CHARACTERIZATION OF HISTONE-LIKE PROTEIN GENE FAMILIES IN

FRITILLARIA LILIACEA

A University Thesis Presented to the Faculty

of

California State University, Hayward

In Partial Fulfillment

ofthe Requirements for the Degree

Master ofScience in Biological Science

By

Rishali Gadkari

March, 2002 Abstract

The genome size ofplants shows a thousand fold variation from the 150 Mb genome ofArabidopsis to the 140,000 Mb genome ofFritillaria. Much ofthis variation in genome size is due to changes in the amount ofnon-coding DNA. Genome complexity, in contrast to genome size, is determined in large part by the number ofgenes but gene number and family organization are poorly characterized in most organisms. In this study I have characterized the number and type offamily members from the histone-like protein gene family in Fritillaria liliacea. The experimental approach involves exhaustive polymerase chain reaction (peR) amplification followed by cloning. Selected clones were sequenced and phylogenetic analyses were performed to determine the relationship among family members. The histone-like gene family in Fritillaria liliacea consists oftwo functional genes, which may be allelic and 12 processed pseudogenes. In contrast the histone-like protein gene family in Arabidopsis consists ofonly one functional gene without any pseudogenes. During the course ofthis study, a new histone­ like protein related gene family was identified. This gene family consists of5-8 functional genes and 4 classical pseudogenes.

11 CHARACTERIZATION OF HISTONE-LIKE PROTEIN GENE FAMILIES IN

FRlT1LLARlA LILIACEA

By

Rishali Gadkari

Date:

I~'J I J r , , VCJVCj, 'dOO \ I

l1l Acknowledgments

My sincere thanks to Dr. Chris Baysdorfer for the inspiration and guidance that he has given me to do this research work. I am grateful to Dr. Kelly Steele for helping me with the phylogenetic analysis ofmy data and Dr. Laura Marschall for her guidance. I also want to thank my family for their support and encouragement.

IV Table of contents

Page

1. List ofTables '" vi

2. List ofFigures vii

3. Introduction 1 General Introduction 1 Gene Families '" 2 Pseudogenes 6 Experimental Organism 18 Histone-like Protein Gene Family 19 Experimental Question 20

4. Material and Methods '" '" 21

5. Results 29

6. Data Analysis 34

7. Discussion 93

8. Reference 99

9. Appendix 112 Raw Sequence Data 112 BLAST N database search ofhistone-like protein genomic clones from Fritillaria liliacea 166 BLAST N database search with processed pseudogene clones from Fritillaria liliacea 169 Intron Exon Structure ofhistone-like gene and new histone-like gene from Fritillaria liliacea 171

v List ofTables

Page

1. Pseudogene composition ofvarious gene families from different plants and animals 9

2. PCR primers used in the analysis 22

3. Comparison ofhistone-like protein 54

VI List ofFigures

Page

1. Initial PCR amplification ofFritillaria liliacea genomic DNA 30

2. PCR amplification ofFritillaria liliacea genomic DNA at lower annealing temperature 31

3. PCR Amplification ofFritillaria liliacea genomic DNA with initial and new histone-like gene specific primers 33

4. Graphical overview ofnucleotide alignment in BLAST N database search from histone-like protein genomic clones from Fritillaria liliacea and histone-like protein cDNA from Fritillaria agrestis 35

5. Graphical overview ofnucleotide alignment in BLAST N database search from histone-like protein processed pseudogenes clones from Fritillaria liliacea and histone-like protein cDNA from Fritillaria agrestis 36

6. BLAST P results ofhistone-like protein gene ofFritillaria liliacea 36

7. Translation ofthe group-l pseudogenes clones from Fritillaria liliacea ...... 39

8. Translations ofthe group 2 and 3 pseudogenes clones from Fritillaria liliacea 39

9. Multiple alignment ofboth genomic clones ofFritillaria liliacea 40

10. Multiple alignment ofgenomic-l clones ofFritillaria liliacea 42

11. Multiple alignment ofgenomic-2 clones ofFritillaria liliacea 46

12. Multiple alignment ofhistone-like protein from Fritillaria liliacea, Fritillaria agrestis and Lilium longiflorum 56

13. Multiple alignment ofhistone-like protein Group 1 pseudogenes clones in Fritillaria liliacea '" '" '" 58

14. Multiple alignment ofhistone-like protein group 2 pseudogenes clones in Fritillaria liliacea 61

VB 15. Multiple alignment ofhistone-like protein group 3 pseudogenes clones in Fritillaria liliacea 65

16. Multiple alignment ofgroup 1 group 2 and group 3 pseudogenes 66

17. Phylogenetic tree ofhistone-like protein gene family from Fritillaria liliacea 74

18. BLASTN database search ofnew histone-like protein from Fritillaria liliacea 76

19. Graphical overview ofhistone-like protein gene and new histone-like protein gene alignment From Fritillaria liliacea 77

20. Multiple alignment ofnew histone-like protein 78

21. Multiple alignment ofnew histone-like group 1 clones from Fritillaria liliacea 80

22. Multiple alignment ofnew histone-like group 2 clones from Fritillaria liliacea 82

23. Multiple alignment ofnew histone-like protein group 3 clones from Fritillaria liliacea 84

24. Multiple alignment ofnew histone-like gene family 86

25. Phylogenetic tree ofnew histone-like protein gene family from Fritillaria liliacea 92

26. Intron exon structure ofhistone-like protein cDNA sequence of Fritillaria agrestis and Arabidopsis putative histone gene sequence 95

Vlll 1

General Introduction

The genome size ofeukaryotes shows a tenthousand-fold variation from 12-140,000

Mb. The complexity ofthe genome is probably not due to the number ofgenes but to the amount ofnon-coding DNA. For example, yeast genome size is 12 Mb and 70 % ofthe genome is encode proteins. In contrast, the genome size ofthe lungfish is 140,000 Mb and the only 0.4-1.2 % ofthe total genome encode proteins (Cavalier-Smith, 1985). In plants, genome size shows a 1000-fold variation between species (Joseph, 1990). For example, the genome size ofArabidopsis thaliana is about 150 Mb with a coding region of31 %. However, the genome size ofFritillaria is 140,000 Mb with coding region of only 0.02 %. (Cavalier-Smith, 1985).

Fritillaria belongs to the family Liliaceae, which includes several other genera with large genomes. These include Tulipa, which has a genome size ofabout 12,000 - 22,000

Mb and Lilium with a genome size of 30-40,000 Mb (Royal Botanic gardens, Kew­

Angiosperm DNA C-Value database-http://www.rbgkew.org.uk). These large genomes mainly consist ofnon-coding DNA, including tandemly and dispersed repeats (Joseph,

1990). The tandem repeats include satellite DNA and rRNA genes, while dispersed repeats mainly consist oftransposable elements. In Lilium henryi there are more than

13000 copies ofthe transposable element dell (a LTR-retrotransposon) that make up about 0.4 % ofthe genome, while in Lilium longiflorum, 1 % ofthe genome consists of dell elements (Smyth, 1991 & Joseph, 1990). Another transposable element del2 element, (a non-LTR retrotransposons) accounts for 4 % ofthe Lilium speciosum genome 2

and is present in approximately 250,000 copies. Although 4 % is a small value compared to the large genome size ofLilium, this sequence is equivalent to ten copies ofthe A. thaliana genome (Smyth, 1991 & Leeton, 1993). These examples show that repeated sequences, mainly retrotransposons, can be responsible for increase in the genome size of the family Liliaceae.

Gene Families

As mentioned above, wide differences in genome size are probably primarily due to changes in the amount ofrepetitive DNA with changes in gene number being a less important factor in determining genome size. Nonetheless, gene numbers do vary somewhat within major taxonomic groups. An increase in gene number is, however one ofthe major factors influencing genome complexity. Three different mechanisms have been proposed for increasing gene numbers (Holland, 1999).

1. Gene Duplication: Duplication ofan ancestral gene can arise by unequal

crossover during recombination in a germ cell precursor or by replication

slippage. Tandem gene duplication creates gene clusters but translocations break

such clusters and scatter their constituent genes around the genome. For example,

the beta globin and Hox gene clusters have remained intact in many evolutionary

lineages. Conversely the RUNX (Runt-related transcription factor 1) gene family

encoding human leukemia associated transcription factor consists ofthree genes

dispersed on different chromosomes. Members ofthis family have 'runt domain' 3

(RD), which directs the binding ofRUNX transcription factors to the consensus

sequence oftarget genes. RUNXI is located on human Chr 21, RUNX2 on

human Chr 6 and RNUX3 on human Chr 1. (Levanon, 2001).

2. Whole genome duplication (polyploidy): Polyploidy events have clearly played a

role in the evolution ofsome eukaryotic genomes, such as maize and yeast

(Shimeld, 1999). Polyploidy is common in plants, but rare in animals. Two types

ofpolyploidy events are described, autopolyploidy and allopolyploidy.

Autopolyploidy occurs within one species by chromosomal doubling, and can be

seen in tetraploid cranberry, Vaccinium OXYcoccos (Mahy, 2000) and Gooseberry­

leaved alumroot, Heuchera grossulariifolia (Segraves, 1999). Allopolyploidy is

the result offusion between parents ofdifferent species and may arise from the

fusion ofabnonnal gametes or from fusion ofnonnal haploid gametes followed

by chromosomal doubling. Examples ofallopolyploidy are cotton, Gossypium

hirsutum (Cronn, 1999) and wheat, Triticum aestivum (Leitch, 1997).

3. Retrotransposition: This is a mechanism where processed RNA is reverse

transcribed into DNA, and the complementary DNA is then inserted back into the

genome at a new site. In this process a copy ofthe original gene is generated at a

different locus in the genome.

An increase in gene number results in an expansion ofgene families and all the mechanisms discussed above have been implied in this process. Gene number varies

significantly within multigene families from as low as two to as many as 800 (in tRNA genes). After gene duplication each member evolves independently and acquires 4

mutations. Ifa single copy gene is sufficient, then the new copy is automatically redundant. In this case the newly duplicated gene is free ofselective constraints and accumulates mutations. Ifthese mutations are advantageous then it may slightly alter the gene function as found in the case ofhemoglobin genes. Ifthese acquired mutations are deleterious then these newly duplicated copies become pseudogenes.

After duplication, gene family members evolve independently. In cotton, Cronn, et

al (1999) have postulated that the duplicated genes evolve independently after polyploid

formation. These authors have proposed a model where these species originated from a

single polyploidation event involving genome A from one parent and genome D from

the other parent. In their study, 9 different gene families were evaluated and only 2 of

these gene families showed the presence ofpseudogenes. Some ofthese pseudogenes

were absent from both the parents. This pseudogene formation might be a later event

after polyploidation.

A gene duplication event can occur after speciation in one ofthe lineage. Forster et al

(1999) have identified the lipoxygenase (LOX) pseudogene in peas (Pisum sativum and

P.fulvum). Two major seed LOX polypeptides (LOX-2 and LOX-3) are found in peas.

Lox enzyme is important in the production offatty acid hydroperoxides that are metabolized either to jasmonate or to volatile aldehydes that are part ofplant defense systems and impart taste and aromas to fruits and vegetables. Genes for both polypeptides are present at the same genomic region. However a Lox pseudogene has been found that contains rearranged LOX-2 and LOX-3 homologous regions and an unidentified tract ofDNA. This fragment is present in P. sativum genome but absent from 5

P. fulvum. This Lox pseudogene appears to have originated in the P. sativum genome after speciation.

Riedel et al (1996) have characterized the signal recognition particle (SRP) RNA gene family from four tomato cultivars. SRPs are essential for the translocations of secretory, lysosomal and membrane proteins through membrane systems. Southern blot analysis has indicated that there are at least 10 different SRP RNA genes. Apart from these 10 genes two highly truncated pseudogenes were observed in two cultivars. From

10 characterized genes, two were pseudogenes whose putative RNA transcript cannot

fold into a biologically active secondary structure. The remaining 8 genes appear to be potentially active.

Independent evolution ofa gene family is not only found between species but is also reported within different strains ofthe same species. Mouse high mobility group I and Y gene family (HmgI) consists of3 HmgI related loci. The high mobility group proteins

are non-histone chromosome associated proteins. HMG proteins bind DNA cooperatively with sequence specific transcription factors, stabilizing multiprotein

complexes that regulate transcription ofneighboring gene. High mobility protein Y and I

are alternative splice products ofa single gene. Only one ofthe three loci is present in all

the strains examined and represents the active functional HmgI gene. Two additional

HmgI related sequences are present in certain mouse strains and thus represents pseudogenes (Johnson, 1992).

The above examples clearly demonstrate an independent evolution and diversification process within family members. 6

Pseudogenes

A pseudogene is a DNA sequence with similarity to a functional gene but contains some deleterious mutations that prevent its expression. In other words, it is a non­ functional copy ofa functional gene. This 'lack offunction' is a result ofeither failure of transcription, translation or the production ofa protein that is missing a functional domain. Pseudogenes can be classified into two types, classical pseudogenes and processed pseudogenes or retroposons. Both classical pseudogene and processed pseudogene members are common in multigene families.

Classical pseudogenes: Classical pseudogenes usually arise by general or segmental genome duplication and differentiation. These pseudogenes are very similar to their functional counterparts with respect to intron and exon structures. After duplication each accumulates mutations independently ofthe other copy. Ifthese mutations cause loss of function ofa gene, then this nonfunctional copy ofa gene is termed as pseudogene. If this defective sequence is harmless, it is retained in the genome as a classical pseudogene.

Usually classical pseudogenes are found close to functional genes.

Processed pseudogenes: Processed pseudogenes arise by retrotransposition event.

They are also called as retroposons or retro-pseudogenes. A processed pseudogene is a double stranded copy ofDNA derived from processed RNA by reverse transcription.

Typical characteristics ofprocessed pseudogenes are the absence of5' promoter sequences and introns and the presence offlanking direct repeats and 3' po1yadeny1ation tract. Like a classical pseudogene it accumulates random mutations after insertion. Unlike classical pseudogenes, processed pseudogenes are inserted into the genome at random 7

locations. Usually cDNA insertion is observed at the site ofthe chromosomal double strand break (Moore, 1996; Teng, 1996). Occasionally classical pseudogenes from an intronless gene family are mistaken for processed pseudogenes. These pseudogenes can be identified as processed pseudogenes ifthey show characteristics such as a poly A tail, absence of5' promoter sequences and presence offlanking direct repeats etc; otherwise they are categorized as classical pseudogenes. Processed pseudogenes can be transcribed ifthey happen to be inserted next to an active promoter. Ifthese pseudogenes have an intact reading frame, then there is a possibility that they might produce a functional protein. Genes that generate processed pseudogenes share common important characteristics: 1) widely expressed, 2) highly conserved, 3) short and 4) GC-poor

(Goncalves, 2000).

Table 1 and 2 list, data on the numbers ofgenes in selected gene families as well as the percentage ofthese that are classical or processed pseudogenes. A summary ofthis data is presented below:

Plant data:

Total number ofgenes characterized: 295 Total number ofpseudogenes: 91 (30.84%). Classical pseudogenes: 74 (81.32%) Processed pseudogenes: 17 (18.68%) 8

Animal data:

Human:

Total number ofgenes characterized: 626 Number ofpseudogenes: 347 (55.43%) Classical pseudogenes: 298 (87.87%) Processed pseudogenes: 49 (14.12%)

Mouse-

Total number ofgenes characterized: 49 Number ofpseudogenes: 36 (73.47%) Classical pseudogenes: 4 (11.11 %) Processed pseudogenes: 32 (88.88%) Table 1- Pseudogene composition ofvarious gene families from different plants and animals. Total # ofgenes- The number indicates the total gene family members that have been identified in this or other studies. ND- Not determined. # of genes charatterized- The number represents the subset offamily members that have been characterized.

Table 1: Plant Data

Arabidopsis thaliana I,..'-(;I\"'V"~"~_V_I ~I ~'"' \U IIv"1 4 I 4 I 1 I Classical I 25.0% I Jost, 2000

Arabidopsis thaliana allllllv""Y"'IV~1 v~al 1'1::::;- I I 5 I 2 I 1 Classical 50.0% Liang, 1995

Arabidopsis thaliana I S gene family I 6 I 6 I 2 Classical 33.3% Owyer1997

Atropa belladonna I lJv~vlallllllv v fJ- NO 2 1 Classical 50.0% Suzuki 1999 Belladonna hydrqxylase lH6H) Brassica S gene fal1)ily 3 3 2 Classical 66.7% Suzuki,1997 Brassica napus Myrosinase Il.lA ....__ \ 4 1 1 Classical 100.0% Lenman, 1993 Canola Brassica oleracea I S-receptor kinase I NO 6 1 Classical 16.7% Kumar, 1993 Cabbage I I I I I Cucumis sativus L.. ~ __ ~ ~~:..:,:~ ..___ J NO 2 1 Classical 50.0% Matsui,2000 Cucumber I I I I I Capsicum annuum Oefensin like Protein I NO 2 1 Classical 50.0% I Houlne, 1998 SweetPaper I I I I Clarkia mildrediae Phosphoglucose 2 2 1 Classical 50.0% I Gottlieb, 1997 Clarkia isomerase I I I I I Coix lacryma Jobi a coixin prolamin 3& 3 2 Classical 66.7% I Ottoboni, 1997 Job's Tears I I I I I Daucus carota Proliferating Cell NO 2 0.0% Hata, 1992 Carrot nuclear antigen I I I - I - I I Eucalyptus globulus LeaFy NO 2 1 Not Classified I 50.0% jsoutherton, 19981 Eucalvotus I I I I

\0 Table 1: Plant Data

Glycine max Em like Lea 5 5 1 Classical 20.0% Calvo, 1997 So bean I I I I I I Ginkgo biloba Seed storage 2-3 2 1 Classical 50.0% Hager, 1995 Gink 0 lobulin I I I I I I Gossypium hirsutum hmg-coA- reductase I 7-9 1 1 Processed 100.0% ILoguercio, 1998 Cotton I I I I Hordeum vulgare a -glucosidase 3 '1 2 Not classified 200.0% Tibbot, 1996 Barley I I I I I I I Lycopersicon esculentum U1 RNA NO 1 1 Processed 100.0% Kiss, 1989 Tomato I I I I I I I Lycopersicon esculentum I NBS-LRR 75 75 7 Classical 9.3% Pan,2001 Tomato I I I I I I Lycopersicon esculentum I Aldehyde Oxidase I 5 5 2 Classical 40.0% Min, 2000 Tomato I I I I I Lycopersicon esculentum L210cus 7 3 2 Classical 66.7% I Simons, 1998 Tomato I I I I I Lycopersicon esculentum Alcohol I NO 3 2 Classical 66.7% ILonghurst, 1994 Tomato deh dro enase 2 I I I I Lycopersicon esculentum SRP RNA NO 10 2 Classical 20% Riedel, 1996 Tomato I I I I I I Lactuca sativa RGC2 24 9 3 Classical 33.3% Meyers 1998 Lettuce Lens culinaris Saenz de Miera Vicilin NO 5 1 Classical 20.0% Lentil 1999 Nicotiana tabacum Pathogenesis related NO 3 2 Classical 66.7% Pfitzner, 1991 Tobacco Drotein Phyllostachys aurea Classical- Prolamin NO 2 1 50.0% Hilu,1998 Fishoole Bamboo intronless I I Pinus Class II Chitinase 2-4 2 1 Classical 50.0% WU,1997 Pine I I Populus hitinaselWin proteir'1 NO 3 1 Classical 33.3% Davis, 1991 Po lar I I I I I Posidonia oceanica Type II NO 3 1 Processed 33.3% Giordani,2000 Sea rass metallothioneins ...- 0 Table 1: Plant Data

Picea sitchensis Kvarnheden, Cdc2 10 10 5 Processed 50.0% Spruce 1998 Picea engelmannii Kvarnheden, Cdc2 10 10 2 Processed 20.0% Soruce 1998 Picea abies Kvarnheden, Cdc2 10 10 6 Processed 60.0% Spruce 1998 Psophocarpus Kunitz chymotrypsin, tetragonolobus I 7 7 , 3 Classical , 42.9% Habu, 1992 inhibitor- WCI I I I Winged bean Ricinus communis Ricin/RCA , 8 5 , 3 Classical , 60.0% Tregear, 1992 Castor bean I I I Spinacia oleracea Basic Leucine Zipper, NO 4 , 3 Classical , 75.0% Bolle, 1998 S inach Protein bZIP' I I I Solanum tuberosum Patatin , 70 2 , 1 Classical , 50.0% Nap, 1992 Potato I I I Solanum tuberosum , U1snRNA , NO , 10 , 3 Classical , 30.0% Vaux, 1992 Potato I I Solanum tuberosum , U2 snRNA , 25-40· , 11 , 1 Classical , 9.1% Waugh,1991 Potato I I Solanum tuberosum Actin 6 6 1 Processed 16.7% Drouin, 1987 Potato Triticum aestivum Low molecular Benmoussa, 3 3 2 Classical 66.7% ~eat weiqht qlutenin 2000 Cre Triticum aestivum 3 nematode 2 , 2 1 , Classical , 50.0% , Lagudah, 1997 Wheat I I resistance locus Triticum aestivum a-gliadin (Prolamin) 150 , 27 , 10 Classical , 37% Wheat I I 'Anderson, 1997 Zea mays , a -zein NO , 2 , 1 Classical , Maize I I 50.0% 'Thompson, 1992 - Table 1: Animal Data

Homo sapiens I Arp NO 17 0 0.0% Pollard,2001 Human I I I I - I I Homo sapiens Actin NO 36 23 Not Classified 63.9% Pollard, 2001 Human Neurofibromatosis Luijten, 2000 & Homo sapiens NO 9 8 Classical 88.9% Human type I (NFl) Cummings, 1996

Homo sapiens Olfactory Receptor 500 87 63 Classical 72.4% Glusman, 2000 Human Homo sapiens Carnitine I 6 6 1 Classical 16.7% I van der Leij, 2000 Human Acyltransferase I I I I Tubulin tyrosine Homo sapiens ligase like 1 4 4 3 Classical 75.0% Trichet, 2000 Human I I I I I I 'TILL1 UDP- Homo sapiens lucuronosyltranfe-j NO 13 5 Classical 38.5% Carrier, 2000 Human I I I I I -rase 2 8 Homo sapiens Immunoglobulin- I 125 125 88 Classical 70.4% Kawasaki,2000 Human VA I I I I I Immunoglobulin Homo sapiens heavy chain 123 123 79 Classical 64.2% Matsuda, 2000 Human I I I I I I variable region MHC class I Parra-Cuadrado, Homo sapiens NO 2 1 Classical 50.0% I Human related MR1 I I I I I 2000 Endothelin Homo sapiens converting enzymel NO 3 2 Classical 66.7% Valdenaire, 2000 Human I I I I I like 1 Homo sapiens Macrophage I 9 9 8 Classical 88.9% I van der Drift, 1999 Human stimulating p~otein I I I. I Homo sapiens Novel class of I 4 4 3 Classical 75.0% Frattini, 1997 Human prenylated prutein I I I I I Homo sapiens p47-phox NO 3 2 Classical 66.7% Gorlach,1997 Human

...... N Table 1: Animal Data

urm • 'S-_·,CIa' Homo sapiens I IL-9 receptor NO 5 4 Classical 80.0% Kermouni, 1995 Human I I I I I I Homo sapiens Tyrosine kinase NO 95 5 Processed 5.3% Robinson, 2000 Human I I I I I I Homo sapiens Ribosomal protein I NO 3 2 Processed 66.7% Cmejla, 2000 Human S19 I I I I I Homo sapiens Serine protease I 18 18 5 Processed 27.8% Gan, 2000 Human I I I I I Homo sapiens y-tubulin 3 3 1 Processed 33.3% I O'Neal Wise, 2000 Human I I I I I Copper Homo sapiens transmembrane I NO 2 1 Processed 50.0% Moller, 2000 Human I I I I I ransport protein -1 H . IMitochondrial outell Hernandez, 1999 & omo sapiens membrane 5 5 4 Processed 80.0% I Human receptor Tom20 I III 2000 Heterogeneous Homo sapiens I nuclear I NO 2 1 Processed 50.0% Romanelli,2000 Human ribonucleoprotein I I I I I tvoe I Homo sapiens Necdin NO 2 1 Processed 50.0% Nakada, 2000 Human I I I I I I Homo sapiens ATP Synthase NO 2 1 Processed 50.0% TU,2000 Human ATP5E I I I I I I Homo sapiens Ubiquitin fusion I NO 2 1 Processed 50.0% Kirschner, 2000 Human Qene Uba80 I I I I I Cytochrome P450 Homo sapiens lanosterol 14a- I NO 3 2 Processed 66.7% Rozman, 1996 Human I I I I I demethylase Willenbrink, 1995 & Homo sapiens Cyclophilin A NO 5 4 Processed 80.0% Human Haendler, 1990 Homo sapiens Glycerol Kinase 7 7 4 Processed 57.1% Sargent, 1994 Human ...... w Table 1: Animal Data

Homo sapiens Heat shock protein, NO 3 , 2 , Processed 66.7% , Durkin, 1993 Human 90 I I Ubiquitin/52 Homo sapiens residue ribosomal' 9 , 9 , 8 Processed , 88.9% Baker, 1992 Human I I rotein UbA52 Homo sapiens Phosphoglycerate I 7 3 2 Processed 66.7% McCarrey, 1987 Human kinase I I I I I Spondyloepiphyse Homo sapiens 2-Processed, al dysplasis tarda 8 8 7 I 87.5% Gecz, 2000 Human 5-Classical I (SEDL) Glutamate 2 - Classical, , Homo sapiens NO 5 4 80.0% , Michaelidis, 1993 Human dehydrogenase 2 - Processed 1 - Classical, Homo sapiens Radixin NO 3 2 I 66.7% I Wilgenbus, 1993 Human 1 - Processed Betaine Mus musculus homocysteine S- NO 2 1 Processed 50.0% Neece,2000 Mouse I I meth Itransferase Functional Mus musculus Glycerol kinase NO 2 0 I 0.0% I Pan, 1999 Mouse processed Macrophage Mus musculus 10 10 9 Processed I 90.0% I Kozak, 1995 Mouse inhibitory factor Mus musculus Int6 NO 7 4 Processed 57.1% Miyazaki, 1995 Mouse I I I I I I Mus musculus Stathmin 3 3 2 Processed 66.7% Okazaki,1993 Mouse I I I I I I Mus musculus Ribosomal protein I 16-17 16 15 Processed 93.8% Dudov, 1984 Mouse L32 r L32 I I I I I Mus musculus Cellular tumour I 2 2 1 Processed 50.0% Zakut-Houri, 1983 Mouse anti en 53 I I I I I Mus musculus Angiogenin- NO 4 2 . Classical 50.0% Brown, 1995 Mouse related rotein

-.j::>. Table 1: Animal Data

I High mobility MUS';WSCUIUS group I & Y proteinl 3 I 3 I 2 I Classical I 66.66% I Johnson, 1992 ouse Hmgl

Bovidae Bovine ~-~~~~~~s~~;e~a~~1 3 I 3 I 2 I Processed I 66.7% I Mercier, 1999

Drosophila IRamos-onsins, 1998 melanogaster Cecropin NO 6 2 Classical 33.3% Kylsten, 1990 Fruit fly I Bombyxmori Classical Bombyxin 38 38 5 13.2% Kondo, 1996 Silk moth Intronless genes' I

...... VI 16

The data presented above show that pseudogenes are common in both plants as well as in animals. Arabidopsis genome contains 25,498 genes and approximately 3 % of these genes are classified as pseudogenes (The Arabidopsis Genome Initiative, 2000).

Pseudogenes are common within multigene families but it is not easy to quantify the number ofpseudogenes within a particular genome unless it has been completely sequenced. Nevertheless, an estimate ofthe number ofgene family members can be made using various techniques:

1) PCR (Polymerase Chain Reaction) can be used to estimate the gene number as

well as to characterize the family members. Using this technique potentially all

the gene family members can be amplified. Due to divergence, not all family

members are amplified with the same set ofprimers, but related genes can be

amplified with different sets ofgene specific primers. Amplified gene products

are then cloned into E. coli to separate the individual genes and then sequenced

to determine the number as well as the type ofgenes identified.

2) Southern blot hybridization can be used to estimate the number offamily

members. Here, genomic DNA is digested, denatured and hybridized with a

gene-specific probe at low stringency conditions to detect all related loci.

Although this technique is very good in estimating the number of family

members, it cannot characterize each family member unless there is a size

difference, as with classical pseudogenes and processed pseudogenes. 17

3) In situ hybridization or fluorescence in situ hybridization (FISH) provides a

mechanism for estimating gene numbers as well as for determining genomic

organization and chromosomal location. In this procedure a gene specific probe

is labeled with a fluorochrome and hybridized to chromosomes attached to

microscope slides. As with the Southern blot, this technique also cannot

differentiate between functional genes and classical pseudogenes. 18

Experimental Organism

The genus Fritillaria belongs to the family Liliaceae and consists ofapproximately

100 species found in the Northern Hemisphere, primarily in high mountain grasslands.

All Fritillaries are perennial herbs arising from a bulb or a rhizome. The plant height ranges from 8" to 36" and the plant have a short growing season. Most Fritillaries are spring blooming and are adapted to habitats where all growth, flowering and seed production need to be completed before the long summer, hence their growing season is short and the plant spend most ofthe year underground in "hibernation." Most California

Fritillaria species are on the California Native Plant (CNPS) Society endangered list due to limiting habitat, overgrazing and land development.

Fritillaria liliacea, also called as "fragrant fritillary", is a perennial herb that is endemic to California. It is on the endangered list and has received habitat protection in several parks and preserves. The Fragrant Fritillary reaches a height of5 to 15 inches.

The flowers are whitish with green stripes and face outward or downward. It prefers open grassland habitat and grows in heavier (clay) soils, often derived from serpentine. 19

Histone-like Protein Gene Family

In this study I have characterized the histone-like protein gene family from Fritillaria liliacea. Histones are conserved nuclear proteins that participate in the organization of chromatin and are encoded by multigene families. Histones are divided into five subtypes, HI, H2A, H2B, H3, and H4. Two copies ofeach H2A, H2B, H3, and H4 form an octamer which associates with ~ 160 bp DNA to form a nucleosome. Nucleosomes are further connected to each other by a linker DNA. The length ofthe linker DNA varies from 15-55bp. The fifth histone HI interacts with the linker DNA and adjacent nucleosomes and further condenses the chromatin (Lodish, 1999). In higher eukaryotes, there are a number ofnon-allelic variants ofeach histone that are encoded by distinct histone genes (Levine, 1988). The Histone-like protein is a HI variant. In Lilium longiflorum this histone-like protein (HI histone variant) is associated with repression of transcription (Tanaka et ai, 1999). Tanaka et al have isolated a novel histone variant

(p35) from nucleoli ofLilium longiflorum, which strongly binds to ribosomal DNA in vitro. The protein is present in all higher plants including monocots and dicots, and might be responsible for the organization ofthe nucleolar higher order chromatin. 20

Experimental Question

As discussed above, the genome size or C-value (amount ofDNA per haploid genome) can vary greatly without concomitant changes in genetic or morphological complexity. In other words, the Fritillaria genome is 30 times larger than the human genome, but is it 30 times more complex? To address this question I have looked at the gene copy number ofthe histone-like protein gene family in Fritillaria with the goal of determining whether evolution has increased the size ofthe gene family in proportion to the size ofthe genome. 21

Material and Methods

Plant Material:

Leaves from Fritillaria liliacea were obtained by Dr. Baysdorfer from Nicasio

Reservoir, Marin county (population voucher number, CAS635332) and stored at -70° C.

Plant DNA Isolation:

Genomic DNA from Fritillaria liliacea was isolated using a QIAGEN DNeasy Plant

Mini Kit. Procedure was followed as per the protocol provided with the kit. Plant tissue was ground in lysis buffer API containing RNase, followed by incubation at 65°C for 10 minutes for cell lysis. Next, precipitation buffer AP2 was added to the lysate to precipitate the detergents, proteins and polysaccharides.

After precipitation, the clear lysate was applied to a QIA shredder spin column and centrifuged for 2 minutes at maximum speed. Elute from the previous step was transferred to a new tube and a halfofthe volume ofbinding buffer AP3 and 1 volume of

100% ethanol was added to the clear lysate. The mixture was then applied to a DNeasy mini spin column and centrifuged for 1 minute at 8000 rpm and the flow-through was discarded. Wash buffer AW was added to the DNeasy column and again centrifuged for

2 minutes at maximum speed. Preheated elution buffer AE was added directly onto

DNeasy column and centrifuged for 1 minute at 8000rpm to elute the DNA. The eluted

DNA was stored at -20°C. 22

PCR:

Different primers were used for PCR amplification. The initial set ofprimers (His F and His R) was designed by Dr. Baysdorfer from the histone-like protein cDNA sequence ofFritillaria agrestis. Additional sets ofprimers (external and internal to the original primers) were designed using Oligo 4. An external primer pair was designed to amplify the entire coding region while an internal primer pair amplifies part ofcoding region that includes the intron. These primer pairs were used with genomic DNA from Fritillaria liliacea. PCR was done using genomic DNA, forward and reverse primers (lmM/L),

PCR buffer (50mM KCL, 10mM Tris-HCI pH8.3,), 2.5mM Mgcl2, 0.8mM dNTP mix, water, and 0.05U/~1 units ofDNA polymerase (Amplitaq Gold 5U/~I). The general PCR parameters were: Initial denaturation at 94° C for 10 minutes, 40 cycles at 94° C for 30 seconds (denaturation), 50° C for 30 seconds (annealing) and 72° C for 2 minutes

(elongation) with a final elongation at 72° C for 7 minutes. Annealing temperatures were varied from 45°C - 60°C.

Table 2: PCR primers used in the analysis

Name Forward primer (5'-3') Reverse primer (5'-3')

Grf 5'- TGAGAAGTIAAGCGCCAGCC - 3' 5'- GATCGAGCAGAAGGAGGAGA - 3'

rL25 5'- GTIGCAGCATAAGGACTAAT - 3' 5'- GACAATCCAAACACAAGTIC - 3'

rS16 5'- CGGAAGAAGACGGCTGTAGC - 3' 5'- GCACCACGCCCACCAAACTI - 3'

HIS 5'- CAGCCGTIGCAATCGAGACT - 3' 5'- GTIGTIGCCTICTICCCAGC - 3'

His Ext 5'- AACCGCAACAGTCTCTTICC - 3' 5'- CATCCCTCCAATCCAAACCC - 3'

His Int 5'- GCTCTCCATCCTACCTATCT - 3' 5'- CCACTGGAGCAGCCTICTTI - 3'

M13 5'- GTAAAACGACGGCCAG - 3' 5'- CAGGAAACAGCTATGAC - 3' 23

Agarose Gel Electrophoresis:

The PCR reactions were analyzed on 1% Agarose gels (Sambrook et aI, 1989) run at

100V for 45 min. After electrophoresis, the gel was stained in ethidium bromide solution for 40 minutes and destained in deionised water for 30 minutes. A photograph ofthe gel was taken with a Polaroid camera under UV light.

TOPO TA Cloning:

Selected PCR products were cloned into the Tapa vector using a Tapa TA Cloning

Kit from Invitrogen. Fresh PCR products were mixed with Tapa vectors in presence ofa dilute salt solution. The reaction mixture was incubated at room temperature for 5 minutes for ligation ofthe PCR products and the Tapa vector. After incubation, ligated vector was transformed into E. coli cells. Here the Tapa cloning reaction was gently mixed with chemically competent E. coli, incubated on ice for 30 minutes, and then heat shocked for 30 seconds at 42°C. After transformation, sac media was added to the cells and incubated in a shaking incubator at 37°C for 1 hour. After incubation, the reaction tube was centrifuged and excess sac media was removed. 50111 oftransformation reaction was plated onto prewarmed LB plate containing kanamycin (50llg/ml) and incubated overnight at 37°C. After 16-20 hours ofincubation, clones were isolated and inoculated in 100111 ofLB broth with kanamycin. After 8 hours ofincubation 50111 ofcell, suspension was mixed with 50% glycerol and stored at -70°C. The remaining cell suspension was analyzed by PCR. 24

peR ofTA Clones:

PCR reagents and parameters were the same as described above. In this PCR, vector specific (M13 forward and Ml3 reverse) primers were used. Plasmid DNA-Tapa vector with an insert (bacterial cell suspension) was used as a template. The bacterial cell suspension from the Tapa cloning reaction was diluted I: I0 and 2/-l1 was used for alOul

PCR reaction.

Plasmid DNA Isolation:

20/-l1 ofbacterial glycerol stock was inoculated in 5ml ofLB broth with kanamycin

(50J..lg/ J..lI) to obtain an overnight culture for plasmid DNA isolation. After 20 hours of incubation at 37°C, bacterial cells were pelleted by centrifugation and plasmid DNA was purified using a QIAprep spin Miniprep kit from QIAGEN. The pelleted cells were first resuspended in resuspension buffer PI containing RNase and the cells are lysed using buffer P2 (lysis buffer). Adding neutralizing buffer N3 neutralizes the lysis reaction and clear lysate was then obtained by centrifugation. Clear lysate was added to a QIAprep column, which has a silica-gel membrane for DNA adsorption. The column was washed with wash buffer PB and buffer PE to remove contaminants. Finally, plasmid DNA was eluted using elution buffer EB (Tris-CI pH 8.5). Eluted plasmid DNA was stored at ­

20°C. 25

Restriction Digestion:

To determine the size ofthe insert, the plasmid DNA was digested with EcoRI. The

TOPO vector was designed in such a way that the insert is flanked by EcoRI sites on both sides. 5111 ofplasmid DNA was mixed with 1111 ofEcoRI, 1ul of lOX EcoRI buffer and

3111 ofH20. The reaction mixture was incubated at 37°C for 45 minutes. The restriction digestion samples were analyzed by agarose gel electrophoresis.

Cycle Sequencing:

2111 ofplasmid DNA was mixed with 2111 ofBig dye terminator reaction mix (ABI) and three pmole ofvector specific primers (either M13 or reverse). The cycle sequencing reaction was done in a thermocycler using the following parameters. Initial denaturation at 96° C for 10 seconds, 25 cycles at 96° C for 10 seconds (denaturation), 45° C for 5 seconds (annealing) and 60° C for 4 minutes (elongation).

Sequencing Clean Up:

Isopropanol precipitation was performed to precipitate the extension products ofthe sequencing reaction. 35111 ofdeionized water and 60111 of 100% isopropanol were added to the sequencing reaction. The final isopropanol concentration was 60%. The tubes are left at room temperature for 15 minutes to precipitate the extension products. The orientation oftubes was marked in the microcentrifuge and centrifuged for 20 minutes at maximum speed. Supernatants were aspirated from each sample completely. 250111 of

75% isopropanol was added to each tube and vortexed briefly. Tubes were centrifuged

C/~.L STATE UNIVERSITY HAYWARD LIBRARY 26

with the same orientation as before for 5 minutes at maximum speed. Supernatants were removed carefully and samples were dried for 30 - 45 minutes at room temperature.

DNA Sequencing:

Purified extension products after cycle sequencing were sequenced on an ABI 377

DNA Sequencer (Perkin-Elmer). Long Ranger Singel packs (FMC) were used for preparation ofthe sequencing gel. The gel pack contains 50% gel solution, IX TBE, 6M

Urea, 0.05% APS, 0.07% TEMED and 5% Long Ranger.

Dried extension products from the cycle sequencing reaction were resuspended in

1.5/-11 ofre-suspension buffer (1:3 formamide: 25mM EDTA plus blue dextran). Re­ suspended samples were denatured at 90°C for 2 minutes just before loading. 1/-11 ofthe sample was loaded onto the sequencing gel and electrophores at 1200 V at 52°C for 7 hours using sequence run module 36E-1200.

Sequence Analysis:

Sequence data from the ABI 377 was analyzed using Sequencer (Gene Codes).

Sequence data for each insert in forward and reverse orientation was edited manually and assembled to obtain a contig. Consensus sequence from each contig was used for BLAST

N database search at NCBI (http://www.ncbi.nlm.nih.gov). BLAST search analysis confirmed that sequenced inserts were actually histone-like genes or were non-specific amplification products. In BLAST analysis, alignments with a bit-score over 100 were analyzed further. This bit-score is derived from the raw alignment score that is calculated 27

as the sum ofsubstitutions and the gap score. The bit score is normalized with respect to the scoring system, therefore it can be used to compare the alignment scores from different searches. The higher the score the better the alignment, but the significance of the alignment cannot be deduced from the score alone. Highly significant scores have expect (E) value close to zero, the lower the E value, the more significant is the score.

The E value represents the probability ofthe match appearing by chance. In addition, from the database search, we could identify histone-like genomic DNA and cDNA inserts.

Once all histone-like genes were identified, they were compared to each other by multiple alignment using Sequencer. Multiple alignment helped to detect the single base

substitutions as well as insertions and deletions ofnucleotides (collectively called as indels) within the sequences.

Data Analysis:

Once all these sequences were characterized, all family members were classified as

functional genes or pseudogenes. Pseudogenes were further classified into conventional

and processed pseudogenes variants. Finally, a gene tree was constructed to determine the number ofsubstitutions using PAUP [Phylogenetic Analysis Using Parsimony],

(Swofford, 2001). This program can construct a phylogenetic tree using distance

methods (Neighbour joining and UPGMA) or discrete methods (Maximum Parsimony

and Maximum likelihood). Maximum parsimony was selected because I was interested

in the evolution ofindividual sites in a group ofclosely related sequences. Maximum 28

parsimony chooses the tree that requires fewest evolutionary changes. Parsimony analysis can allow one to locate where in the tree each site changes. Discrete methods do not always produce an optimal tree, especially for large and complex data sets, but I have relatively few sequences from one gene family that are not particularly divergent. A bootstrap analysis was performed to put confidence limits on groups found in the phylogenetic trees. In bootstrap analysis resamples are taken from the data. Each resample is a pseudoreplicate. From each pseudoreplicte tree was constructed and this process was repeated 100 times, resulting in a set ofbootstrap trees. A bootstrap consensus tree was assembled from the set ofbootstrap trees representing the commonality among a set oftrees. 29

Results

peR Amplification of Genomic DNA

Initial PCR studies were concerned with identifying a suitable gene for further analysis. In this part ofthe work four different gene-specific primer pairs were investigated. These primers pairs amplified the 14-3-3 protein (Grf), ribosomal proteins rS16 (rS16) and rL25 (rL25) and histone-like protein (His). These primer pairs were designed by Dr. Baysdorfer from a Fritillaria agrestis cDNA sequences. Since Fritillaria agrestis and Fritillaria liliacea are closely related species, these primer pairs should be able to amplify respective gene families from Fritillaria liliacea genomic DNA.

Jnitial PCR Amplification

Fritillaria liliacea genomic DNA was amplified with the four sets ofprimers, at an annealing temperature of50°C (other PCR parameters were same as those described in material and methods). After amplification, PCR reactions were analyzed by 1% agarose gel electrophoresis (Fig.1). Only rS 16 and His primer pairs generated multiple amplification products, and hence these genes seem to be good candidates for a multigene family. 30

1 kb 1 - 1 kb ladder 3 -Grf 5 -rL2S 6 -rS16 7 -His

Fig. 1. Initial peR amplification of Fritillaria liliacea genomic DNA. Primers used are 3) 14-3-3 protein (Grf), 5) ribosomal protein rL25 (rL25), 6) ribosomal protein rS16 (rSI6) and 7) histone-like protein (His).

PCR Amplification at Lower Annealing Temperature

To extend the results ofthe first PCR, another PCR amplification was performed at an annealing temperature of45°C with the same sets ofprimers. As with the first PCR, the His and rS 16 primers generated multiple bands (Fig.2). Considering the results of both PCR amplifications, the histone-like gene family was chosen for further analysis.

This gene family seems to be the ideal candidate to study a multigene family as multiple bands were observed in both the PCR amplifications. In Fritillaria agrestis, the histone- like protein cDNA is ~lkb with coding region of71O bases. Since it is a cDNA it does not include intron, but it has 5' and 3' untranslated regions. The His primer pair is designed to amplify only the coding region, therefore histone-like protein genes from 31

Fritillaria liliacea do not have 5' and 3' untranslated regions. The 1kb band in Fig-1 and

Fig-2 could be the histone-like protein gene with intron, while other bands could be other members ofthe histone-like gene family or non-specific amplifications.

1 kb

1 - 1 kb ladder 2-Grf 3 -rL25 4 -r816 5 -His

Fig.2. peR amplification ofFritillaria liliacea genomic DNA at lower annealing temperature. Primers used are 2) 14-3-3 protein (Grt), 3) ribosomal protein rL25 (rL25), 4) ribosomal protein r816 (r816) and 5) histone-like protein (His). 32

PCR Amplification with Initial and New Histone-like Gene Specific Primers.

After the analysis ofPCR products from first two PCR reactions, new primer sets, external and internal to the initial histone primers were designed by using Oligo 4.

External primers were designed to amplify the entire coding region, while the internal primer pair was designed to amplify the part ofcoding region that includes the intron.

In the third PCR, different combinations ofinitial and new primer pairs were used to amplify all members ofthe gene family at annealing temperature ofSO°C. The amplification products were observed for only the following combinations ofprimers

(Fig.3). External forward + internal reverse, internal forward + internal reverse, initial

His forward + internal reverse and internal forward + initial His reverse. No amplification products were observed with the external sets ofprimers. All the amplified

PCR products were cloned in the Tapa vector for further analysis. There is a possibility that, since the external primers are outside the coding region, these sequences might not be conserved. 33

1- 1 Kb ladder 2 - Ext f + Ext r 3 - Ext f + Int r 4 - Int f + Int r 5 - Int f + Ext r 6 - His f + Int r 7 - Int f + His r 8 - His f + Ext r 9 - Ext f + His r

Fig. 3. peR amplification ofFritillaria liliacea genomic DNA with initial and new histone-like gene specific primers. Primers used were Ext f- external forward, Ext r- external reverse, Int f- internal f, Int r­ internal reverse, His f- initial histone-like protein forward and His r- initial histone-like protein reverse.

Tapa TA Cloning

PCR amplification products ofthe histone-like protein from all PCR reactions were cloned into the Tapa vector. Approximately 100 colonies from each PCR reaction were isolated. After screening, approximately 200 clones were selected for plasmid preparation from each initial PCR preps.

Sequencing

Cycle sequencing reactions were performed on a total of 175 clones. 34

Data Analysis

Sequence data for each insert in forward and reverse orientation was edited manually and assembled to obtain a contig. The consensus sequence from each contig was used for

BLAST N and BLAST P database search at NCBI. Clones that showed any similarity to histone-like protein cDNA sequence from Fritillaria agrestis and Lilium longiflorum were selected for further analysis, other clones that did not show any similarity to histone-like protein were classified as non-specific amplifications.

In the database search, some ofthe clones were identified as either histone-like protein genes or processed pseudogenes based on their alignment with Fritillaria agrestis histone-like protein cDNA sequence. Some ofthe clones have a discontinuous alignment with Fritillaria agrestis sequence. Fig. 4 shows a graphical overview ofthe

BLAST N database search results ofhistone-like protein genomic clones from Fritillaria liliacea (BLAST N database search results have given in the appendix p.166). Sequence comparison between the two revealed that these clones have an intron with the correct splice sites (GT-AG). Thus, these clones appear to be histone-like protein genomic sequences from Fritillaria liliacea. 35

# I # 135 # 827 Intron # 321 Fritillaria liliacea histone-like Exon I # 136 # 32°1 Exon protein genomic clone Fritillaria agrestis histone-like Exon Exon protein cDNA gb # AF03 I547 # 100 # 232 # 233 # 741

Fig. 4. Graphical overview of nucleotide alignment in BLAST N database search from histone-like protein genomic clones from Fritillaria liliacea and histone-like protein eDNA from Fritillaria agrestis. Numbers in the above figure represents the nucleotide numbers in respective sequences from alignment.

In contrast to these genomic clones, some ofthe clones were continuous and nearly identical to Fritillaria agrestis cDNA. Fig. 5 shows a graphical overview ofthe BLAST

N database search results ofhistone-like protein processed pseudogene clones from

Fritillaria liliacea (BLAST N database search results are in the appendix p.169). These clones lack the intron found in genomic clones, so they were classified as processed pseudogenes. Finally multiple alignment ofgenomic clones and processed pseudogenes was performed using Sequencer (Gene Codes). The results ofthe multiple alignments are described below. A BLAST P database search confirmed that all the genomic clones have a complete open reading frame (Fig- 6). Some ofthe clones from the processed pseudogene groups have a complete open reading frame, while others have inframe stop codons (Fig.7 & Fig. 8). 36

# 1 # 642 Fritillaria liliacea histone-like protein processed pseudogenes Exon Exon clone Fritillaria agrestis histone-like Exon Exon # protein cDNA gb AF031547 # 100 # 741

Fig. 5. Graphical overview of nucleotide alignment in BLAST N database search from histone-like protein processed pseudogenes clones from Fritillaria liliacea and histone-like protein cDNA from Fritillaria agrestis. Numbers in the above figure represents the nucleotide numbers in respective sequences from alignment.

>giI2641211IgbIAAB86857.11 (AF031547) histone-like protein [Fritillaria agrestisJ Length = 236

Score = 163 bits (413), Expect = ge-40 Identities = 198/208 (95%), positives = 201/208 (96%)

Query: 1 PAFAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYLEMISEAIASLKERTGS 60 PAFAPVPVARDEPVAKP KVTKAKAPKEKKAS+AKKPALHPTYLEMISEAIASLKERTGS Sbjct: 10 PAFAPVPVARDEPVAKPGKVTKAKAPKEKKASVAKKPALHPTYLEMISEAIASLKERTGS 69

Query: 61 SQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKISAKPTAAVKPRSA 120 SQYAIAKFVEDKHKSHLPANFKKLLLVQL+KLTAAGKLTKVKNSYKISAKPT A KP+SA Sbjct: 70 SQYAIAKFVEDKHKSHLPANFKKLLLVQLQKLTAAGKLTKVKNSYKISAKPTPAAKPKSA 129

Query: 121 AVKPKSAVAKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVKPKSKPAALKPNTVTKSKTVA 180 AVKPKSA KLKSAAKKVKKAAVKPKPKSAAVKPKAPAV KSKPAALKPNTVTKSKTVA Sbjct: 130 AVKPKSAATKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVNMKSKPAALKPNTVTKSKTVA 189

Query: 181 LKGKTAGRPAKAAKTSVKAAPGKKAAPV 208 LKGKTAGRPAKAAKTSVKAAPGKKAAPV Sbjct: 190 LKGKTAGRPAKAAKTSVKAAPGKKAAPV 217

>gi164749501dbj IBAA87331.11 (AB012694) variant of histone Hl [Lilium longiflorumJ Length 231

Score = 117 bits (294), Expect = 4e-26 Identities = 142/214 (66%), positives = 156/214 (72%), Gaps = 5/214 (2%)

Query: 1 PAFAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYLEMISEAIASLKERTGS 60 PAF PV V AK K K+ + KPALHPTYLEMISEAIASLKERTGS Sbjct: 10 PAFTPVAVDPPAAKPAKAKKAKVPKEKKASVA---KPALHPTYLEMISEAIASLKERTGS 66

Query: 61 SQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKISAKPTAAVKPRSA 120 SQ AI+KFVE+KHK+HLPANFKKLLLVQLRKLTAAGKLTKVKNSYKISAKPT A KP+ Sbjct: 67 SQIAISKFVENKHKAHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKISAKPTTATKPKKT 126 37

Query: 121 AVKPKSAVAKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVKPKSKPAALKPNTVTKSKTVA 180 + K + VAK KSAA K K A K K + KPK+ AVKPK++PAA KP V+K K VA Sbjct: 127 SAK-STTVAKPKSAAAKPKSTAAKVKKAAVKPKPKSAAVKPKAEPAAPKPKAVSKPKAVA 185

Query: 181 LKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKAK 214 K KTAG PAK AKTS K +P KKAAPVA KKAK Sbjct: 186 PKPKTAG-PAKKAKTSAKPSPSKKAAPVASKKAK 218

>gi141066961dbj IBAA36284.11 (AB021872) ribosome-sedimenting protein [Pisum sativum]

Length = 295

Score = 71.6 bits (174), Expect = 4e-12 Identities = 63/105 (60%), positives = 73/105 (69%), Gaps = 5/105 (4%)

Query: 3 FAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYLEMISEAIASLKERTGSSQ 62 F PV +EP AKP KK K+ A HPTY EM+ EAI +LKER GSSQ Sbjct: 23 FPPVVNESEEPTAKPKKAPKEPKAKKAPAKPRT----HPTYEEMVKEAIVALKERNGSSQ 78

Query: 63 YAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKI 107 YAIAKF+E+KHK LP+NFKKLLLVQ+RKL A+GKL KVK SYK+ Sbjct: 79 YAIAKFIEEKHK-QLPSNFKKLLLVQIRKLVASGKLVKVKASYKL 122

>gi149965671dbj IBAA78535.11 (AB021873) ribosome-sedimenting protein [Pisum sativum]

Length = 297

Score = 71.2 bits (173), Expect = 5e-12 Identities = 63/105 (60%), positives = 73/105 (69%), Gaps = 5/105 (4%)

Query: 3 FAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYLEMISEAIASLKERTGSSQ 62 F PV +EP AKP KK K+ A HPTY EM+ EAI +LKER GSSQ Sbjct: 25 FPPVVNESEEPTAKPKKAPKEPKAKKAPAKPRT----HPTYEEMVKEAIVALKERNGSSQ 80

Query: 63 YAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKI 107 YAIAKF+E+KHK LP+NFKKLLLVQ+RKL A+GKL KVK SYK+ Sbjct: 81 YAIAKFIEEKHK-QLPSNFKKLLLVQIRKLVASGKLVKVKASYKL 124

>giI13540395IgbIAAK29451.1IAF352248_1 (AF352248) histone HI [Pisum sativum] Length = 301

Score = 67.4 bits (163), Expect = 8e-ll Identities = 60/103 (58%), positives = 72/103 (69%), Gaps = 5/103 (4%)

Query: 5 PVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYLEMISEAIASLKERTGSSQYA 64 PV +EP AKP KK K+ A HPTY EM+ EAI +LKER GSSQYA Sbjct: 25 PVVNESEEPTAKPKKAPKEPKAKKAPAKPRT----HPTYEEMVKEAIVALKERNGSSQYA 80

Query: 65 IAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKI 107 IAKF+E+KH + LP+NFKKLLLVQ++KL A+GKL KVK SYK+ Sbjct: 81 IAKFIEEKH-TQLPSNFKKLLLVQIKKLVASGKLVKVKASYKL 122

>giI13540391IgbIAAK29449.1IAF352246_1 (AF352246) histone Hl [Pisum sativum]

Length = 296

Score = 67.0 bits (162), Expect = le-l0 Identities = 61/103 (59%), positives = 72/103 (69%), Gaps 5/103 (4%) 38

Query: 5 PVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYLEMISEAIASLKERTGSSQYA 64 PV +EP AKP KK K+ A HPTY EM+ EAI +LKER GSSQYA Sbjct: 25 PVVNESEEPTAKPKKAPKEPKAKKAPAKPRT----HPTYEEMVKEAIVALKERNGSSQYA 80

Query: 65 IAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKI 107 IAKF+E+KHK LP+NFKKLLLVQ++KL A+GKL KVK SYK+ Sbjct: 81 IAKFIEEKHK-QLPSNFKKLLLVQIKKLVASGKLVKVKASYKL 122

>giI5230785!gbIAAD41007.1IAF107024_1 (AF107024) histone H1 WH1B.1 [Triticum aestivum] Length = 275

Score = 66.6 bits (161), Expect = 1e-10 Identities = 66/110 (60%), positives = 74/110 (67%), Gaps = 6/110 (5%)

Query: 5 PVPVARDEPVAKPAKVTKAKAPKEKKASIAKKP------ALHPTYLEMISEAIASLKERT 58 PV EP AAKK KA P HPTY EM+SEAI +LKERT Sbjct: 20 PVVETTAEPAAGDANAAKETKAKAAKAKKPSAPRKPRAAPAHPTYAEMVSEAITALKERT 79

Query: 59 GSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKIS 108 GSS YAIAKFVEDKHK+HLPANF+K+L VQL+KL A+GKLTKVK SYK+S Sbjct: 80 GSSPYAIAKFVEDKHKAHLPANFRKILSVQLKKLVASGKLTKVKASYKLS 129

giI1343059SlgbIAAK25921.1IAF360211_1 (AF3602II) putative histone HI protein [Arabidopsis thalianaJ Length = 273

Score = 52.0 bits (123), Expect = 3e-06 Identities = 100/233 (42%), positives = 124/233 (52%), Gaps = 29/233 (12%)

Query: 9 ARDEPVAKPAKVTKAKAPKE------KKASIAKKPALHPTYLEMISEAlAS 53 ADVPK AK K + K + HPTY EMI +AI + Sbjct: 16 AADTTVKSPEKKPAAKGGKSKKTTTAKATKKPVKAAAPTKKKTTSSHPTYEEMIKDAIVT 75

Query: 54 LKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSYKISAKPTA 113 LKERTGSSQYAI KF+E+KHKS LP F+KLLLV L++L A+ KL KVK S+KI + +A Sbjct: 76 LKERTGSSQYAIQKFIEEKHKS-LPPTFRKLLLVNLKRLVASEKLVKVKASFKIPSARSA 134

Query: 114 AVKPRSAAV------KPKSAVAKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVKPKSKP 165 A +A V KPK VA + AK A KP + V KPK+K Sbjct: 135 ATPKPAAPVKKKATVVAKPKGKVAAAVAPAKAKAAAKGTKKPAAKVVAKAKVTAKPKAKV 194

Query: 166 AALKPNT-----VTKSKTVALKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKA 213 A KP + V+K+K VA KK RPAKA++TS + +PGKK AAKA Sbjct: 195 TAAKPKSKSVAAVSKTKAVAAKPKAKERPAKASRTSTRTSPGKKVAAPAKKVA 247

Fig. 6. BLAST P results of histone-like protein gene of Fritillaria liliacea. Query: The histone-like protein genomic clone from Fritillaria liliacea used for database search. Sbjct: Matching sequence from the database. Score: The Bit score (see material and methods). Expect: This value represents the probability ofthe match appearing by chance. Identities: total number of identical residues in common. Positives: Number ofresidues in common where the nature is conserved. 39

1 PAFAPVPVAR DEPVAKPGKV TKAKAPKEKK ASVAKKPALH PTYLEMISEA

51 IASLKERTGS SQYAIAKFVE DKHKSHLPAN FKKLLLVQLQ KLTAAGKLTK

101 VKNSYKISAK PTPAAKPKSA AVKPKSAATK LKSAAKKVKK AAVKPKPKSA

151 AVKPKAPAVK PKSKPAALKP NTVTKSKTVA LKGKTAGRPA KAAKTSVKAA

201 PGKKAAPVAL KKAK

Fig. 7. Translation of the group-l pseudogenes clones from Fritillaria liliacea. Translation data indicates that group-l pseudogenes have intact open reading frame. Translations ofthe nucleic acid data for the group 1 clones were obtained by using SeQWeb-GCG sequence analysis software.

1 LFVLFSLFYF *FP*NVRSRC N*DSRLCSGP CCRR*SSGKA DQGDEGQGP*

51 GEEGLYCEEA CSPSYLSRDD **SDRFAEGA DWIEPVRYCK VC*KQA*VPS

101 PGELQEASPC PVAETHCCWQ THQGQEFYVI SAKPTPAVKP KSAAVEPMSA

151 ATKPKSAAKK V*KAAVKPKS KPAAPKTKTV TKPKAVALKT KTVGRPAKAA

201 KISVKAAP

Fig. 8. Translations of the group 2 and 3 pseudogenes from Fritillaria liliacea. Translation data indicates that group-2 and 3 pseudogenes have inframe stop codons. Translations ofthe nucleic acid data for the group 2 and group 3 clones were obtained by using SeQWeb-GCG sequence analysis software. *- stop codons. 40

The Histone-like protein gene family from Fritillaria liliacea

The Fritillaria liliacea histone-like gene family consists oftwo functional genes and

12 processed pseudogenes. Since the peR primers used are designed from coding regions, all ofthe clones have incomplete 5' and 3' ends. Sets ofinternal primers were

also used to amplify some clones.

Functional genes in Histone-like gene family

I have identified at least 2 functional genes, labeled genomic-1 and genomic-2 (Fig.9).

Both clones contain two exons and one intron. The 5' end of first exon and the 3' end of

second exon are incomplete. The intron is 184 bp long. Genomic-1 and genomic-2 are

97% similar at the nucleotide level and 96% similar at the amino acid level.

genomic 1 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC genomic 2 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG CGGCGAAGCC

1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG YGGCGAAGCC *

genomic 1 #51 GGCCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCATTG genomic 2 #51 GGCC::: ::: : ::AAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCGTTG

51 GGCCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCRTTG ****** ***

genomic 1 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TTGAGGTCTG ATCCAGCCAC genomic 2 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TCGAGGTCTG ATCCAGCCAC

101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TYGAGGTCTG ATCCAGCCAC *

genomic 1 #151 TATTTCCTCT AGATTTGTTA ATTTATCGAA TTTGTGCAGT CCAAATTTGT genomic 2 #151 TATTTCCTCT AGATTTGTTA ATTTATTGAA TTTGTGCAGT CCAAATTTGT

#151 TATTTCCTCT AGATTTGTTA ATTTATYGAA TTTGTGCAGT CCAAATTTGT * 41

genomic 1 #201 GTACTTCCAC CAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG genomic 2 #201 GTACTTCCTC TAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG ...... #201 GTACTTCCWC YAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG *

genomic 1 #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG genomic 2 #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG ...... #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG

genomic 1 #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATTGC TTCGCTGAAG genomic 2 #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATCGC TTCGCTGAAG ...... #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATYGC TTCGCTGAAG *

genomic 1 #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA genomic 2 #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA ...... #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA

genomic 1 #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT genomic 2 #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT ...... #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT

genomic 1 #451 TGCGGAAACT CACTGCTGCT GGCAAACTCA CGAAGGTGAA GAACTCCTAC genomic 2 #451 TGCGGAAGCT CACTGCTGCT GGCAAGCTCA CAAAGGTGAA GAATTCCTAC ...... #451 TGCGGAARCT CACTGCTGCT GGCAARCTCA CRAAGGTGAA GAAYTCCTAC * *

genomic 1 #501 AAGATCTCTG CCAAACCAAC CGCTGCTGTG AAGCCTAGAT CCGCTGCTGT genomic 2 #501 AAGATCTCTG CCAAACCGAC CCCTGCTGCG AAGCCTAAAT CAGCTGCTGT ...... #501 AAGATCTCTG CCAAACCRAC CSCTGCTGYG AAGCCTARAT CMGCTGCTGT * *

genomic 1 #551 GAAGCCAAAG TCTGCTGTTG CTAAGCTCAA GTCCGCTGCC AAGAAGGTGA genomic 2 #551 GAAGCCAAAG TCTACTGCTA GTAAGCTCAA GTCCGCTGCC AAGAAGGTGA ...... #551 GAAGCCAAAG TCTRCTGYTR STAAGCTCAA GTCCGCTGCC AAGAAGGTGA

genomic 1 #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA genomic 2 #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA ...... #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA

genomic 1 #651 GCCCCTGCCG TGAAACCGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC genomic 2 #651 GCCCCTGCCG TGAACATGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC ...... #651 GCCCCTGCCG TGAAMMYGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC ***

genomic 1 #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGAAAGACT GCTGGCCGTC genomic 2 #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGGAAGACT GCTGGCCGTC ...... #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGRAAGACT GCTGGCCGTC * 42

genomic 1 #751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT genomic 2 #751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT

#751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT

genomic 1 #801 GCTCCAGTGG CTCTGAAGAA GGCTAAG genomic 2 #801 GCTCCAGTGG CTCTGAAGAA GGCTAAG

#801 GCTCCAGTGG CTCTGAAGAA GGCTAAG

Fig. 9. Multiple alignment of both genomic clones of Fritillaria liliacea. *- Nucleotide difference in the alignment, :- Gap in the sequence.

Genomic-l

The sequence ofgenomic-l was assembled from five clones (FL HL GA-l, FL HL

GA-2, FL HL GA-3, FL HL GA-4 and FL HL GA-5) (Fig. 10). These clones have only a few base differences, which could be allelic variations or peR errors. The genomic-l consensus sequence is 97% similar at the nucleotide level to Fritillaria agrestis histone like protein cDNA sequence (Genbank accession #AF031547).

FL HL 1 GA-1 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC FL HL 1 GA-2 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC FL HL 1 GA-3 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC FL HL 1 GA-4 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC ...... #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC

FL HL 1 GA-1 #51 GGCCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCATTG FL HL 1 GA-2 #51 GGCCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCATTG FL HL 1 GA-3 #51 GGCCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCATTG FL HL 1 GA-4 #51 GGCCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCATTG ...... #51 GGCCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCATTG

FL HL 1 GA-1 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TTGAGGTCTG ATCCAGCCAC FL HL 1 GA-2 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TTGAGGTCTG ATCCAGCCAC FL HL 1 GA-3 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TTGAGGTCTG ATCCAGCCAC FL HL 1 GA-4 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TTGAGGTCTG ATCCAGCCAC FL HL 1 GA-5 #1 TGAGGTCTG ATCCAGCCAC ...... #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TTGAGGTCTG ATCCAGCCAC 43

FL HL 1 GA-1 #151 TATTTCCTCT AGATTTGTTA ATTTATCGAA TTTGTGCAGT CCAAATTTGT FL HL 1 GA-2 #151 TATTTCCTCT AGATTTGTTA ATTTATCGAA TTTGTGCAGT CCAAATTTGT FL HL 1 GA-3 #151 TATTTCCTCT AGATTTGTTA ATTTATCGAA TTTGTGCAGT CCAAATTTGT FL HL 1 GA-4 #151 TATTTCCTCT AGATTTGTTA ATTTATCGAA TTTGTGCAGT CCAAATTTGT FL HL 1 GA-5 #20 TATTTCCTCT AGATTTGTTA ATTTATCGAA TTTGTGCAGT CCAAATTTGT ...... #151 TATTTCCTCT AGATTTGTTA ATTTATCGAA TTTGTGCAGT CCAAATTTGT

FL HL 1 GA-1 #201 GTACTTCCAC CAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG FL HL 1 GA-2 #201 GTACTTCCAC CAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG FL HL 1 GA-3 #201 GTACTTCCAC CAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG FL HL 1 GA-4 #201 GTACTTCCAC CAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG FL HL 1 GA-5 #70 GTACTTCCAC CAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG ...... #201 GTACTTCCAC CAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG

FL HL 1 GA-1 #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG FL HL 1 GA-2 #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG FL HL 1 GA-3 #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG FL HL 1 GA-4 #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG FL HL 1 GA-5 #120 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG ...... #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG

FL HL 1 GA-1 #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATTGC TTCGCTGAAG FL HL 1 GA-2 #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG GAGCGATTGC TTCGCTGAAG FL HL 1 GA-3 #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATTGC TTCGCTGAAG FL HL 1 GA-4 #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATTGC TTCGCTGAAG FL HL 1 GA-5 #170 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATTGC TTCGCTGAAG ...... #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATTGC TTCGCTGAAG *

FL HL 1 GA-1 #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA FL HL 1 GA-2 #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA FL HL 1 GA-3 #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA FL HL 1 GA-4 #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA FL HL 1 GA-5 #220 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA ...... #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA

FL HL 1 GA-1 #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT FL HL 1 GA-2 #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT FL HL 1 GA-3 #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT FL HL 1 GA-4 #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT FL HL 1 GA-5 #270 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT ...... #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT

FL HL 1 GA-1 #451 TGCGGAAACT CACTGCTGCT GGCAAACTCA CGAAGGTGAA GAACTCCTAC FL HL 1 GA-2 #451 TGCGGAAACT CACTGCTGCT GGCAAACTCA CGAAGGTGAA GACCTCCTAC FL HL 1 GA-3 #451 TGCGGAAACT CACTGCTGCT GGCAAACTCA CGAAGGTGAA GAACTCCTAC FL HL 1 GA-4 #451 TGCGGAAACT CACTGCTGCT GGCAAACTCA CGAAGGTGAA GAACTCCTAC FL HL 1 GA-5 #320 TGCGGAAACT CACTGCTGCT GGCAAACTCA CGAAGGTGAA GAACTCCTAC ...... #451 TGCGGAAACT CACTGCTGCT GGCAAACTCA CGAAGGTGAA GAACTCCTAC 44

FL HL 1 GA-1 #501 AAGATCTCTG CCAAACCAAC CGCTGCTGTG AAGCCTAGAT CCGCTGCTGT FL HL 1 GA-2 #501 AAGATCTCTG CCAAACCAAC CGCTGCTGTG AAGCCTAGAT CCGCTGCTGT FL HL 1 GA-3 #501 AAGATCTCTG CCAAACCAAC CGCTGCTGTG AAGCCTAGAT CCGCTGCTGT FL HL 1 GA-4 #501 AAGATCTCTG CCAAACCAAC CGCTGCTGTG AAGCCTAGAT CCGCTGCTGT FL HL 1 GA-5 #370 AAGATCTCTG CCAAACCAAC CGCTGCTGTG AAGCCTAGAT CCGCTGCTGT ...... #501 AAGATCTCTG CCAAACCAAC CGCTGCTGTG AAGCCTAGAT CCGCTGCTGT

FL HL 1 GA-1 #551 GAAGCCAAAG TCTGCTGTTG CTAAGCTCAA GTCCGCTGCC AAGAAGGTGA FL HL 1 GA-2 #551 GAAGCCAAAG TCTGCTGTTG CTAAGCTCAA GTCCGCTGCC AAGAAGGTGA FL HL 1 GA-3 #551 GAAGCCAAAG TCTGCTGTTG CTAAGCTCAA GTCCGCTGCC AAGAAGGTGA FL HL 1 GA-4 #551 GAAGCCAAAG TCTGCTGTTG CTAAGCTCAA GTCCGCTGTC AAGAAGGTGA FL HL 1 GA-5 #420 GAAGCCAAAG TCTGCTGTTG CTAAGCTCAA GTCCGCTGCC AAGAAGGTGA ...... #551 GAAGCCAAAG TCTGCTGTTG CTAAGCTCAA GTCCGCTGCC AAGAAGGTGA *

FL HL 1 GA-1 #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA FL HL 1 GA-2 #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA FL HL 1 GA-3 #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA FL HL 1 GA-4 #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA FL HL 1 GA-5 #470 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA ...... #601 AGAAAGCAGC TGTGAAGCCA AAGCCTAAAT CTGCTGCCGT GAAGCCAAAA

FL HL 1 GA-1 #651 GCCCCTGCCG TGAAACCGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC FL HL 1 GA-2 #651 GCCCCTGCCG TGAAACCGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC FL HL 1 GA-3 #651 GCCCCTGCCG TGAAACCGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC FL HL 1 GA-4 #651 GCCCCTGCCG TGAAACCGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC FL HL 1 GA-5 #520 GCCCCTGCCG TGAAACCGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC ...... #651 GCCCCTGCCG TGAAACCGAA ATCCAAGCCT GCTGCCCTGA AGCCAAATAC

FL HL 1 GA-1 #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGAAAGACT GCTGGCCGTC FL HL 1 GA-2 #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGAAAGACT GCTGGCCGTC FL HL 1 GA-3 #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGAAAGACT GCTGGCCGTC FL HL 1 GA-4 #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGAAAGACT GCTGGCCGTC FL HL 1 GA-5 #570 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGAAAGACT GCTGGCCGTC ...... #701 AGTGACAAAA TCAAAGACTG TAGCTCTGAA GGGAAAGACT GCTGGCCGTC

FL HL 1 GA-1 #751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT FL HL 1 GA-2 #751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT FL HL 1 GA-3 #751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT FL HL 1 GA-4 #751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT FL HL 1 GA-5 #620 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG ...... #751 CAGCAAAGGC GGCAAAGACA TCCGTCAAAG CTGCTCCGGG AAAGAAGGCT

FL HL 1 GA-1 #801 GCTCCAGTGG CTCTGAAGAA GGCTAAG FL HL 1 GA-2 #801 GCTCCAGTGG CTCTGAAGAA GGCTAAG FL HL 1 GA-3 #801 GCTCCAGTGG CTCTAAAGAA GGCTAAG FL HL 1 GA-4 #801 GCTCCAGTGG CTCTGAAGAA GGCTAAG ...... #801 GCTCCAGTGG CTCTGAAGAA GGCTAAG *

Fig. 10. Multiple alignment of genomic-1 clones of Fritillaria liliacea. * -Nucleotide difference in the alignment, : -. Gap in the sequence 45

Clone FL HL 1 GA-l

This clone is 827 base pairs (bp) long and was amplified by His forward and His reverse pnmers. The sequence ofthis clone is used as the reference for the discussion below.

Clone FL HL 1 GA-2

This clone is 827 bp long and was amplified by His forward and His reverse primers.

It has 2 base changes compared to the reference sequence. At position 331, A has changed to G which has replaced the amino acid glutamic to glycine. At position 493, A has changed to C, this change has replaced the amino acid asparagine to threonine.

Clone FL HL 1 GA-3

This clone is 827 bp long and was amplified by His forward and His reverse primers.

Its sequence is identical to the reference sequence.

Clone FL HL 1 GA-4

This clone is 827 bp long and was amplified by His forward and His reverse primers.

It has one base change compared to the reference sequence. At position 589, C has

changed to T, which has replaced the amino acid alanine to valine. 46

Clone FL HL I GA-5

This clone is 659 bp long and was amplified by internal forward and internal reverse primers. Its sequence is identical to clone FL HL I GA-I.

Genomic 2

Genomic-2 is 818 bp long and 97% similar to Fritillaria agrestis histone-like protein eDNA sequence (Genbank accession #AF031547) and is 97% similar to genomic 1. It has a 9 bp deletion at position 55-63 bp (Fig.9). This deletion has not altered the reading frame. Genomic-2 was assembled from ten clones (FL HL 1GB-I, FL HL I GB-2, FL

HL I GB-3, FL HL I GB-4, FL HL I GB-5, FL HL I GB-6, FL HL I GB-7, FL HL I

GB-8, FL HL I GB-9 and FL HL 1GB-I0) (Fig-II). These clones differ by only a few bases. As with genomic-I, these differences could be allelic variations or PCR errors.

FL HL 1 GB-1 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG CGGCGAAGCC FL HL 1 GB-4 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG CGGCGAAGCC FL HL 1 GB-6 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG CGGCGAAGCC

#1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG CGGCGAAGCC

FL HL 1 GB-1 #51 GGCCAAGGCC AAGGCCCCTA AGGAGAAGAA GGCCTCCGTT GCGAAGAAGC FL HL 1 GB-4 #51 GGCCAAGGCC AAGGCCCCTA AGGAGAAGAA GGCCTCCGTT GCGAAGAAGC FL HL 1 GB-6 #51 GGCCAAGGCC AAGGCCCCTA AGGAGAAGAA GGCCTCCGTT GCGAAGAAGC

#51 GGCCAAGGCC AAGGCCCCTA AGGAGAAGAA GGCCTCCGTT GCGAAGAAGC 47

FL HL 1 GB-1 #101 CTGCTCTCCA TCCTACCTAT CTCGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-2 #1 CGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-3 #1 CGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-4 #101 CTGCTCTCCA TCCTACCTAT CTCGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-5 #1 CGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-6 #101 CTGCTCTCCA TCCTACCTAT CTCGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-7 #1 CGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-8 #1 CGAGGTCT GATCCAGCCA CCATTTCCTC FL HL 1 GB-9 #1 CGAGGTCT GATCCAGCCA CTATTTCCTC FL HL 1 GB-10 #1 CGAGGTCT GATCCAGCCA CTATTTCCTC ...... #101 CTGCTCTCCA TCCTACCTAT CTCGAGGTCT GATCCAGCCA CTATTTCCTC *

FL HL 1 GB-1 #151 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-2 #29 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-3 #29 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-4 #151 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-5 #29 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-6 #151 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-7 #29 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-8 #29 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-9 #29 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT FL HL 1 GB-10 #29 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT ...... #151 TAGATTTGTT AATTTATTGA ATTTGTGCAG TCCAAATTTG TGTACTTCCT

FL HL 1 GB-1 #201 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-2 #79 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-3 #79 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-4 #201 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-5 #79 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-6 #201 CTAGATCTGT TAATTTACTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-7 #79 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-8 #79 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-9 #79 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC FL HL 1 GB-10 #79 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC ...... #201 CTAGATCTGT TAATTTATTG AATTTATGCA GTCCAATTTT GTGTACTTCC

FL HL 1 GB-1 #251 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-2 #129 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-3 #129 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-4 #251 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-5 #129 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-6 #251 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-7 #129 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-8 #129 TCTAGATTTG TTAATTTATG lUl.AXI'AATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-9 #129 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT FL HL 1 GB-10 #129 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT ...... #251 TCTAGATTTG TTAATTTATG AAATTAATGT AGTCTAATTT GGTCTACTTT 48

FL HL 1 GB-1 #301 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-2 #179 CTAAATCTCA GATGATCAGT GAAGCGATCG CTCCGCTGAA GGAGCGGACT FL HL 1 GB-3 #179 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-4 #301 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-5 #179 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-6 #301 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-7 #179 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-8 #179 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-9 #179 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT FL HL 1 GB-10 #179 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT ...... #301 CTAAATCTCA GATGATCAGT GAAGCGATCG CTTCGCTGAA GGAGCGGACT *

FL HL 1 GB-1 #351 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-2 #229 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-3 #229 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-4 #351 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-5 #229 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC i"L HL 1 GB-6 #351 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-7 #229 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-8 #229 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-9 #229 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC FL HL 1 GB-10 #229 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC ...... #351 GGATCGAGCC AGTACGCTAT TGCAAAGTTT GTTGAAGACA AGCACAAGTC

FL HL 1 GB-1 #401 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-2 #279 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-3 #279 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-4 #401 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-5 #279 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-6 #401 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-7 #279 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-8 #279 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-9 #279 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC FL HL 1 GB-10 #279 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC ...... #401 TCATCTCCCG GCGAACTTCA AGAAGCTTCT CCTTGTCCAG TTGCGGAAGC

FL HL 1 GB-1 #451 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-2 #329 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-3 #329 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-4 #451 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-5 #329 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-6 #451 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-7 #329 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-8 #329 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-9 #329 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT FL HL 1 GB-10 #329 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT ...... #451 TCACTGCTGC TGGCAAGCTC ACAAAGGTGA AGAATTCCTA CAAGATCTCT

FL HL 1 GB-1 #501 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-2 #379 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-3 #379 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-4 #501 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-5 #379 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-6 #501 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-7 #379 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-8 #379 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-9 #379 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA FL HL 1 GB-10 #379 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA ...... #501 GCCAAACCGA CCCCTGCTGC GAAGCCTAAA TCAGCTGCTG TGAAGCCAAA 49

FL HL 1 GB-1 #551 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-2 #429 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-3 #429 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-4 #551 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-5 #429 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-6 #551 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-7 #429 GTCTACTGCC AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-8 #429 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-9 #429 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG FL HL 1 GB-10 #429 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG ...... #551 GTCTACTGCT AGTAAGCTCA AGTCCGCTGC CAAGAAGGTG AAGAAAGCAG

FL HL 1 GB-1 #601 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-2 #479 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-3 #479 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-4 #601 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-5 #479 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-6 #601 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-7 #479 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-8 #479 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC FL HL 1 GB-9 #479 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCTAAA AGCCCCTGCC FL HL 1 GB-10 #479 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAATCCAAA AGCCCCTGCC ...... #601 CTGTGAAGCC AAAGCCTAAA TCTGCTGCCG TGAAGCCAAA AGCCCCTGCC **

FL HL 1 GB-1 #651 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-2 #529 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGGCAAA FL HL 1 GB-3 #529 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-4 #651 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-5 #529 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-6 #651 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-7 #529 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-8 #529 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-9 #529 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA FL HL 1 GB-10 #529 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA ...... #651 GTGAACATGA AATCCAAGCC TGCTGCCCTG AAGCCAAATA CAGTGACAAA *

FL HL 1 GB-1 #701 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-2 #579 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-3 #579 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-4 #701 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-5 #579 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-6 #701 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-7 #579 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-8 #579 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-9 #579 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG FL HL 1 GB-10 #579 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG ...... #701 ATCAAAGACT GTAGCTCTGA AGGGGAAGAC TGCTGGCCGT CCAGCAAAGG 50

FL HL 1 GB-1 #751 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG GAAAGAAGGC TGCTCCAGTG FL HL 1 GB-2 #629 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG G FL HL 1 GB-3 #629 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG G FL HL 1 GB-4 #751 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG G FL HL 1 GB-5 #629 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG GAAAGAAGGC TGCTCCAGTG FL HL 1 GB-6 #751 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG GAAAGAAGGC TGCTCCAGTG FL HL 1 GB-7 #629 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG G FL HL 1 GB-8 #629 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG GAAAGAAGGC TGCTCCAGTG FL HL 1 GB-9 #629 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG GAAAGAAGGT TGCTCCAGTG FL HL 1 GB-10 #629 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG GAAAGAAGGC TGCTCCAGTG ...... #751 CGGCAAAGAC ATCCGTCAAA GCTGCTCCGG GAAAGAAGGC TGCTCCAGTG *

FL HL 1 GB-1 #801 GCTCTGAAGA AGGCTAAG FL HL 1 GB-5 #679 GCTCTGAAGA AGGCTAAG FL HL 1 GB-6 #801 GCTCTGAAGA AGGCTAAG FL HL 1 GB-8 #679 GCTCTGAAGA AGGCTAAG FL HL 1 GB-9 #679 GCTCTGAAGA AGGCTAAG FL HL 1 GB-10 #679 GCTCTGAAGA AGGCTAAG ...... #801 GCTCTGAAGA AGGCTAAG

Fig. 11. Multiple Alignment of genomic-2 clones of Fritillaria liliacea. *- Nucleotide difference in the alignment, : -. Gap in the sequence

FLHL 1 GB-l

This clone is 818 bp long and was amplified by His forward and reverse primers. The

sequence ofthis clone is used as the reference for the discussion below.

FLHL 1 GB-2

This clone is 659 bp long and was amplified by internal forward and reverse primers.

Its sequence is identical to the corresponding region ofreference sequence. 51

FL HL 1 GB-3

This clone is 659 bp long and was amplified by internal forward and reverse primers.

It has 2 base differences compared to the corresponding region ofreference sequence. At position 333, T has changed to C, replacing the amino acid serine to proline. At position

696, A has changed to G, changing the amino acid threonine to alanine.

FLHL 1 GB-4

This clone is 781 bp long and was amplified by original His forward and internal reverse primers. Its sequence is identical to the reference sequence.

FL HL 1 GB-5

This clone is 696 bp long and was amplified by internal forward and His reverse primers. Its sequence is identical to the reference sequence.

FLHL 1 GB-6

This clone is 818 bp long and was amplified by His forward and His reverse primers.

It has one base difference compared to the corresponding region ofreference sequence.

At position 218, T has changed to C. This change is in the intron and therefore will not affect the encoded protein. 52

FL HL 1 GB-7

This clone is 659 bp long and was amplified by internal forward and reverses primers.

It has one base change compared to the corresponding region ofreference sequence. At position 560, T has changed to C. Being a synonymous substitution, it has not changed the overlaying amino acid; therefore it will not affect the encoded protein.

FL HL 1 GB-8

This clone is 696 bp long and was amplified by internal forward and internal reverse primers. It has one base change compared to the corresponding region ofreference sequence. At position 142, T has changed to C. This base change is in the intron so it will not affect the encoded protein.

FLHL 1 GB-9

This clone is 696 bp long and was amplified by internal forward and internal reverse primers. It has 2 base changes compared to the corresponding region ofreference sequence. At position 637, and 790, C has changed to T. The first change has replaced the amino acid leucine by proline and the second change has replaced the amino acid alanine by valine. 53

FL HL 1 GB-IO

This clone is 696 bp long and was amplified by internal forward and reverse primers.

It has one base change compared to the corresponding region ofreference sequence. At position 635, G has changed to T. This has changed the amino acid lysine to asparagine. 54

Characterization of Histone-like Protein in Fritillaria liliacea.

Table 3- Comparison of histone-like protein: Comparison ofhistone-like protein from Fritillaria liliacea, Fritillaria agrestis and Lilium longiflorum. P35 protein from Lilium longiflorum is a nucleolar histone variant.

Nucleotide Amino Acid Similarity Amino Acid Similarity to Histone-like protein Length in Similarity to to F. agrestis Protein L. longiflorum p35 in F. liliacea AA F. agrestis protein

Genomic 1 214 97% 96% 82%

Genomic 2 211 97% 98% 83%

In the Fritillaria liliacea samples, none ofthe clones have complete 5' and 3' ends, therefore all amino acid sequences are truncated at 5' and 3' ends. Comparison of histone-like protein from Fritillaria liliacea, Fritillaria agrestis and Lilium longiflorum revealed that histone-like protein from Fritillaria liliacea does not have the first nine 5'or

N-terminal amino acids and last thirteen 3' or carboxyl terminus amino acids (Fig. 12).

The total length ofthe histone-like protein from Fritillria agrestis is 236 amino acids and its complete amino acid sequence is available in the database (genbank accession #-

AAB86857). Since Fritillaria liliacea and Fritillaria agrestis are closely related species and share high nucleotide similarity (sequence identity between two nucleotide/amino acid sequences, sequence similarity does not indicate that two sequences are identical or have common ancestry.) (Table 3), the Fritillaria agrestis amino acid sequence can be used to characterize the histone-like protein from Fritillaria liliacea. 55

The Fritillaria agrestis histone-like protein amino acid sequence is 80% similar to the nucleolar p35 histone-like protein from Lilium longiflorum. Also, the histone-like proteins from both species have the same amino acid length (Fig 12). Fritillaria and

Lilium are closely related genera so the similarity between the two proteins suggests that histone-like protein from Fritillaria agrestis might also be a nucleolar protein. lfthe

protein is associated with nucleoli, its protein sequence should have a nuclear localization

signal. This is indeed the case in Fritillaria agrestis. The nuclear localization signal in

Fritillaria agrestis peptide is located at position 220 (Using PSORT (version 6.4) at

Expasy). Nuclear localization signal is "KK AKAGKKVTTP KKAKK" and is located at

the carboxyl terminus (Fig 12).

Nuclear localization signals are not conserved, but are generally rich in basic residues

(Cokol, 2000). Nuclear localization signal in Fritillaria agrestis histone-like protein is

also rich in basic amino acid lysine. PSORT software uses the same information to

determine whether a protein is nuclear or cytoplasmic. lfthe sum ofthe basic residues is

higher than 20%, then protein is categorized as having a high possibility ofbeing nuclear

than cytoplasmic. PSORT software showed 0.706 certainty for nuclear localization of

histone like protein from Fritillaria liliacea. Also lnterproscan at Expasy (finds

conserved protein domains) identified a Hl&H5 histone signature (at position 36-106) in

the histone-like protein sequence from F. liliacea. HI & H5 histone signature or domain

is a conserved motif found in all HI histones. H5 is a HI variant found in the nucleated

red blood cells ofbirds. These results and similarity between histone like protein from 56

Fritillaria agrestis. Fritillaria liliacea and Lilium longiflorum suggest that the histone-

like protein from Fritillaria liliacea might be a nucleolar histone-like protein. Nucleolar

localization ofhistone like protein from Fritillaria liliacea can be investigated using histone-like protein specific antibodies in future.

Agrestis_pep 1 IsAAIIDiIi genomic_2 1 genomic1 1 lilium T1 1 consensus 1 AKPakvtKAKaPKEKKASvAkKPALHP

Agrestis_pep 51 YLEMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLe genomic_2 39 TYLEMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLR genomic1 42 TYLEMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLR lilium T1 48 TYLEMISEAIASLKERTGSSQ I KFVE KHKlHLPANFKKLLLVQLR HI & H5 histone consensus 61 TYLEMISEAIASLKERTGSSQyAlaKFVEdKHKSHLPANFKKLLLVQLrK domain

Agrestis_pep 101 LTAAGKLTKVKNSYKISAKPTPAAKP SAAVKPKS KLKS genomic 2 89 LTAAGKLTKVKNSYKISAKPTPAAKP SAAVKPKS KLKS genomic1 92 LTAAGKLTKVKNSYKISAKPT~ mKP SAAVKPKS+KLKS lilium T1 98 LTAAGKLTKVKNSYKISAKPT KP KTSAKS 'KPKSAAA KS consensus 181 LTAAGKLTKVKNSYKISAKPTpAaKPk saavKPKSaaaK1KSaA

Agrestis_pep 145 KKVKKAAVKPKPKSAAVKPKAPAVNMKSKPAALKPNTVTKSKTVALKGKT genomic 2 133 KKVKKAAVKPKPKSAAVKPKAPAVNMKSKPAALKPNTVTKSKTVALKGKT genomic1 136 KKVKKAAVKPKPKSAAVKPKAPA KSKPAALKPNTVTKSKTVALKGKT lilium T1 148 'KVKKAAVKPKPKSAAVKP P KP' K~ KT consensus 301 kKVKKAAVKPKPKSAAVKPKApavnmkskPAA1KPntVtKsKtVA1KgKT

Agrestis_pep 195 genomic 2 183 genomic1 186 lilium T1 191 consensus 361 Nuclear localization signal

Fig. 12. Multiple alignment of histone-like protein from Fritillaria liliacea, Fritillaria agrestis and Lilium longijlorum. Amino acid sequences ofhistone-like protein from Fritillaria liliacea, Fritillaria agrestis and Lilium longiflorum are aligned using BOX Shade program. This program shows the identical amino acids from alignment in a shaded box. -- - HI and H5 histone domain, -- - Nuclear localization signal 57

Pseudogenes in Histone-like gene family from Fritillaria liliacea

In the histone-like gene family from Fritillaria liliacea, apart from 2 functional genes, 3 groups ofpseudogenes are observed. All pseudogenes are processed pseudogenes as they lack introns (Fig.5). These 3 groups are significantly different from each other and are classified based on their unique patterns ofindels. Group-l pseudogenes do not have any inde1s, while group-2 pseudogenes have a 48 bp deletion at position 588-635 and group-3 pseudogenes have a 17 bp insertion at position 534-550.

Group 1- Pseudogenes

This group includes clones FL HL 1 PA-l, FL HL 1 PA-2 and FL HL 1 PA-3 (Fig.

13). Clones from this group have a complete open reading frame and share 98-96 % similarity at the nucleotide level and 95-99 % similarity at the amino acid level with functional genomic sequences. Although these sequences have a complete open reading frame, it is unlikely that they are functional. Processed pseudogenes are cDNA copies of a processed mRNA, which gets inserted randomly into the genome. To produce a functional protein, they have to be inserted next to an active promoter. Since this insertion is random, pseudogenes with open reading frame are usually not expressed.

Over time these genes acquire mutations, which will eventually interrupt their open reading frame. Group 1 pseudogenes lack the intron but have an open reading frame, therefore they appear to be recently inserted into the genome. 58

FL HL 1 PA-1 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC FL HL 1 PA-2 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC FL HL 1 PA-3 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC ...... #1 CCCGCCTTTG CTCCGGTCCC TGTTGCCAGA GATGAACCGG TGGCGAAGCC

FL HL 1 PA-1 #51 GGGCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCGTCG FL HL 1 PA-2 #51 GGGCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCGTCG FL HL 1 PA-3 #51 GGGCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCGTCG ...... #51 GGGCAAGGTG ACGAAGGCCA AGGCCCCTAA GGAGAAGAAG GCCTCCGTCG

FL HL 1 PA-1 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TCGAGATGAT CAGTGAAGCG FL HL 1 PA-2 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TCGAGATGAT CAGTGAAGCG FL HL 1 PA-3 #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TCGAGATGAT CAGTGAAGCG ...... #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TCGAGATGAT CAGTGAAGCG

FL HL 1 PA-1 #151 ATCGCTTCGC TGAAGGAGCG GACTGGATCG AGCCAGTACG CTATTGCGAA FL HL 1 PA-2 #151 ATCGCTTCGC TGAAGGAGCG GACTGGATCG AGCCAGTACG CTATTGCGAA FL HL 1 PA-3 #151 ATCGCTTCGC TGAAGGAGCG GACTGGATCG AGCCAGTACG CTATTGCGAA ...... #151 ATCGCTTCGC TGAAGGAGCG GACTGGATCG AGCCAGTACG CTATTGCGAA

FL HL 1 PA-1 #201 GTTTGTTGAA GACAAGCACA AGTCTCATCT CCCGGCGAAC TTCAAGAAGC FL HL 1 PA-2 #201 GTTTGTTGAA GACAAGCACA AGTCTCATCT CCCGGCGAAC TTCAAGAAGC FL HL 1 PA-3 #201 GTTTGTTGAA GACAAGCACA AGTCTCATCT CCCGGCGAAC TTCAAGAAGC ...... #201 GTTTGTTGAA GACAAGCACA AGTCTCATCT CCCGGCGAAC TTCAAGAAGC

FL HL 1 PA-1 #251 TTCTCCTTGT CCAGTTGCAG AAACTCACTG CTGCTGGCAA ACTCACGAAG FL HL 1 PA-2 #251 TTCTCCTTGT CCAGTTGCAG AAACTCACTG CTGCTGGCAA ACTCACGAAG FL HL 1 PA-3 #251 TTCTCCTTGT CCAGTTGCAG AAACTCACTG CTGCTGGCAA ACTCACGAAG ...... #251 TTCTCCTTGT CCAGTTGCAG AAACTCACTG CTGCTGGCAA ACTCACGAAG

FL HL 1 PA-1 #301 GTGAAGAATT CCTACAAGAT CTCTGCCAAA CCAACCCCTG CTGCGAAGCC FL HL 1 PA-2 #301 GTGAAGAATT CCTACAAGAT CTCTGCCAAA CCAACCCCTG CTGCGAAGCC FL HL 1 PA-3 #301 GTGAAGAATT CCTACAAGAT CTCTGCCAAA CCAACCGCTG CTGTGAAGCC ...... #301 GTGAAGAATT CCTACAAGAT CTCTGCCAAA CCAACCCCTG CTGCGAAGCC *

FL HL 1 PA-1 #351 TAAATCCGCT GCTGTGAAGC CAAAGTCTGC TGCTACTAAA CTCAAGTCCG FL HL 1 PA-2 #351 TAAATCCGCT GCTGTGAAGC CAAAGTCTGC TGCTACTAAA CTCAAGTCCG FL HL 1 PA-3 #351 TAGATCCGCT GCTGTGAAGC CAAAGTCTGC TGTTGCTAAG CTCAAGTCCG ...... - ...... #351 TAAATCCGCT GCTGTGAAGC CAAAGTCTGC TGCTACTAAA CTCAAGTCCG * * *

FL HL 1 PA-1 #401 CTGCCAAGAA GGTGAAGAAA GCAGCTGTGA AGCCAAAGCC TAAATCTGCT FL HL 1 PA-2 #401 CTGCCAAGAA GGTGAAGAAA GCAGCTGTGA AGCCAAAGCC TAAATCTGCT FL HL 1 PA-3 #401 CTGCCAAGAA GGTGAAGAAA GCAGCTGTGA AGCCAAAGCC TAAATCTGCT ...... #401 CTGCCAAGAA GGTGAAGAAA GCAGCTGTGA AGCCAAAGCC TAAATCTGCT 59

FL HL 1 PA-1 #451 GCCGTGAAGC CAAAAGCCCC TGCCGTGAAC ATGAAATCCA AGCCTGCTGC FL HL 1 PA-2 #451 GCCGTGAAGC CAAAAGCCCC TGCCGTGAAA CCGAAATCCA AGCCTGCTGC FL HL 1 PA-3 #451 GCCGTGAAGC CAAAAGCCCC TGCCGTGAAA CCGAAATCCA AGCCTGCTGC ...... #451 GCCGTGAAGC CAAAAGCCCC TGCCGTGAAA CCGAAATCCA AGCCTGCTGC

FL HL 1 PA-1 #501 CCTGAAGCCA AATACAGTGA CAAAATCAAA GACTGTAGCT CTGAAGGGGA FL HL 1 PA-2 #501 CCTGAAGCCA AATACAGTGA CAAAATCAAA GACTGTAGCT CTGAAGGGAA FL HL 1 PA-3 #501 CCTGAAGCCA AATACAGTGA CAAAATCAAA GACTGTAGCT CTGAAGGGAA ...... #501 CCTGAAGCCA AATACAGTGA CAAAATCAAA GACTGTAGCT CTGAAGGGAA *

FL HL 1 PA-1 #551 AGACTGCTGG CCGTCCAGCA AAGGCGGCAA AGACATCCGT CAAAGCTGCT FL HL 1 PA-2 #551 AGACTGCTGG CCGTCCAGCA AAGGCGGCAA AGACATCCGT CAAAGCTGCT FL HL 1 PA-3 #551 AGACTGCTGG CCGTCCAGCA AAGGCGGCAA AGACATCCGT CAAAGCTGCT ...... #551 AGACTGCTGG CCGTCCAGCA AAGGCGGCAA AGACATCCGT CAAAGCTGCT

FL HL 1 PA-1 #601 CCGGGAAAGA AGGCTGCTCC AGTGGCTCTG AAGAAGGCTA AG FL HL 1 PA-2 #601 CCGGGAAAGA AGGCTGCTCC AGTGGCTCTG AAGAAGGCTA AG FL HL 1 PA-3 #601 CCGGGAAAGA AGGCTGCTCC AGTGGCTCTG AAGAAGGCTA AG ...... #601 CCGGGAAAGA AGGCTGCTCC AGTGGCTCTG AAGAAGGCTA AG

Fig. 13. Multiple alignment of histone-like protein Group 1 pseudogenes clones in Fritillaria liliacea. *-Nucleotide difference in the alignment, : -. Gap in the sequence

Group 2- Pseudogenes

This group includes clones FL HL 1 PB-I, FL HL 1 PB-2, FL HL 1 PB-3, FL HL 1

PB-4, FL HL 1 PB-5, FL HL 1 PB-6, FL HL 1 PB-7, FL HL 1 PE-I and FL HL 1 PF-I

(Fig-I 4). Each has a 48 bp indel at position 588-635 (Fig-16). None ofthese clones have a complete open reading frame. Many base changes and indels in individual clones have introduced stop codons in the reading frame. Most ofthese clones differ from each other by a few base changes. Clone FL HL 1 PE-I and FL HL 1 PF-1 have their own unique indels. Clone FL HL I PB-3 and FL HL I PB-5 are identical. Clone FL HL 1 PB-I and

FL HL I PB-2 have only one difference at position 568. This difference could represent allelic variation or PCR error. Similarly, clone FL HL 1 PB-6 and FL HL 1 PB-7 have 60

only one difference at position 353 and it could represent a PCR error. Clones with significant differences were considered for further analysis. The selected clones are FL

HL 1 PB-1, FL HL 1 PB-3, FL HL 1 PB-6, FL HL 1 PE-1, FL HL 1 PF-l.

FL HL 1 PE-1

This clone is 537 bp in length. It has a 59 bp insertion at position 227-284 compared to group-2 consensus sequence (Fig-14). This insertion has a 27 bp direct repeat of position 227-253, at position 285-312. Also at position 444-460 there is a 17 bp insertion, which is a direct repeat. Both ofthese direct repeats could result from transposable element insertion/excision or could result from polymerase error during

PCR.

FL HL 1 PF-1

This clone is 731 bp long. Although it is similar to the other Group 2 clones, it has a

138 bp insertion at position 742 (Fig-14). Immediately after position 741, there is sequence similarity to His reverse primer followed by 35 base pairs ofnon-homologous sequence. At position 801-879, there appears to be a direct repeat ofposition 663-74l.

Considering the similarity to the primer sequence and the direct repeat ofthe end sequence, this appears to be a PCR error. 61

FL HL 1 PB-3 #1 TTATTTGTTC TATTTTCCCT CTTTTACTTT TAATTTCCTT GAAATGTCCG

#1 TTATTTGTTC TATTTTCCCT CTTTTACTTT TAATTTCCTT GAAATGTCCG

FL HL 1 PB-3 #51 CAGCCGTTGC AATTGAGACT CCCGCCTTTG CTCCGGTCCC TG:TTGCCGG FL HL 1 PB-1 #1 CCCGCCTTTG CTCCGGTCCC TGTTTGCCGG FL HL 1 PB-2 #1 CCCGCCTTTG CTCCGGTCCC TGTTGCC:GG FL HL 1 PF-1 #1 CTCACCTTTG CTTCGGTCCC TG:TCGCCAG

#51 CAGCCGTTGC AATTGAGACT CCCGCCTTTG CTCCGGTCCC TGTTTGCCGG ** * * ** **

FL HL 1 PB-3 #101 AGATGATCTA GCGGCAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA FL HL 1 PB-1 #31 AGATGATCTA GCGGCAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA FL HL 1 PB-2 #31 AGATGATCTA GCGGCAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA FL HL 1 PF-1 #31 AGATGATCTG ACGGAAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA

#101 AGATGATCTA GCGGCAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA

FL HL 1 PB-3 #151 AGGAGAAGAA GGCCTCTATT GCGAAGAAGC CTGCTCTCCA TCCTACCTAT FL HL 1 PB-1 #81 AGGAGAAGAA GGCCTCTATT GCGAAGAAGC CTGCTCTCCA TCCTACCTAT FL HL 1 PB-2 #81 AGGAGAAGAA GGCCTCTATT GCGAAGAAGC CTGCTCTCCA TCCTACCTAT FL HL 1 PF-1 #81 AGAAGAAGAA GGCCTCTGTT ACGAAGAAGC CTGCTCTCCA TTCTACCTAT

#151 AGGAGAAGAA GGCCTCTATT GCGAAGAAGC CTGCTCTCCA TCCTACCTAT * *

FL HL 1 PB-3 #201 CTCGAGATGA TTAGTGAAGC GATCGC:::: ::::::::: : ::::::::: : FL HL 1 PB-1 #131 CTCGAGATGA TTAGTGAAGC GATCGC:::: ::::::::: : ::::::::: : FL HL 1 PB-2 #131 CTCGAGATGA TTAGTGAAGC GATCGC: ::: ::::::::: : ::::::::: : FL HL 1 PB-4 #1 CGAGATGA TTAGTGAAGT GATCGC: ::: ::::::::: : FL HL 1 PB-5 #1 CGAGATGA TTAGTGAAGC GATCGC: ::: ::::::::: : ::::::::: : FL HL 1 PB-6 #1 CGAGATGA TTAGTGAAGT GATCGC:::: ::::::::: : ::::::::: : FL HL 1 PB-7 #1 CGAGATGA TTAGTGAAGT GATCGC:::: ::::::::: : ::::::::: : FL HL 1 PF-1 #131 CTCGAGATGA TTAGTGAAGC GATCGC: ::: ::::::::: : ::::::::: : FL HL 1 PE-1 #1 TGAGATAA TTAGTGAAGG GATAGATTTG CTGAAGGAGC AGACTGGATC

#201 CTCGAGATGA TTAGTGAAGC GATCGCTTTG CTGAAGGAGC AGACTGGATC ** ***

FL HL 1 PB-3 #251 ::::::::: : ::::::::: : ::: :TTTGCT :GAAGGAGCA FL HL 1 PB-1 #181 ::::::::: : ::::::::: : : :: :TTTGCT :GAAGGAGCA FL HL 1 PB-2 #181 ::::::::: : ::::::::: : : :: :TTTGCT :GAAGGAGCA FL HL 1 PB-4 #49 ::::::::: : ...... ::::::::: : ::: :TTTGCT :GAAGGAGTA FL HL 1 PB-5 #49 ::::::::: : ::::::::: : ::: :TTTGCT :GAAGGAGCA FL HL 1 PB-6 #49 ::::::::: : ::::::::: : :: : :TTTGCT :GAAGGAGTA FL HL 1 PB-7 #49 ::::::::: : ::::::::: : ::::::::: : ::: :TTTGCT TGAAGGAGTA FL HL 1 PF-1 #181 ::::::::: : ::::::::: : ::: :TTTGCT :GAAGGAGCA FL HL 1 PE-1 #49 GAGCACCTAT CGAGATGATT AGTGAAGCGA TAAATTTGCT :GAAGGAGCA

#251 GAGCACCTAT CGAGATGATT AGTGAAGCGA TAAATTTGCT :GAAGGAGCA ** 62

FL HL 1 PB-3 #301 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-1 #231 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTG:A AACAAGCATA FL HL 1 PB-2 #231 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-4 #99 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-5 #99 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-6 #99 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-7 #99 GCCTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PF-1 #231 GACTGGATCA AACCAGTACG ATATTGTAAA GTTTGTTGAA AACAAGCATA FL HL 1 PE-1 #99 GACTGGATTG GGCCAGTACG CTATGGCAAA GTTTGTTGAA AACAAGTATA ...... #301 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA * ** ** *** *

FL HL 1 PB-3 #351 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TTCCCCTTGT CCAGTTGCGG FL HL 1 PB-1 #281 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TT:CCCTTGT CCAGTTGCGG FL HL 1 PB-2 #281 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TTCCCCTTGT CCAGTTGCGG FL HL 1 PB-4 #149 AGTCCCATCT CCCGGCGAAC TTCAAGAAGT TTCCCCTTGT CCAGTTGCGG FL HL 1 PB-5 #149 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TTCCCCTTGT CCAGTTGCGG FL HL 1 PB-6 #149 AGCCCCATCT CCCGGCGAAC TTCAAGAAGT TTCCCCTTGT CCAGTTACGG FL HL 1 PB-7 #149 AGTCCCATCT CCCGGCGAAC TTCAAGAAGT TTCCCCTTGT CCAGTTACGG FL HL 1 PF-1 #281 AGTCCCATCT CCCGACGAAC TTCAAGAAGC TTCCTCTTGT CCAGTTGTGG FL HL 1 PE-1 #149 AGTCCCATCT CCCGGCAAAC TTCAAGAAGC TTCTCCTTGT CCAGTTACGG ...... #351 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TTCCCCTTGT CCAGTTGCGG * * *** **

FL HL 1 PB-3 #401 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT CTA:::::: : FL HL 1 PB-1 #331 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT CTA:::::: : FL HL 1 PB-2 #331 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT CTA:::::: : FL HL 1 PB-4 #199 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT CTA:::::: : FL HL 1 PB-5 #199 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT CTA:::::: : FL HL 1 PB-6 #199 AAACTCACTG TTGCTGGCAA ACTCACCGAG GTCAAGAATT CTA:::::: : FL HL 1 PB-7 #199 AAACTCACTG TTGCTGGCAA ACTCACCGAG GTCAAGAATT CTA:::::: : FL HL 1 PF-1 #331 AAACTCACTG TTGCTGGCAA ACTCACCAAG ATCAAGAATT CTA:::::: : FL HL 1 PE-1 #199 AAACTCACTG TTGCTGACAA ACTCACCAAG GTCAAGAATT CTACATGATC ...... #401 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT CTACATGATC **

FL HL 1 PB-3 #451 ::::::::: : CGTGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG FL HL 1 PB-1 #381 ::::::::: : CGTGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG FL HL 1 PB-2 #381 ::::::::: : CGTGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG FL HL 1 PB-4 #249 ::::::::: : CGTGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG FL HL 1 PB-5 #249 ::::::::: : CGTGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG FL HL 1 PB-6 #249 ::::::::: : CATGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG FL HL 1 PB-7 #249 ::::::::: : CATGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG FL HL 1 PF-1 #381 ::::::::: : CATGATCTCT GCCAAACCAA CCCCTACTGT GAAGCCCAAG FL HL 1 PE-1 #249 TCTGCCAAAC CAAGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG ...... #451 TCTGCCAAAC CGTGATCTCT GCCAAACCAA CCCCTGCTGT GAAGCCCAAG ** *

FL HL 1 PB-3 #501 TCCGCCGCTG TGGAGCCGAT GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC FL HL 1 PB-1 #431 TCCGCCGCTG TGGAGCCGAT GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC FL HL 1 PB-2 #431 TCCGCCGCTG TGGAGCCGAT GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC FL HL 1 PB-4 #299 TCCGCCGCTG TGGAGCCGAT GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC FL HL 1 PB-5 #299 TCCGCCGCTG TGGAGCCGAT GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC FL HL 1 PB-6 #299 TCTGCCGCTG TGGAGCCGAA GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC FL HL 1 PB-7 #299 TCTGCCGCTG TGGAGCCGAA GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC FL HL 1 PF-1 #431 TCCGCCGCTG TGGAGCCGAA GTCTGCTGCT ACCAAGCCCA TGTCTACTGC FL HL 1 PE-1 #299 TCCGTCACTG TGGAGCTGAA TTCTGCTACT ATCAAGCCCA AGTCTGCTGC ...... #501 TCCGCCGCTG TGGAGCCGAT GTCTGCTGCT ACCAAGCCCA AGTCTGCTGC *** **** * * 63

FL HL 1 PB-3 #551 CAAGAAGGTG TAGAAAGCAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC FL HL 1 PB-1 #481 CAAGAAGGTG TAGAAAGTAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC FL HL 1 PB-2 #481 CAAGAAGGTG TAGAAAGCAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC FL HL 1 PB-4 #349 CAAGAAGGTG TAGAAAGCAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC FL HL 1 PB-5 #349 CAAGAAGGTG TAGAAAGCAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC FL HL 1 PB-6 #349 CAAGAAGGTG TAGAAAGCAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC FL HL 1 PB-7 #349 CAAGAAGGTG TAGAAAGCAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC FL HL 1 PF-1 #481 CAAGAAGGTG TAGAAAGCAG CTGTGAAACC GAAATCCAAG CCTGTTGCCC FL HL 1 PE-1 #349 CAAGAAGGTG TAGAAAGCAG TTGTGAAGCC GAAATCCAAG CCTGCTGTCC ...... #551 CAAGAAGGTG TAGAAAGCAG CTGTGAAGCC GAAATCCAAG CCTGCTGCCC * ** * *

FL HL 1 PB-3 #601 CGAAGACAAA GACAGTGACA AAACCAAAGG CAGTAGCTCT GAAGACAAAG FL HL 1 PB-1 #531 CGAAGACAAA GACAGTGACA AAATCAAAGG CAGTAGCTCT GAAGACAAAG FL HL 1 PB-2 #531 CGAAGACAAA GACAGTGACA AAATCAAAGG CAGTAGCTCT GAAGACAAAG FL HL 1 PB-4 #399 CGAAGACAAA GACAGTGACA AAATCAAAGG CAGTAGCTCT GAAGACAAAG FL HL 1 PB-5 #399 CGAAGACAAA GACAGTGACA AAACCAAAGG CAGTAGCTCT GAAGACAAAG FL HL 1 PB-6 #399 TGAAGTCAAA GACAGTGATA AAATC:AAGG CAGTAGCTCT GAAGCCAAAG FL HL 1 PB-7 #399 TGAAGTCAAA GACAGTGATA AAATC:AAGG CAGTAGCTCT GAAGCCAAAG FL HL 1 PF-1 #531 CGAAGCTAAA GACAGTGACA AAATCAAAGG CAGTAGCTCT GAAGCCAAAG FL HL 1 PE-1 #399 CGAGGCCAAA GACAGTGACA AAATCCAAGG CAGTAGCTCT GAAGCCAAAT ...... #601 CGAAGACAAA GACAGTGACA AAATCAAAGG CAGTAGCTCT GAAGACAAAG ** ** ** *

FL HL 1 PB-3 #651 ACTGTTGGCC GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PB-1 #581 ACCGTTGGCC GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PB-2 #581 ACCGTTGGCC GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PB-4 #449 ACCGTTGGCC GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PB-5 #449 ACTGTTGGCC GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PB-6 #449 ACTGGTGGCT GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PB-7 #449 ACTGGTGGCT GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PF-1 #581 ACTGCTGGCC GTCTAGCAAA GATGGCGAAG ATATCTGTTA AAGCTGCTCC FL HL 1 PE-1 #449 ATTGTTGGCC GTCCGGCAAA GGCGGTGAAG ACATCTGTTA AAGCTGCTCC ...... #651 ACTGTTGGCC GTCCAGCAAA GGCGGCGAAG ATATCTGTTA AAGCTGCTCC ** * ** ** * *

FL HL 1 PB-3 #701 GAG FL HL 1 PB-1 #631 GAGAAAGAAG GTCGGCTCCA GTGGCCCTGA AGGAAGCTAA G FL HL 1 PB-2 #631 GAGAAAGAAG GTCG:CTCCA GTGGCCCTGA AGGAAGCTAA G FL HL 1 PB-4 #499 GAG FL HL 1 PB-5 #499 GAG FL HL 1 PB-6 #499 GAG FL HL 1 PB-7 #499 GAG FL HL 1 PF-1 #631 GAGAAAGAAG GTCG:CTCCA GTGGCCCTGA AGGAAGCTAA GGCTGGGAAG FL HL 1 PE-1 #499 GGGAAA:AAG GTCG:CTTCA GTGGCCCTGA AGGAAGCTAA G ...... #701 GAGAAAGAAG GTCG:CTCCA GTGGCCCTGA AGGAAGCTAA GGCTGGGAAG *

FL HL 1 PF-1 #681 GTGGTACTCA GAGTCAATCA TATTTCTGGG AAGAAGTTGA TGCTTCATCG ...... #751 GTGGTACTCA GAGTCAATCA TATTTCTGGG AAGAAGTTGA TGCTTCATCG 64

FL HL 1 PF-1 #731 GCCAGCAAAG ATGGCGAAGA TATCTGTTAA AGCTGCTCCG AGAAAGAAGG

#801 GCCAGCAAAG ATGGCGAAGA TATCTGTTAA AGCTGCTCCG AGAAAGAAGG

FL HL 1 PF-1 #781 TCGCTCCAGT GGCCCTGAAG GAAGCTAAG

#851 TCGCTCCAGT GGCCCTGAAG GAAGCTAAG

Fig. 14. Multiple alignment of histone-like protein group 2 pseudogenes clones in Fritillaria liliacea. *- Nucleotide difference in the alignment, : -. Gap in the sequence

Group 3- Pseudogenes

This group includes clones FL HL 1 PC-2, FL HL 1 PC-3, FL HL 1 PA-4 and FL HL

1 PD-l (Fig-15). This group has a 17 bp indel at position 534-550 in all clones except FL

HL 1 PA-4 (Fig-l 6). None ofthe clones have a complete open reading frame. All these clones are quite similar to each other. Clone FL HL 1 PA-4 and clone FL HL 1 PD-l each have a set ofunique indels.

FLHL 1 PA-4

This clone is 510 bp long. It is similar to the rest ofgroup 3 except it does not have the 17 bp indel at position 261-276.

FL HL 1 PD-l

This clone is 495 bp long. It has 5 bp indel at 197. 65

FL HL 1 PA-4 #1 CGAGATGATT AGTGAAGCGA TCGCTTTGCT GAAGGAGCAG ACTGGATCAA FL HL 1 PC-3 #1 CAAGATGATT AGTGATGCGA TCACTTTGCT GAAGGAGCAG ACTGGATAGA FL HL 1 PC-2 #1 CAAGATGATT AGTAAAGCGA TCACTTTGCT GAAGGAGCAG ACTGGATAGA FL HL 1 PD-1 #1 CAAGATGATT AGTGATGCGA TCACTTTGCT GAAGGAGCAG ACTGGATAGA

#1 CAAGATGATT AGTGAWGCGA TCACTTTGCT GAAGGAGCAG ACTGGATAGA *** **

FL HL 1 PA-4 #51 ACCAGTACGA TATTGTAAAG TTTGTTGAAA ACAAGCATAA GTCCCATCTC FL HL 1 PC-3 #51 GCCAGTACGC TATTGCAAAG TTTGTTGAAA TTAAGCATAA GTCCCATCTC FL HL 1 PC-2 #51 GCCAGTACGC TATTGCAAAG TTTGTTAAAA ATAAGCATAA GTCCCATCTC FL HL 1 PD-1 #51 GCCAGTACGC TATTGCAAAG TTTGTTGAAA TTAAGCATAA GTCCCATCTC

#51 GCCAGTACGC TATTGCAAAG TTTGTTGAAA WTAAGCATAA GTCCCATCTC * * **

FL HL 1 PA-4 #101 CCGACGAACT TCAAGAAGCT TCCTCTTGTC CAGTTGTGGA AACTCACTGT FL HL 1 PC-3 #101 CCAATGAACT TCAAGAAA:T TCTCCTTATT CAGTTGCGGA AACTCACTTT FL HL 1 PC-2 #101 CCGACAAACT TCAAGAAACT TCTCCTTGTT CAGTTGCAGA AACTCACTGT FL HL 1 PD-1 #101 CCAATGAACT TCAAGAAA:T TCTCCTTATT CAGTTGCGGA AACTCACTTT

#101 CCRAYGAACT TCAAGAAACT TCTCCTTRTT CAGTTGCGGA AACTCACTKT * ** ** ** ** *

FL HL 1 PA-4 #151 TGCTGGCAAA CTCACCAAGA TCAAGAA:TT CTACATGATC TCTGCC:::: FL HL 1 PC-3 #151 TGCTGGAAAA GTAACTAAGG TCAAGAATTT CTACAAGATC TCTGCC:::: FL HL 1 PC-2 #151 TGCTGAAAAA CTCACTAAGG TCAAGAATTT CTACAAGATC TCTGCC: ::: FL HL 1 PD-1 #151 TGCTGGAAAA GTAACTAAGG TCAAGAATTT CTACAAGATC TCTGCCAACC

#151 TGCTGGAAAA STMACTAAGG TCAAGAATTT CTACAAGATC TCTGCC: ::: ** *** * * ****

FL HL 1 PA-4 #201 :AAACCAACC CCTACTGTGA AGCCCAAGTC CGCCGCTGTG GAGCCGAAGT FL HL 1 PC-3 #201 :AACCCAACC CCTGCTGTGA AACCCAAGTC TGTCACTGCA GAGCTGAAGT FL HL 1 PC-2 #201 :AAACCAACC CCTGCTGTGA AACCCAATTC TGCCGCTGCA GAGCTGAAGT FL HL 1 PD-1 #201 CAACCCAACC CCTGCTGTGA AACCCAAGTC TGTCACTGCA GAGCTGAAGT

#201 :AAMCCAACC CCTGCTGTGA AACCCAAGTC TGYCRCTGCA GAGCTGAAGT ** * *** ** *

FL HL 1 PA-4 #251 CTGCTGCTAC ::::: ::::: :::::: :CAA GCCCATGTCT ACTGCCAAGA FL HL 1 PC-3 #251 CTGTTGCTAC CAAGCTCAAG TCAGCAGCAA GCCCAAGTCT TCTGCCAAGA FL HL 1 PC-2 #251 CTGTTGCTAC CAAGCCCAAG TCAGTAGCAA GCCCAAGTCT TCTGCCATGA FL HL 1 PD-1 #251 CTGTTGCTAC CAAGCTCAAG TCAGCAGCAA GCCCAAGTCT TCTGCCAAGA

#251 CTGTTGCTAC CAAGCTCAAG TCAGCAGCAA GCCCAAGTCT TCTGCCAAGA * * **

FL HL 1 PA-4 #301 AGGTGAAGAA AGCAGCTGTG AAGCCGAAGT CTAAATCTGC TGCCGTGAAA FL HL 1 PC-3 #301 AGGTGAAGAA AGCAGCTATA AAGTTGAAGT CTAAATCTAC TGCCGTGAAA FL HL 1 PC-2 #301 AGGTGAAGAA AGCAACTATG AAGTCGAAGC CTAAATCTGC TGCCGTAAAA FL HL 1 PD-1 #301 AGGTGAAGAA AGCAGCTATA AAGTTGAAGT CTAAATCTAC TGCCGTGAAA

#301 AGGTGAAGAA AGCAGCTATR AAGTYGAAGT CTAAATCTRC TGCCGTGAAA *** **

FL HL 1 PA-4 #351 CTAAATGCTC CTACTGTGAA GCTGAAATCC AAGACTACTG CCCCGAAGCC FL HL 1 PC-3 #351 CCAAAAGCTC ACGCTGTGAA GCCAAAATCC AAGACTACTG CCCCGAAGCC FL HL 1 PC-2 #351 CCAAAAGCTC ATGCTGTGAA GCCGAAATCC AAGACTACTG CCCCGAAGCC FL HL 1 PD-1 #351 CCAAAAGCTC ATGCTGTGAA GCCAAAATCC AAGACTACTG CCCCGAAGCC

#351 CCAAAAGCTC ATGCTGTGAA GCCRAAATCC AAGACTACTG CCCCGAAGCC * * *** ** 66

FL HL 1 PA-4 #401 AAAGACAGTG ATAAAATCAA AGGTTGTAGC TCTAAAGCCA AAGACTGCTG FL HL 1 PC-3 #401 AAAGACAGTG ACAAAATCAA AGGGTGTATC TCTAAAGCCA AAGACTGCTG FL HL 1 PC-2 #401 AAAGACAGTG ACAAAATCAA AGGGTGTAGC TCTAAATCCA AAGACTGCTG FL HL 1 PD-1 #401 AAAGACAGTG ACAAAATCAA AGGGTGTATC TCTAAAGCCA AAGACTGCTG ...... #401 AAAGACAGTG ACAAAATCAA AGGGTGTAKC TCTAAAGCCA AAGACTGCTG * **

FL HL 1 PA-4 #451 GCCGTCCAGC AAAGTCGATG AAGACATATG TTAAAGCTGC TTTGGGAAAG FL HL 1 PC-3 #451 GCTGTCCAGC AAAGTTGGCG AAGACATATG TTAAAGCTGC TTTGGG FL HL 1 PC-2 #451 GCTGTCCAGC AAAGTCGGTG AAGACATATG TTAAAGCTGC TTTGGG FL HL 1 PD-1 #451 GCTGTCCAGC AAAGTTGGCG AAGACATATG TTAAAGCTGC TTTGGG ...... #451 GCTGTCCAGC AAAGTYGGYG AAGACATATG TTAAAGCTGC TTTGGGAAAG * **

FL HL 1 PA-4 #501 AAGGTCACTC TAGCGGCTCT GAAGAAATAT AAA ...... #501 AAGGTCACTC TAGCGGCTCT GAAGAAATAT AAA

Fig. 15. Multiple alignment of histone-like protein group 3 pseudogenes clones in Fritillaria liliacea. *- Nucleotide difference in the alignment, : -. Gap in the sequence

FL HL 1 PB-3 #1 TTATTTGTTC TATTTTCCCT CTTTTACTTT TAATTTCCTT GAAATGTCCG ...... #1 TTATTTGTTC TATTTTCCCT CTTTTACTTT TAATTTCCTT GAAATGTCCG

FL HL 1 PA-2 #1 CCCGCCTTTG CTCCGGTCCC TGTT:GCCAG FL HL 1 PA-3 #1 CCCGCCTTTG CTCCGGTCCC TGTT:GCCAG FL HL 1 PB-3 #51 CAGCCGTTGC AATTGAGACT CCCGCCTTTG CTCCGGTCCC TGTT:GCCGG FL HL 1 PB-1 #1 CCCGCCTTTG CTCCGGTCCC TGTTTGCCGG FL HL 1 PF-1 #1 CTCACCTTTG CTTCGGTCCC TGTC:GCCAG ...... #51 CAGCCGTTGC AATTGAGACT CCCGCCTTTG CTCCGGTCCC TGTT:GCCAG * ** *

FL HL 1 PA-2 #31 AGATGAACCG GTGGCGAAGC CGGGCAAGGT GACGAAGGCC AAGGCCCCTA FL HL 1 PA-3 #31 AGATGAACCG GTGGCGAAGC CGGGCAAGGT GACGAAGGCC AAGGCCCCTA FL HL 1 PB-3 #101 AGATGATCTA GCGGCAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA FL HL 1 PB-1 #31 AGATGATCTA GCGGCAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA FL HL 1 PF-1 #31 AGATGATCTG ACGGAAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA ...... #101 AGATGATCTG GCGGCAAAGC CGACCAAGGT GACGAAGGCC AAGGTCCCTA * ** ** **

FL HL 1 PA-2 #81 AGGAGAAGAA GGCCTCCGTC GCGAAGAAGC CTGCTCTCCA TCCTACCTAT FL HL 1 PA-3 #81 AGGAGAAGAA GGCCTCCGTC GCGAAGAAGC CTGCTCTCCA TCCTACCTAT FL HL 1 PB-3 #151 AGGAGAAGAA GGCCTCTATT GCGAAGAAGC CTGCTCTCCA TCCTACCTAT FL HL 1 PB-1 #81 AGGAGAAGAA GGCCTCTATT GCGAAGAAGC CTGCTCTCCA TCCTACCTAT FL HL 1 PF-1 #81 AGAAGAAGAA GGCCTCTGTT ACGAAGAAGC CTGCTCTCCA TTCTACCTAT ...... #151 AGGAGAAGAA GGCCTCTGTT GCGAAGAAGC CTGCTCTCCA TCCTACCTAT * ** ** * 67

FL HL 1 PD-1 #1 CAAGATGA TTAGTGATGC GATCAC::: : ::::::::: : ::::::::: : FL HL 1 PC-3 #1 CAAGATGA TTAGTGATGC GATCAC::: : ::::::::: : ::::::::: : FL HL 1 PC-2 #1 CAAGATGA TTAGTAAAGC GATCAC: : :: ::::::::: : ::::::::: : FL HL 1 PA-2 #131 CTCGAGATGA TCAGTGAAGC GATCGC::: : ::::::::: : ::::::::: : FL HL 1 PA-3 #131 CTCGAGATGA TCAGTGAAGC GATCGC::: : ::::::::: : ::::::::: : FL HL 1 PA-4 #1 CGAGATGA TTAGTGAAGC GATCGC::: : ::::::::: : ::::::::: : FL HL 1 PB-3 #201 CTCGAGATGA TTAGTGAAGC GATCGC::: : ::::::::: : ::::::::: : FL HL 1 PB-1 #131 CTCGAGATGA TTAGTGAAGC GATCGC: ::: ::::::::: : ::::::::: : FL HL 1 PF-1 #131 CTCGAGATGA TTAGTGAAGC GATCGC: : :: ::::::::: : ::::::::: : FL HL 1 PB-6 #1 CGAGATGA TTAGTGAAGT GATCGC::: : ::::::::: : ::::::::: : FL HL 1 PE-1 #1 TGAGATAA TTAGTGAAGG GATAGATTTG CTGAAGGAGC AGACTGGATC ...... #201 CTCGAGATGA TTAGTGAAGC GATCGCTTTG CTGAAGGAGC AGACTGGATC ** ** ** ***

FL HL 1 PD-1 #49 ::::::::: : ::::::::: : ::::::::: : ::: : :TTTGC TGAAGGAGCA FL HL 1 PC-3 #49 ::::::::: : ::::::::: : ::::::::: : :: :: :TTTGC TGAAGGAGCA FL HL 1 PC-2 #49 ::::::::: : ::::::::: : ::::::::: : :::: :TTTGC TGAAGGAGCA FL HL 1 PA-2 #181 ::::::::: : ::::::::: : ::::::::: : :::: :TTCGC TGAAGGAGCG FL HL 1 PA-3 #181 ::::::::: : ::::::::: : ::::::::: : :: :: :TTCGC TGAAGGAGCG FL HL 1 PA-4 #49 ::::::::: : ::::::::: : ::::::::: : :::::TTTGC TGAAGGAGCA FL HL 1 PB-3 #251 ::::::::: : ::::::::: : ::::::::: : :::::TTTGC TGAAGGAGCA FL HL 1 PB-1 #181 ::::::::: : ::::::::: : ::::::::: : ::: : :TTTGC TGAAGGAGCA FL HL 1 PF-1 #181 ::::::::: : ::::::::: : ::::::::: : :::: :TTTGC TGAAGGAGCA FL HL 1 PB-6 #49 ::::::::: : ::::::::: : ::::::::: : ::: ::TTTGC TGAAGGAGTA FL HL 1 PE-1 #49 GAGCACCTAT CTGAGATGAT TAGTGAAGCG ATAAATTTGC TGAAGGAGCA ...... #251 GAGCACCTAT CTGAGATGAT TAGTGAAGCG ATAAATTTGC TGAAGGAGCA * **

FL HL 1 PD-1 #99 GACTGGATAG AGCCAGTACG CTATTGCAAA GTTTGTTGAA ATTAAGCATA FL HL 1 PC-3 #99 GACTGGATAG AGCCAGTACG CTATTGCAAA GTTTGTTGAA ATTAAGCATA FL HL 1 PC-2 #99 GACTGGATAG AGCCAGTACG CTATTGCAAA GTTTGTTAAA AATAAGCATA FL HL 1 PA-2 #231 GACTGGATCG AGCCAGTACG CTATTGCGAA GTTTGTTGAA GACAAGCACA FL HL 1 PA-3 #231 GACTGGATCG AGCCAGTACG CTATTGCGAA GTTTGTTGAA GACAAGCACA FL HL 1 PA-4 #99 GACTGGATCA AACCAGTACG ATATTGTAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-3 #301 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-1 #231 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA :ACAAGCATA FL HL 1 PF-1 #231 GACTGGATCA AACCAGTACG ATATTGTAAA GTTTGTTGAA AACAAGCATA FL HL 1 PB-6 #99 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA FL HL 1 PE-1 #99 GACTGGATTG GGCCAGTACG CTATGGCAAA GTTTGTTGAA AACAAGTATA ...... #301 GACTGGATCG AGCCAGTACG CTATTGCAAA GTTTGTTGAA AACAAGCATA ** * * ** * *** **

FL HL 1 PD-1 #149 AGTCCCATCT CCCAATGAAC TTCAAGAA:A TTCTCCTTAT TCAGTTGCGG FL HL 1 PC-3 #149 AGTCCCATCT CCCAATGAAC TTCAAGAA:A TTCTCCTTAT TCAGTTGCGG FL HL 1 PC-2 #149 AGTCCCATCT CCCGACAAAC TTCAAGAAAC TTCTCCTTGT TCAGTTGCAG FL HL 1 PA-2 #281 AGTCTCATCT CCCGGCGAAC TTCAAGAAGC TTCTCCTTGT CCAGTTGCAG FL HL 1 PA-3 #281 AGTCTCATCT CCCGGCGAAC TTCAAGAAGC TTCTCCTTGT CCAGTTGCAG FL HL 1 PA-4 #149 AGTCCCATCT CCCGACGAAC TTCAAGAAGC TTCCTCTTGT CCAGTTGTGG FL HL 1 PB-3 #351 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TTCCCCTTGT CCAGTTGCGG FL HL 1 PB-1 #281 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TTC:CCTTGT CCAGTTGCGG FL HL 1 PF-1 #281 AGTCCCATCT CCCGACGAAC TTCAAGAAGC TTCCTCTTGT CCAGTTGTGG FL HL 1 PB-6 #149 AGCCCCATCT CCCGGCGAAC TTCAAGAAGT TTCCCCTTGT CCAGTTACGG FL HL 1 PE-1 #149 AGTCCCATCT CCCGGCAAAC TTCAAGAAGC TTCTCCTTGT CCAGTTACGG ...... #351 AGTCCCATCT CCCGGCGAAC TTCAAGAAGC TTCTCCTTGT CCAGTTGCGG **** ** ** * *** 68

FL HL 1 PD-1 #199 AAACTCACTT TTGCTGGAAA AGTAACTAAG GTCAAGAATT TCTACAAGAT FL HL 1 PC-3 #199 AAACTCACTT TTGCTGGAAA AGTAACTAAG GTCAAGAATT TCTACAAGAT FL HL 1 PC-2 #199 AAACTCACTG TTGCTGAAAA ACTCACTAAG GTCAAGAATT TCTACAAGAT FL HL 1 PA-2 #331 AAACTCACTG CTGCTGGCAA ACTCACGAAG GTGAAGAATT CCTACAAGAT FL HL 1 PA-3 #331 AAACTCACTG CTGCTGGCAA ACTCACGAAG GTGAAGAATT CCTACAAGAT FL HL 1 PA-4 #199 AAACTCACTG TTGCTGGCAA ACTCACCAAG ATCAAGAATT :CTACATGAT FL HL 1 PB-3 #401 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT :CTACGTGAT FL HL 1 PB-1 #331 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT :CTACGTGAT FL HL 1 PF-1 #331 AAACTCACTG TTGCTGGCAA ACTCACCAAG ATCAAGAATT :CTACATGAT FL HL 1 PB-6 #199 AAACTCACTG TTGCTGGCAA ACTCACCGAG GTCAAGAATT :CTACATGAT FL HL 1 PE-1 #199 AAACTCACTG TTGCTGACAA ACTCACCAAG GTCAAGAATT :CTACATGAT

#401 AAACTCACTG TTGCTGGCAA ACTCACCAAG GTCAAGAATT :CTACATGAT ** * * ** ** * **

FL HL 1 PD-1 #249 CTCTGCCAAC CCAA:::::: ::::: :CCCA ACCCCTGCTG TGAAACCCAA FL HL 1 PC-3 #249 CTCTGCCAAC :::::::::: ::::: ::CCA ACCCCTGCTG TGAAACCCAA FL HL 1 PC-2 #249 CTCTGCCAAA :::::::::: :::::: :CCA ACCCCTGCTG TGAAACCCAA FL HL 1 PA-2 #381 CTCTGCCAAA :;:::::::: ::;::;:CCA ACCCCTGCTG CGAAGCCTAA FL HL 1 PA-3 #381 CTCTGCCAAA :::::::::: ::: ::: :CCA ACCGCTGCTG TGAAGCCTAG FL HL 1 PA-4 #249 CTCTGCCAAA :::::::::: :::::: :CCA ACCCCTACTG TGAAGCCCAA FL HL 1 PB-3 #451 CTCTGCCAAA :: :::::::: ::::: ::CCA ACCCCTGCTG TGAAGCCCAA FL HL 1 PB-1 #381 CTCTGCCAAA :::::::::: :::::: :CCA ACCCCTGCTG TGAAGCCCGA FL HL 1 PF-1 #381 CTCTGCCAAA :::::::::: ::::: ::CCA ACCCCTCATG TGAAGCCCAA FL HL 1 PB-6 #249 CTCTGCCAAA :::::::::: ::::: ::CCA ACCCCTGCTG TGAAGCCCAA FL HL 1 PE-1 #249 CTCTGCCAAA CCAAGATCTC TGCCAAACCA ACCCCTGCTG TGAAGCCCAA

#451 CTCTGCCAAA CCAAGATCTC TGCCAAMCCA ACCCCTGCTG TGAAGCCCAA * * * ***

FL HL 1 PD-1 #299 GTCTGTCACT GCAGAGCTGA AGTCTGTTGC TACCAAGCTC AAGTCAGCAG FL HL 1 PC-3 #299 GTCTGTCACT GCAGAGCTGA AGTCTGTTGC TACCAAGCTC AAGTCAGCAG FL HL 1 PC-2 #299 TTCTGCCGCT GCAGAGCTGA AGTCTGTTGC TACCAAGCCC AAGTCAGTAG FL HL 1 PA-2 #431 ATCCGCTGCT GTGAAGCCAA AGTCTGCTGC TAC::::::: :::::::::: FL HL 1 PA-3 #431 ATCCGCTGCT GTGAAGCCAA AGTCTGCTGT TGC::::::: :::: ::: ::: FL HL 1 PA-4 #299 GTCCGCCGCT GTGGAGCCGA AGTCTGCTGC TAC:: ::::: ::: :::: ::: FL HL 1 PB-3 #501 GTCCGCCGCT GTGGAGCCGA TGTCTGCTGC TAC:: ::::: ::: ::::::: FL HL 1 PB-1 #431 ATCCGCCGCT GTGGAGCCGA TGTCTGCTGC TAC::::::: :::::::::: FL HL 1 PF-1 #431 GTCCGCCGCT GTGGAGCCGA AGTCTGCTGC TAC::::::: :: :::::::: FL HL 1 PB-6 #299 GTCTGCCGCT GTGGAGCCGA AGTCTGCTGC TAC::::::: :: :::::::: FL HL 1 PE-1 #299 GTCCGTCACT GTGGAGCTGA ATTCTGCTAC TAT::::::: ::::::::::

#501 GTCCGCCGCT GTGGAGCCGA AGTCTGCTGC TACCAAGCTC AAGTCAGCAG * *** ** ** ** * *

FL HL 1 PD-1 #349 CAAGCCCAAG TCTTCTGCCA AGAAGGTGAA GAAAGCAGCT ATAAAGTTGA FL HL 1 PC-3 #349 CAAGCCCAAG TCTTCTGCCA AGAAGGTGAA GAAAGCAGCT ATAAAGTTGA FL HL 1 PC-2 #349 CAAGCCCAAG TCTTCTGCCA TGAAGGTGAA GAAAGCAACT ATGAAGTCGA FL HL 1 PA-2 #481 TAAACTCAAG TCCGCTGCCA AGAAGGTGAA GAAAGCAGCT GTGAAGCCAA FL HL 1 PA-3 #481 TAAGCTCAAG TCCGCTGCCA AGAAGGTGAA GAAAGCAGCT GTGAAGCCAA FL HL 1 PA-4 #349 CAAGCCCATG TCTACCC: :A AGAAGGTGAA GAAAGCAGCT GTGAAGCCGA FL HL 1 PB-3 #551 CAAGCCCAAG TCTGCC:::A AGAAGGTGTA GAAAGCA::: ::::::::: : FL HL 1 PB-1 #481 CAAGCCCAAG TCTGCCC::A AGAAGGTGTA GAAAGTA::: ::::::::: : FL HL 1 PF-1 #481 CAAGCCCATG TCTACTGCC: : :AAGGT::A GAAAGCA::: ::::::::: : FL HL 1 PB-6 #349 CAAGCCCAAG TCTGCCC::A AGAAGTGGTA GAAAGCA::: ...... FL HL 1 PE-1 #349 CAAGCCCAAG TCTGCTGCCA AGAAGGTGTA GAAAGCA: :: ::::::::: :

#551 CAAGCCCAAG TCTGCTGCCA AGAAGGTGAA GAAAGCAGCT RTGAAGYCGA *** ** ***** ** **** ** ** *** 69

FL HL 1 PD-1 #399 AGTCTAAATC TACTGCCGTG AAACCAAA:G CTCATGCTGT GAAGCCAAAA FL HL 1 PC-3 #399 AGTCTAAATC TACTGCCGTG AAACCAAAAG CTCACCTGTG GAAGCCGAAA FL HL 1 PC-2 #399 AGCCTAAATC TGCTGCCGTA AAACCAAAAG CTCATGCTGT GAAGCCGAAA FL HL 1 PA-2 #531 AGCCTAAATC TGCTGCCGTG AAGCCAAAAG CCCCTGCCGT GAAACCGAAA FL HL 1 PA-3 #531 AGCCTAAATC TGCTGCCGTG AAGCCAAAAG CCCCTGCCGT GAAACCGAAA FL HL 1 PA-4 #399 AGTCTAAATC TGCTGCCGTG AAACTAAATG CTCCTACTGT GAAGCTGAAA FL HL 1 PB-3 #601 ...... :::::::::: :::::::::: :::: :GCTGT GAAGCCGAAA FL HL 1 PB-1 #531 ::::::::: : :::::::::: :::::::::: :::: :GCTGT GAAGCCGAAA FL HL 1 PF-1 #531 :::::::::: :::::::::: ::: ::GCTGT GAAACCGAAA FL HL 1 PB-6 #399 ::::::::: : :::::::::: :::::::::: ::: ::GCTGT GAAGCCGAAA FL HL 1 PE-1 #399 ...... :::::::::: :::::::::: ::: ::GTTGT GAAGCCGAAA

#601 AGYCTAAATC TGCTGCCGTG AAACCAAAAG CTCMTGCTGT GAAGCCGAAA * * * ******* * **

FL HL 1 PD-1 #449 TCCAAGACTA CTGCCCCGAA GCCAAA:GA: CAGTGACAAA ATCAAAGGGT FL HL 1 PC-3 #449 TCCAAGACTA CTGCCCCGAA GCCAAA:GA: CAGTGACAAA ATCAAAGGGT FL HL 1 PC-2 #449 TCCAAGACTA CTGCCCCGAA GCCAAA:GA: CAGTGACAAA ATCAAAGG:: FL HL 1 PA-2 #581 TCCAAGCCTG CTGCCCTGAA GCCAAA:TA: CAGTGACAAA ATCAAAGACT FL HL 1 PA-3 #581 TCCAAGCCTG CTGCCCTGAA GCCAAA:TA: CAGTGACAAA ATCAAAGACT FL HL 1 PA-4 #449 TCCAAGACTA CTGCCCCGAA GCCAAA:GA: CAGTGATAAA ATCAAAGGTT FL HL 1 PB-3 #651 TCCAAGCCTG CTGCCCCGAA GACAAA:GA: CAGTGACAAA ACCAAAGGCA FL HL 1 PB-1 #581 TCCAAGCCTG CTGCCCCGAA GACAAA:GAA CAGTGACAAA ATCAAAGGCA FL HL 1 PF-1 #581 TCCAAGCCTG TTGCCCCGAA GCTAAA:GA: CAGTGACAAA ATCAAAGGCA FL HL 1 PB-6 #449 TCCAAGCCTG CTGCCCTGAA GTCAAAAGA: CAGTGATAAA ATCAA:GGCA FL HL 1 PE-1 #449 TCACAGCCTG CTGTCCCGAG GCCAAA:GA: CAGTGACAAA ATCCAAGGCA

#651 TCCAAGCCTG CTGCCCCGAA GCCAAA:GA: CAGTGACAAA ATCAAAGGCW * ** * * ** * ***

FL HL 1 PD-1 #499 GTATCTCTAA AGCCAAAGAC TGCTGGCTGT CCAGCAAAGT TGGC: :GAAG FL HL 1 PC-3 #499 GTATCTCTAA AGCCAAAGAC TGCTGGCTGT CCAGCAAAGT TGGC::GAAG FL HL 1 PC-2 #499 GTAGCTCTAA ATCCAAAGAC TGCTGGCTGT CCAGCAAAGT CGGTGTGAAG FL HL 1 PA-2 #631 GTAGCTCTGA AGGGAAAGAC TGCTGGCCGT CCAGCAAAGG CGGC: :AAAG FL HL 1 PA-3 #631 GTAGCTCTGA AGGGAAAGAC TGCTGGCCGT CCAGCAAAGG CGGC: :AAAG FL HL 1 PA-4 #499 GTAGCTCTAA AGCCAAAGAC TGCTGGCCGT CCAGCAAAGT CGAT: :GAAG FL HL 1 PB-3 #701 GTAGCTCTGA AGACAAAGAC TGTTGGCCGT CCAGCAAAGG CGGC: :GAAG FL HL 1 PB-1 #631 GTAGCTCTGA AGACAAAGAC CGTTGGCCGT CCAGCAAAGG CGGC: :GAAG FL HL 1 PF-1 #631 GTAGCTCTGA AGCCAAAGAC TGCTGGCCGT CTAGCAAAGA TGGC: :GAAG FL HL 1 PB-6 #499 GTAGCTCTGA AGCCAAAGAC TGGTGGCTGT CCAGCAAAGG CGGC: :GAAG FL HL 1 PE-1 #499 GTAGCTCTGA AGCCAAATTA TGTTGGCCGT CCGGCAAAGG CGGT: :AAAG

#701 GTAGCTCTGA AGCCAAAGAC TGCTGGCCGT CCAGCAAAGG CGGC: :GAAG * * *** *** ** * * *****

FL HL 1 PD-1 #549 ACATATGTTA AAGCTGCTTT GGG FL HL 1 PC-3 #549 ACATATGTTA AAGCTGCTTT GGG FL HL 1 PC-2 #549 ACATATGTTA AAGCTGCTTT GGG FL HL 1 PA-2 #681 ACATCCGTCA AAGCTGCTCC GGGAAAGAAG GCTG:CTCCA GTGGCTCTGA FL HL 1 PA-3 #681 ACATCCGTCA AAGCTGCTCC GGGAAAGAAG GCTG:CTCCA GTGGCTCTGA FL HL 1 PA-4 #549 ACATATGTTA AAGCTGCTTT GGGAAAGAAG GTCA:CTCTA GCGGCTCTGA FL HL 1 PB-3 #751 ATATCTGTTA AAGCTGCTCC GAG FL HL 1 PB-1 #681 ATATCTGTTA AAGCTGCTCC GAGAAAGAAG GTCGGCTCCA GTGGCCCTGA FL HL 1 PF-1 #681 ATATCTGTTA AAGCTGCTCC GAGAAAGAAG GTCG:CTCCA GTGGCCCTGA FL HL 1 PB-6 #549 ATATCTGTTA AAGCTGCTCC GAG FL HL 1 PE-1 #549 C:ATCTGTTA AAGCTGCTCC GGGAAAAA:: GTCG:CTTCA GTGGCCCTGA

#751 ACATCTGTTA AAGCTGCTCC GGGAAAGAAG GTCG:CTCCA GTGGCYCTGA ** ** * ** * * ** **** * 70

FL HL 1 PA-2 #731 AGAAGGCTAA G FL HL 1 PA-3 #731 AGAAGGCTAA G FL HL 1 PA-4 #599 AGAAATATAA A FL HL 1 PB-1 #731 AGGAAGCTAA G FL HL 1 PF-1 #731 AGGAAGCTAA GGCTGGGAAG GTGGTACTCA GAGTCAATCA TATTTCTGGG FL HL 1 PE-1 #599 AGGAAGCTAA G

#801 AGRAAGCTAA GGCTGGGAAG GTGGTACTCA GAGTCAATCA TATTTCTGGG * *** *

FL HL 1 PF-1 #781 AAGAAGTTGA TGCTTCATCG GCCAGCAAAG ATGGCGAAGA TATCTGTTAA

#851 AAGAAGTTGA TGCTTCATCG GCCAGCAAAG ATGGCGAAGA TATCTGTTAA

FL HL 1 PF-1 #831 AGCTGCTCCG AGAAAGAAGG TCGCTCCAGT GGCCCTGAAG GAAGCTAAG

#901 AGCTGCTCCG AGAAAGAAGG TCGCTCCAGT GGCCCTGAAG GAAGCTAAG

Fig. 16. Multiple alignment of group 1 group 2 and group 3 pseudogenes from Fritillaria liliacea. * - Nucleotide difference in the alignment, : -. Gap in the sequence 71

Phylogenetic Analysis of histone-like gene family

To support the visual sequence analysis, phylogenetic analyses were perfonned using

PAUP (Phylogenetic Analysis Using Parsimony). The data was analyzed using the parsimony method that chooses the tree that requires fewest evolutionary changes. A bootstrap analysis was perfonned to put the confidence limits on the groups found in the

Phylogenetic trees. Fig-I7 is an unrooted phylogram ofone ofthe two most parsimonious trees ofthe histone-like gene family from Fritillaria liliacea.

The two functional genes and group-I pseudogenes fonn a group supported by 100 % bootstrap values that does not includes group-2 and group-3 pseudogenes. Group-I processed pseudogenes (FL HL 1 PAl, FL HL 1 PA 2 & HL 1 PA 3) fonns a group with two functional genes (FL HL 1GB 1 & FL HL 1GA-I). In bootstrap analysis, FL HL

1GA-I and FL HL 1 PA-3 fonns a group supported by an 86 % bootstrap value, thus FL

HL 1 PA-3 pseudogene could have originated from FL HL 1GA-I mRNA. However, the functional gene FL HL 1GB 1 and pseudogene FL HL 1 PA 2 are clustered with 66 % bootstrap value and pseudogene FL HL 1 PAl are clustered with FL HL 1GB 1 and HL

1 PA 2 with 69 % bootstrap value. Although, bootstrap values are rather low, these two pseudogenes may have an evolutionary relationship with the functional gene FL HL 1GB

1. In addition, group-I is the only group ofpseudogenes with a complete open reading frame. Therefore, group-I pseudogenes could be a recent evolutionary event compared to the other two pseudogene groups.

According to the sequence analysis, group 2 pseudogenes include clones FL HL 1

PB-I, FL HL 1 PB-3, FL HL 1 PB-6, FL HL 1 PE-I and FL HL 1 PF-I. Group 2 72

pseudogenes share a 48 bp deletion, but they are not clustered in a single group.

Although in the most parsimonious trees, clone FL HL 1 PE-l is in a group with clones

FL HL 1 PB-l, FL HL 1 PB-3, FL HL 1 PB-6, this grouping is not supported in the bootstrap analysis. Also, clone FL HL 1 PE-l is not grouped with clones FL HL 1 PB-l,

FL HL I PB-3, and FL HL 1 PB-6 and in bootsrap analysis this grouping is supported by

63 % bootstrap value. In addition, clones FL HL 1 PF-l and FL HL 1 PA-4 forms a group that is suooprted by 50 % bootstrap value. Since these bootstrap values are low, the grouping ofthese clones cannot be resolved and therefore the node indicated as a star

ofsix branches represents a polytomy. Clone FL HL 1 PF-1 has 15 unique apomorphic characters (unique derived characters which are not present in other group 2 clones); therefore it is excluded from the group 2 cluster. It forms a group with clone FL HL 1

PA-4 which is supported by a 70 % bootstrap value.

Clones FL HL 1 PE-l and FL HL 1 PF-1 were separated from the rest ofthe group 2

clones because oftheir unique apomorphic characters. This result can be explained by two hypotheses. The first hypothesis is that a 48 bp deletion event could have occurred

independently in clones FL HL 1 PE-l and FL HL 1 PF-l. The second hypothesis is that

phylogenetic tree in Fig-17 obtained by parsimony method does not represent the true

phylogenetic relationship among these clones as there are not enough informative

characters in the data to determine the actual relationship, therefore a 48 bp deletion

event in clone FL HL 1 PE-l and clone FL HL 1 PF-1 is not an independent event. The

second hypothesis seems more likely. All the pseudogenes in this gene family are

processed pseudogenes, which were generated by retrotransposition. Ifthe first 73

hypothesis is correct then the 48 bp deletion has to take place in two different retrotransposition events. An insertion ofthe same length (48 bp) at the same position in two different retrotransposition events could be rare. Instead, a 48 bp deletion event could have occurred in the ancestral group-2 pseudogene that has then undergone segmental duplication.

In the most parsimonious trees group 3 pseudogenes except clone FL HL 1 PA-4 are found in a monophyletic group supprted by a 100 % bootstrap value. FL HL PA 4 is excluded from group 3, since it does not have a 17 bp insertion, which is a synapomorphic character (shared derived characters) ofgroup 3 pseudogenes. In addition, it has 13 apomorphic characters. FL HL PA 4 forms a group with FL HL 1 PF­

1 supported by a 70% bootstrap value, while the rest ofthe group-3 pseudogenes are in a group supported by a 100 % bootstrap value. Clone FL HL 1 PA 4 could be related to group 2 pseudogenes, but it does not have the 48 bp deletion, which is a synapomorphic character ofthis group. 74

FLHL 1 PC3

FL HL 1 PO 1

100 FL HL 1 PC 2

FL HL 1 PF 1

FL HL 1 GB 1 86

FL HL 1 PA 2 FL HL 1 GA 1 FL HL 1 PA 3

~OmiC + GrouV

---5 changes

Fig. 17. Phylogenetic tree of histone-like protein gene family from Fritillaria liliacea. Phylogenetic tree was constructed using maximum parsimony. Numbers on each branch indicate the percent of bootstrap replicates supporting that node. Note- Node for group 2 pseudogenes represents polytomy. 75

New Histone-like protein gene family from Fritillaria liliacea

During the course ofthis study, a new histone-like protein related gene family was identified. All gene members ofthis family were amplified by internal forward and either internal reverse or initial His reverse primers. Initial His and internal His primer pair sets are designed to amplify only the part ofcoding region, consequently, these clones have incomplete at the 5' and 3' ends. They are classified into three groups, two functional gene groups and one pseudogene group based on their unique inde1 pattern.

All the pseudogenes in this new gene family are conventional pseudogenes. This family either does not have processed pseudogenes or the primer pairs did not amplify processed pseudogenes from this family. All members ofthis gene family showed weak homology to histone-like protein in the BLAST N (Fig. IS) and BLAST P database search. A comparison between histone-like gene family and the new gene family ofFritillaria liliacea revealed that all members from the new gene family have an incomplete intron at the 5' end (Fig. 19). There must be a sequence in the intron, which served as a primer binding site. Also, the internal primer binding site, which flanks the 5' end ofthe intron in the histone-like protein gene family, might have been altered in the new gene family members. This might explain the missing 5'end ofthe intron in this gene family and also the absence ofprocessed pseudogenes. 76

gi126412101gb1AF031547.11AF031547 Fritillaria agrestis histone-like protein mRNA, complete cds Length = 956

Score = 71.9 bits (36), Expect 5e-10 Identities = 147/184 (79%) Strand = Plus / Plus

Query: 114 gtgaggcgatagcatccctgaaggagaggaccgggtcaagccagtatgcaatctcaaagt 173 I11I IIIII II II IIIIIIIII 11II II II IIIIIIII II II I IIII Sbjct: 242 gtgaagcgatcgcttcgctgaaggagcggactggatcgagccagtacgctattgcgaagt 301

Query: 174 ttgttgcagacaagcacaaggttcatctcttggtaaattttaagaagctcctcctcatcc 233 111111 1111111111111 11II111 II II II I1111111 11I11 III Sbjct: 302 ttgttgaagacaagcacaagtctcatctcccggcgaacttcaagaagcttctccttgtcc 361

Query: 234 cacttaggaagctcactgctgctggcaaactcaccaaggccaagaactcctacaagatcc 293 I III 11111111111111111111111 11I1 1I111 111111111111 Sbjct: 362 agttgcagaaactcactgctgctggcaaactcacgaaggtgaagaattcctacaagatct 421

Query: 294 ctgc 297 1111 Sbjct: 422 ctgc 425

Fig. 18. BLAST N database search of new histone-like protein from Fritillaria liliacea. Query- The new histone-like protein clone from Fritillaria liliacea. Sbjct - Matching sequence from the database. Score - Alignment score, which is calculated as the sum ofsubstitution and gap scores. Expect - This value represents the probability ofthe match appearing by chance. Identities- total number ofidentical residues in common. 77

# 1 # 135 # 827 Intron # 321 Fritillaria liliacea histone-like Exon I # 136 # 32°1 Exon protein genomic clone I~on J Fritillaria liliacea new Exon histone-like protein clone # 1 ----,------# 55 # 838

Fig. 19. Graphical overview of histone-like protein gene and new histone-like protein gene alignment from Fritillaria liliacea. The nucleotide alignment of intron exon structure is given in the appendix p. 171.

The two functional gene groups (group1 & group 2) share 85% similarity at the nucleotide level and 75% similarity at the amino acid level. The new gene family members share 64-66% similarity at the amino acid level with histone-like gene family

(Fig.20). 78

genomic 1 1 ------IAFApv&MIR genomic 2 1 ------IAFAP~ GROUP 1 GENE 1 GROUP 2 GENE 1 Sorghum_cDNA 1 ARGAELSSSLSSAHPSSRSPSSSEVQVTALMATDVAETPAlLAE~Elp consensus 1 p p a genomic 1 11 oI!lpvlKlBI

Fig. 20 Multiple alignment of new histone-like protein. Group I and Group 2 protein sequences ofnew histone-like protein from Fritillaria liliacea and protein sequence ofSorghum propinquum floral-induced meristem I cDNA are aligned using BOX Shade program. Identical amino acids are shaded. -- HI and H5 histone domain 79

As all the gene family members lack 5' and 3' ends, a mitochondrial targeting sequence or nuclear localization sequence could not be found. In the expressed sequence tag (EST, database ofpartial cDNA sequences) database search, the new gene family exhibits a 63% similarity at the amino acid level with floral-induced meristem 1 (FM1)

Sorghum propinquum cDNA (Genbank Acc.# BG051000.1). The first 60 out of 171 amino acids have 75% similarity with a Sorghum propinquum cDNA but then similarity drops to 36% for the remaining 111 amino acids (Fig-20). An Interproscan search identified a Histone HI and H5 family signature (conserved domain found in all HI histones) at amino acid position 1-63, in this gene family. Interproscan at Expasy is sequence analysis program that scans a protein sequence against protein family database and protein profile database to find a conserved protein domain. The presence ofa histone signature and the poor match to the EST and the gene bank databases indicates that this could be a new Histone-like gene family.

New histone-like gene family- Group 1

This group includes clones FL HL 2 GA-2, FL HL 2 PA-6 and FL HL 2 PA-7

(Fig.2l). This group has a 73 bp insertion in the intron at position 19-92 (Fig.24). This group shows 68% similarity at the nucleotide level and 66% similarity at the amino acid level with the Histone-like protein gene from Fritillaria liliacea. 80

Clone FL HL 2 PA-7

This clone has 15 bp deletion at position 346-363. There are also other unique

substitutions and small indels (Fig-21).

FL HL 2 PA-7 #1 TGAGGTACCA TATCTGGCCC CAATTTAGTC AGAGCTCTTT TCCTTATTGC FL HL 2 PA-6 #1 TGAGGTCA:A GATCCGGTTC CTATTTAGTC ATAGCTCTTT TCCTTGTTGC FL HL 2 GA-2 #1 TGATGTACCA GATCCGGTCC CAATTTAGTC AGAGCTCTTT TCCTTGTTGC

#1 TGAGGTACCA GATCCGGTCC CAATTTAGTC AGAGCTCTTT TCCTTGTTGC * *** * * ** * *

FL HL 2 PA-7 #51 TATTTTATTT CAATATTGCT CTAATTTTCT AAATTATCCC GATTTTGAAA FL HL 2 PA-6 #51 TATTCTATTT CGATGTTGCC CTAATTTTCT TACTTATACC CAATTTGAAA FL HL 2 GA-2 #51 TATTCTATTT CAATGTTGCC CTAATTTTCT AACTTATCCC GATTTTGAAA

#51 TATTCTATTT CAATGTTGCC CTAATTTTCT AACTTATCCC GATTTTGAAA * * * * **

FL HL 2 PA-7 #101 TCTCAGATGA TCCGTGAGGC GATAGCGTCC CTGAAGGAGA GGGCCGGGTT FL HL 2 PA-6 #101 TCTCAGATGA TCCACGAGGC GATAGCATTC CTGAAGGAGA GGACCGGGTC FL HL 2 GA-2 #101 TCTCAGATAT TCTGTGAGGC GATAGCATCC CTGAAGGAGA GGACCGGGTC

#101 TCTCAGATGA TCCGTGAGGC GATAGCATCC CTGAAGGAGA GGACCGGGTC ** *** * * *

FL HL 2 PA-7 #151 AAGCCAGTAT GCAATCTCGA AATTTGTTGA AGACAAGCAT AAGGCTCACC FL HL 2 PA-6 #151 AAGCCAGTAT GCAGTCTCAA AGTCCATTGA AGACAAGCAC AAGGGTGATC FL HL 2 GA-2 #151 AAGCCAGTAT GCAATCTCAA AGTTTGTTGC AGACAAGCAC AAGGTTCATC

#151 AAGCCAGTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGGBTCATC ** * *** * * * *

FL HL 2 PA-7 #201 TCCCGGCAAA CTATAAGAAG CTCCTCCTCA TCCAGCTTCG GAAGCTCACT FL HL 2 PA-6 #201 TCCTGGTAAA TATTAAGAAG TTCCTCCTCA TCCAGCATCG GAAGCACACT FL HL 2 GA-2 #201 TCTTGGTAAA TTTTAAGAAG CTCCTCCTCA TCCCACTTAG GAAGCTCACT

#201 TCCTGGTAAA TTTTAAGAAG CTCCTCCTCA TCCAGCTTCG GAAGCTCACT * * ** * * FL HL 2 PA-7 #251 GCTGCTGGCA AGCCCACAAA GGTCAAGAAC TCCTACAAGA TCCCTGCCAA FL HL 2 PA-6 #251 GCTGCTGGCA AACTCACCAA GGTCAAGAAC TCTTACAAGA TCCCTGCTAA FL HL 2 GA-2 #251 GCTGCTGGCA AACTCACCAA GGCCAAGAAC TCCTACAAGA TCCCTGCTAA

#251 GCTGCTGGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA ** * * *

FL HL 2 PA-7 #301 GCCCATTGCC GGTGGGAAGA AGACAACTAT CTCTACCGAG CTGAA::::: FL HL 2 PA-6 #301 GCCCGTTCTT TGTGAGATGA AAACAGTTAT CTCTGTAAAG CCAAAGTCTG FL HL 2 GA-2 #301 TCACATTCCT GGTGGGATGA AAAAAATTAT CTCTGTGAAG CCAAAGTCTA

#301 GCCCATTCCT GGTGGGATGA AAACAATTAT CTCTGTVAAG CCAAAGTCTR * * * *** * * * * ** **** ** * 81

FL HL 2 PA-7 #351 :::::::::: : ::GCCAAAG TCCACTACTG TTATGCCAAA GAAGGTGGCT FL HL 2 PA-6 #351 CTGTTGTGAA TCCCAATAAG TCCACTTCTG TTAAACCAAA TAAGTTGCAT FL HL 2 GA-2 #351 CTGTTGTAAA GCCCAATGAG TCCACTGCTG TTAAGCCAAA TAAGTTGGCC

#351 CTGTTGTRAA KCCCAATAAG TCCACTDCTG TTAAGCCAAA TAAGTTGGCT * ***** * ** * * ***

FL HL 2 PA-7 #401 GTGAAGCCGA AGCCAAAATC ATATACTGCA AAACCTAAAG CCAAGTCTAC FL HL 2 PA-6 #401 GTGAAGCCGA AGCCAAAAGC ATCTGCTACA AATCCTAAAT CCAAGTCTGC FL HL 2 GA-2 #401 GTGAAGCCGA AGCCAAAAGC ATCTGCTGCA AAGCCTAAAT CCAAGTCTGC

#401 GTGAAGCCGA AGCCAAAAGC ATCTGCTGCA AADCCTAAAT CCAAGTCTGC **** * *

FL HL 2 PA-7 #451 TGCTGCGAAG CCAGAGACAG CAGCAAAATT GAAATCTGTT GCGCCTAAGC FL HL 2 PA-6 #451 TGCTGTGATG CCAAAGACCG CAGCAAAGTC GAAATCCGTT GCACCTAACT FL HL 2 GA-2 #451 TGCTGCGAAG CCAAAGACCG CAGCGAAGTC AAAATCTGTT GCACCTAAGT

#451 TGCTGCGAAG CCAAAGACCG CAGCAAAGTC GAAATCTGTT GCACCTAAGT * ** * * ** * **

FL HL 2 PA-7 #501 TTAAAACTGC TGGTGGATCG GGGAAGGCAG CAAAGA:CCT CAGCCAAAGC FL HL 2 PA-6 #501 CTAAAGCTTC TAATGGACTG GCAAAGGCAG CAAAGACCCT CAGTCAATGT FL HL 2 GA-2 #501 CTAAAGCTTC TGGTGGACTG ACAAAGGCAG CAAAGA:CCT CAATCAATGT

#501 CTAAAGCTTC TGGTGGACTG GCAAAGGCAG CAAAGA:CCT CAGTCAATGT * ** *** ** **

FL HL 2 PA-7 #551 CACTCC:::T GTCAAGCT FL HL 2 PA-6 #551 CACTCCATCC GCTAAGCT FL HL 2 GA-2 #551 CACTCCCTCC GCCAAGCT

#551 CACTCCMTCC GCCAAGCT **** **

Fig.21. Multiple alignment of new histone-like group 1 clones from Fritillaria liliacea. *- Nucleotide difference in the alignment, : -. Gap in the sequence

New histone-like gene family- Group 2

This group includes clones FL HL 2 GA-3, FL HL 2 GA-4, FL HL 2 GA-5, FL HL 2

GA-6, FL HL 2 GA-7, FL HL 2 GA-8 and FL HL 2 GA-9 (Fig -22). Clone FL HL 2

GA-4 and clone FL HL 2 GA-6 have only one difference at position 23, which could represent a PCR error (Fig -22). This group does not have a 73 bp insertion in the intron as in group 1 (Fig-24). It exhibits a 68% similarity at the nucleotide level and 65% similarity at the amino acid level with the histone-like protein gene family from

Fritillaria liliacea. 82

FL HL 2 GA-3 #1 TGAGGTACCA GATCCCAATT TTGAAATCTC AGATGATCCG TGAGATGATA FL HL 2 GA-4 #1 TGAGGTACCA GATCCCAATT TTAAAATCTC AGATGATCCG TGAGACGATA FL HL 2 GA-5 #1 TGAGGTACCA GATCCCAATT TTGAAATCTC AGATGATCCG TGAGGCGATA FL HL 2 GA-6 #1 TGAGGTACCA GATCCCAATT TTGAAATCTC AGATGATCCG TGAGACGATA FL HL 2 GA-7 #1 TGAGGTACCA GATCCCAATT TTGAAATCAC AGAGGATCCG TGAGGCGATA FL HL 2 GA-B #1 TGAGGTACCA GATCCCAATT TTGAAATCTC AGATGATCCG TGAGGCGATA FL HL 2 GA-9 #1 TGAGGTACCA GATCCCAATT TTGAAATCTC AGATGATCCG TGAGGCGATA ...... #1 TGAGGTACCA GATCCCAATT TTGAAATCTC AGATGATCCG TGAGGCGATA

FL HL 2 GA-3 #51 GCGTCCCTGA AGGAGAGGAT CGGGTCAAGC CACTATGCAA TCTCAAAGTT FL HL 2 GA-4 #51 GCGTCCCTGA AGGAGAGGAT CGGGTCAAGC CACTATGCAA TCTCAAAGTT FL HL 2 GA-5 #51 GCGTCCCTAA AGGAGAGGAT CGGGTCAAGC CAGTATGCAA TCTCAGAGTT FL HL 2 GA-6 #51 GCGTCCCTGA AGGAGAGGAT CGGGTCAAGC CACTATGCAA TCTCAAAGTT FL HL 2 GA-7 #51 GCGTCCCTGA AGGAGAGGAT CGGGTCAAGC CAGTATGCAA TCTCAAAGTT FL HL 2 GA-B #51 GCGTCCCTAA AGGAGAGGAT CGGGTCAAGC CAGTATGAAA TCTCAAAGTT FL HL 2 GA-9 #51 GCGTCCCTGA AGGAGAGGAT CGTGTCAAGC CAGTATGAAA TCTCAAAGTT ...... #51 GCGTCCCTGA AGGAGAGGAT CGGGTCAAGC CAGTATGCAA TCTCAAAGTT * * * *

FL HL 2 GA-3 #101 TGTTGAAGAC AAGCACAAGG GTCATCTCCC GGTAAACTCT AAGAAGTTCC FL HL 2 GA-4 #101 TGTTGAAGAC AAGCACAAGG GTCATCTCCC GGTAAACTCT AAGAAGTTCC FL HL 2 GA-5 #101 TGTTGAAGAC AAGCACAAGG GTCATCTCCC GGTAAACTTT AAGAAGTTCC FL HL 2 GA-6 #101 TGTTGAAGAC AAGCACAAGG GTCATCTCCC GGTAAACACT AAGAAGTTCC FL HL 2 GA-7 #101 TGTTGAAGAC AAGCACAAGG GTCATCTCCT GGTAAACTTT AAGAAGTTCA FL HL 2 GA-B #101 TGTTGAAGAC AAGCACAAGG GTCATCTCCC GGTAAACTTT AAGAAGTTCC FL HL 2 GA-9 #101 TGTTGGAGAC AAGCACAAGG GTCATCTCCC GGTAAACTTT AAGAAGTTCC ...... #101 TGTTGAAGAC AAGCACAAGG GTCATCTCCC GGTAAACTTT AAGAAGTTCC * **

FL HL 2 GA-3 #151 TCATCCAGCT TCGGAAGTTC AATGCTGCTC GCAAACTCAC CAAGGTCAAG FL HL 2 GA-4 #151 TCATCCAGCT TCGGAAGCTC AATGCTGCTC GCAAACTCAC CAAGGTCAAG FL HL 2 GA-5 #151 TCATCCAGCT TTGGAAGCTC AATGCTGCTC GCAAACTCAC CAAGGTCAAG FL HL 2 GA-6 #151 TCATCCAGCT TCGGAAGCTC AATGCTGCTC GCAAACTCAC CAAGGTCAAG FL HL 2 GA-7 #151 TCATCCAGCT TCGGAAGCTC AATGCTGCTC GAAAACTCAC CAAGGTCAAG FL HL 2 GA-B #151 TCATCCAGCT TCGGAAGCTC AATGCTGCTC GCAAACTCAC CAAGGTCAAG FL HL 2 GA-9 #151 TCATCCAGCT TCGGAAGCTC AATGCTGCTC GCAAACTCAC CAAGGTCAAG ...... #151 TCATCCAGCT TCGGAAGCTC AATGCTGCTC GCAAACTCAC CAAGGTCAAG ** *

FL HL 2 GA-3 #201 AACTCCTACA AGATACCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT FL HL 2 GA-4 #201 AACTCCTACA AGATCCCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT FL HL 2 GA-5 #201 AACTCCTACA AGATCCCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT FL HL 2 GA-6 #201 AACTCCTACA AGATCCCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT FL HL 2 GA-7 #201 AACTCCTACA AGATCCCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT FL HL 2 GA-B #201 AACTCCTACA AGATACCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT FL HL 2 GA-9 #201 AACTCCTACA AGATCCCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT ...... #201 AACTCCTACA AGATCCCTGC TAAGCCCATT TCTGGTAGTA TGAAAACAGT

FL HL 2 GA-3 #251 TATCTCTGTG ACGCCAAAGT CTGCTGTTGT GAAACCAAAT AAGTCCACTG FL HL 2 GA-4 #251 TATCTCTGTG ACGCCAAAGT CTGCTGTTGT GAAACCAAAT AAGTCCACTG FL HL 2 GA-5 #251 TATCTCTGTG AAGCCAAAGT CTGCAGTTGT GAAACCAAAT AAGTCAACTG FL HL 2 GA-6 #251 TATCTCTGTG ACGCCAAAGT CTGCTGTTGT GAAACCAAAT AAGTCCACTG FL HL 2 GA-7 #251 TATCTCTGTG AAGCCAAAGT CTGCTGTTGT GAAACCAAAT AAGTCCACTG FL HL 2 GA-B #251 TATCTCTGTG ACGCCAAAGT CTGCTGTTGT GAAACCAAAT AAGTCCACTG FL HL 2 GA-9 #251 TATCTCTGTG AAGCCAAAGT CTGCTGTTGT GAAACCAAAT AAGTCCACTG ...... #251 TATCTCTGTG ACGCCAAAGT CTGCTGTTGT GAAACCAAAT AAGTCCACTG * * 83

FL HL 2 GA-3 #301 CTGTTATGCC AGATAAGGTG GCTGTGAAGC CGAATCAAAA ATCAACTGTT FL HL 2 GA-4 #301 CTGTTATGCC AGATAAGGTG GCTGTGAAGC CGAATAAAAA ATCAACTGTT FL HL 2 GA-5 #301 CTGTCGTGCC AGATAAGGTG GCTGTGAAGC CGAATCCAAA ATCAACTGTT FL HL 2 GA-6 #301 CTGTTATGCC AGATAAGGTG GCTGTGAAGC CGAATAAAAA ATCAACTGTT FL HL 2 GA-7 #301 CTGTTATGCC AGATAAGGTG GCTGTGAAGC CGAATCAAAA ATCAACTGTT FL HL 2 GA-8 #301 CTGTTATGCC AGATAAGGTG GCTGTGAAGC CGAATCAAAA ATCAACTGTT FL HL 2 GA-9 #301 CTGTTATGCC AGATAAGGTG GCTGCGAAGC CGAATCCAAA ATCAACTGTT ...... #301 CTGTTATGCC AGATAAGGTG GCTGTGAAGC CGAATCAAAA ATCAACTGTT ** * **

FL HL 2 GA-3 #351 GCAAAGCCTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TTGCAGTGAA FL HL 2 GA-4 #351 GCAAAGCCTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TTGCAGTGAA FL HL 2 GA-5 #351 GCAAAGCCTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TCGCAGTGAA FL HL 2 GA-6 #351 GCAAAGCCTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TTGCAGTGAA FL HL 2 GA-7 #351 GCAAAGCCTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TTGCAGTGAA FL HL 2 GA-8 #351 GCAAAGCCTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TTGCAGTGAA FL HL 2 GA-9 #351 GCAAAGCTTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TCGCAGTGAA ...... #351 GCAAAGCCTA AATCCAAGTC TGCTGCTGTG AAGCCAAAGA TTGCAGTGAA

FL HL 2 GA-3 #401 GTCGAAACCT GTTGCACCTA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG FL HL 2 GA-4 #401 GTCGATACCT GTTGCACCTA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG FL HL 2 GA-5 #401 GTCGAAACCT GTTGCACCTA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG FL HL 2 GA-6 #401 GTCGATACCT GTTGCACCTA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG FL HL 2 GA-7 #401 GTCGAAACCT GTTGCACCTA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG FL HL 2 GA-8 #401 GTCGAAACCT GTTGCACCTA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG FL HL 2 GA-9 #401 GTCGAAACCT GTTGCACCAA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG ...... #401 GTCGAAACCT GTTGCACCTA TGTCTAAAAC ATCCGGTGGA CTGGCAAAGG * *

FL HL 2 GA-3 #451 TAAAAAAGAC CCCAGTCAGT GTCACTCCTT CCACCAAGCC GAAGATGGCT FL HL 2 GA-4 #451 TAAAAAAGAC CCCAGTCAAT GTCACTCCTT CCACCAAGCC GAAGATGGCT FL HL 2 GA-5 #451 TAACAAAGAC CTCAGTCAAT GTTACTCCTT CCACCAGGCC GAAGATGGCT FL HL 2 GA-6 #451 TAAAAAAGAC CCCAGTCAAT GTCACTCCTT CCACCAAGCC GAAGATGGCT FL HL 2 GA-7 #451 TAAAAAAGAC CCCAGTCAAT GTCACTCCTT CCACCAAGCC GAAGATGGCT FL HL 2 GA-8 #451 TAAAAAAGGC CCCAGTCAAT GTCACTCCTT CCACCAAGCT GAAGATGGCT FL HL 2 GA-9 #451 TAAAAAAGAC CCCAGTCAAT GTCACTCCTT CCACCAAGCT GAAGATGTCT ...... #451 TAAAAAAGAC CCCAGTCAAT GTCACTCCTT CCACCAAGCC GAAGATGGCT ***** ** *

FL HL 2 GA-3 #501 GCTCCAGTTG CGGCCGAGAA GCCGAAGATT GTGAATAAGT CCCCT FL HL 2 GA-4 #501 GCTCCAGTTG CTGCCAAGAA GCCGAAGATT GTGAATAAGT CCCCT FL HL 2 GA-5 #501 GCTCCAGTTG CTGCAAAGAA GCTGAAGATT GTGAATAAAT CCCCT FL HL 2 GA-6 #501 GCTCCAGTTG CTGCCAAGAA GCCGAAGATT GTGAATAAGT CCCCT FL HL 2 GA-7 #501 GCTCCAGTTG CTGCCAAGAA GCCGAAGATT GTGAATAAGT CCCCT FL HL 2 GA-8 #501 GCTCCAGTTG CTGCCAAGAA GCCGAAGATT GTGAATAAGT CCCCT FL HL 2 GA-9 #501 GCTCCAGTTG CTGCCAAGAA GCCGAAGATT GTGAATAAGT CCCCT ...... #501 GCTCCAGTTG CTGCCAAGAA GCCGAAGATT GTGAATAAGT CCCCT ** * * Fig. 22. Multiple alignment of new Histone-like group 2 clones from Fritillaria liliacea. * Nucleotide difference in the alignment, : -. Gap in he sequence 84

New histone-like gene family- Group 3

This group includes pseudogenes. All ofthese pseudogenes are defined as conventional pseudogenes due to the presence ofan intron and the absence ofan open reading frame. This group includes clones FL HL 2 PA-3, FL HL 2 PA-4, FL HL 2 PA-9,

FL HL 2 PA-II (Fig.23).

FL HL 2 PA-3 #1 TGAGGTAC:C GATCCGGTCC TAATTAAGTC AGAGTTCTTT TGCTTGTTGC

FL HL 2 PA-4 #1 TGTGGTATCA GATCCAGTCA CAGTTTAGTC AGAGCTCTTT TCCTGGTTGC FL HL 2 PA-9 #1 TGAGGTACTA GATCCGGTCC CAATTTATTC AAAGATCTTT TCCTTGTTGC FL HL 2 PA-11 #1 TGAGGTACTA GATCTGGTCC CAATTTAGTC AAAGCTCTTT TCCTTGTTAC

#1 TGAGGTACTA GATCCGGTCC CAATTTAGTC ARAGCTCTTT TCCTTGTTGC * *** **** * *

FL HL 2 PA-3 #51 TATTCTATTT CAACATTGCC CTAATTTTCT AACTTATTCC GATTTTGAAA FL HL 2 PA-4 #51 TATTCTATGT CAATGTTGTT CTAATTTTCA AACTTA:CCC TATTTTGAAA FL HL 2 PA-9 #51 TATTCAATTT CAATGTTGCC CTAGTTTTCT AACTTATCCC GATTTGGAAA FL HL 2 PA-11 #51 TATTCAATTT CAATGTTGCC TTAGTTTTCT AACTTATCCC GATTTAGAAA

#51 TATTCWATTT CAATGTTGCC CTARTTTTCT AACTTATCCC GATTTTGAAA ** ** * * *

FL HL 2 PA-3 #101 TCTCTGATGA TCCATGAGGA GATAACATCC CTGAAGGAGA GGACCGGGTC FL HL 2 PA-4 #101 TCTCAGATGA TCCGTGAGGC AATAGCGTCC CCGAAGGAGA GGACCAGGTC FL HL 2 PA-9 #101 TATCAAATGA TCCGTGAGGT GAAAGCGTCC CTGA:GGAGA GGACCGGGTC FL HL 2 PA-11 #101 TATCAAATGA TCCGTGAATT GATAGCGT:C CTGAAGAAGA GGACCGGGTC

#101 TMTCARATGA TCCGTGAGGT GATAGCGTCC CTGAAGGAGA GGACCGGGTC * *** * * * ** *

FL HL 2 PA-3 #151 AAGAAAGTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGACTCATC FL HL 2 PA-4 #151 AAGCCAGTAT GCAATCTCAT AGTTTGATGA AGACAAGCAC AAGACACATA FL HL 2 PA-9 #151 AAGCTAGTAT GAAATCTCAA AGTTTCTTGA AGACAAGCAC AAGGCTCATC FL HL 2 PA-11 #151 ATGACAGTAC GCAATCTTAA CGTCTGTTGA AGACAAGCAC AAGGCTCATC

#151 AAGMCAGTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGRCTCATC * *** * ** ** *

FL HL 2 PA-3 #201 TCCTGATAAA CTTTAAGAAG CTCCTCCTCA TCCAACTTCA GAAGCCCACT FL HL 2 PA-4 #201 TCCCGGTAAA CTTTAAAAAG CTCCACCTCA TCCAGCTTCA GAAGCTCACT FL HL 2 PA-9 #201 TCCCGGTAAA CTTTAAGAAG CTCCTCCTCG TCCAGCTTCG GAAGCTCACT FL HL 2 PA-11 #201 TCCCGGTAAA CTTTAAGAAG CTCCTCCTCG TCCAGCTTTA GAAGCTCACT

#201 TCCCGGTAAA CTTTAAGAAG CTCCTCCTCR TCCAGCTTCA GAAGCTCACT ** * * * ** * 85

FL HL 2 PA-3 #251 GTTGCTCGCA AACTCACCAA GGTCAAGAAT TCCTATAATA TCCCTGCAAA FL HL 2 PA-4 #251 GCTGCTGGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA FL HL 2 PA-9 #251 GCTGCTGGCA AACTCACCCA GGTCAAGAAC TCCTACAAGA TCCATGTTAA FL HL 2 PA-11 #251 ACAGCTGGCA AACTCACCAA GGTCAAGAGC TCCTACAAGA TCCCTGCTAA

#251 GCTGCTGGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA *** * *

FL HL 2 PA-3 #301 TCCCATTCTT GGTGGGATAA AAATA::::: :::::::::: GTTATCTCTG FL HL 2 PA-4 #301 GCCCGTTCAT GGTGGGATGA AAAGAGATGG GATGAAAATA GTTATCTCTG FL HL 2 PA-9 #301 GCCCATTCCT GGTGGGATGA AAACA::::: :::::::::: GTTATCTCTG FL HL 2 PA-11 #301 GCCCGTTCCT GGTGAGATGA AAACA::::: :::::::::: CTTATCTCTG

#301 GCCCRTTCCT GGTGGGATGA AAACAGATGG GATGAAAATA GTTATCTCTG * * * * *

FL HL 2 PA-3 #351 CGAATGCAAA TTCTGCTGTT GTGAAACCTA ATAAGTCCAC TAATCTTAAG FL HL 2 PA-4 #351 TGTAACCAAA GTCTGCTGTT GTGAAGCCCA ATAA: :CCAC TGCTGTTAAG FL HL 2 PA-9 #351 TGAAGCCAAA GTCTGCTGTT GTGAATCCCA AAAAGTCCAC TACTGTTAAG FL HL 2 PA-11 #351 TGAAGCCAAA TTCTGCTGTT GTGAATCCCA AAAAGTCCAC TGCTGTTGAG

#351 TGAAGCCAAA KTCTGCTGTT GTGAATCCCA AWAAGTCCAC TRCTGTTAAG * * ** * * * ** * *

FL HL 2 PA-3 #401 CCAAATAAGG TTGCCGTGAA GCCGAAGCCA AAAGCATCTC CTGTAAAGCC FL HL 2 PA-4 #401 ACAAAAAAGG TGGCTGTGAA GCCAAAGCCA AAAGCATCTG CTGCAAATCA FL HL 2 PA-9 #401 CCAAATAAGG TGGTTGTGAA GCCGAAGCCA AAAGCATCTG CTGCAAAACC FL HL 2 PA-11 #401 TCAAATAAGG TGTCTGTGAA GCCGAAGCCA AAAGCATCTG CTGCAAAACC

#401 CCAAATAAGG TGGCTGTGAA GCCGAAGCCA AAAGCATCTG CTGCAAAACC ** **** * *

FL HL 2 PA-3 #451 TAAATCCAAG CCAGCTGTTG TGAACCCAAA GACAGCAGCG AAGTCAAAAT FL HL 2 PA-4 #451 TAAATCCAAA TCTGCTGCTG CAAAGACAAA GACTGCAGTG AAGTCGGAAT FL HL 2 PA-9 #451 TAAATTCGAG TCTGCTGCTC CGAATCCCAA GACAGCAGCG AAGTCAAAAT FL HL 2 PA-11 #451 TAAATCCAAG TCTGCTGCTC CGAAGCCAAA GACCGCAGCG AAGTCGAAAT

#451 TAAATCCAAG TCTGCTGCTS CGAAGCCAAA GACAGCAGCG AAGTCRAAAT ** *** * * ** ** * * **

FL HL 2 PA-3 #501 ATATTGCACC TAAGTTTAAA GCTTATGGTG GACTGGAAAA GGCAGCAAAG FL HL 2 PA-4 #501 CTGTTGCACC TAAGTCTAAA GCTACTGGTG GACTGGCAAA GGCAGCAAAG FL HL 2 PA-9 #501 CTGTTGCACC TAAATCTAAA GCTTCGGGTT GACTGGCAAA GACAGCAAAG FL HL 2 PA-11 #501 ATGTTGCACC TAAATCTAAA GCTTCTGGTT GACTGGCAAA GGCAGCAAAG

#501 MTGTTGCACC TAARTCTAAA GCTTCTGGTK GACTGGCAAA GGCAGCAAAG ** *** ***

FL HL 2 PA-3 #551 ACCTTAGTCA ATGTCACTCC TTCTGCCAAG CA FL HL 2 PA-4 #551 ATCTCAGTCA ATGTCACTCC TTCCGC FL HL 2 PA-9 #551 ACCACAGTCA ATGTCACTCC CACCGCCAAG TAGAAGAAGA CTGCTCTAGT FL HL 2 PA-11 #551 ACCACAGTCA ATGTCACTCC TACCGCCAAG TAGAAGAAGG CTGCTCCAGT

#551 ACCWCAGTCA ATGTCACTCC TWCCGCCAAG TAGAAGAAGR CTGCTCYAGT * ** ** * * *

FL HL 2 PA-9 #601 TACTGCCAAA AAGCTGAAGA TTGCGAATGA GGCCCCT FL HL 2 PA-11 #601 TGCTGCCAAA AAGCAGAAGA TTGTGAATGA GGACCCA

#601 TRCTGCCAAA AAGCWGAAGA TTGYGAATGA GGMCCCW * * *

Fig. 23. Multiple alignment of new histone-like protein group 3 clones from Fritillaria liliacea. * Nucleotide difference in the alignment, : -. Gap in he sequence 86

FLHL2 PA-3

In this clone, 3' splice site ofthe intron at position 105, has changed from AG to TG.

Also many base substitutions have introduced inframe stop codons.

FLHL 2 PA-4

Although this clone has an intact 3' intron splice site, it does not have an open reading frame. Many base substitutions and small indels have introduced inframe stop codons.

FL HL 2 PA-9 and FL HL 2 PA-ll

In both the clones, 3' splice site ofintron at position 105, has changed from AG to

AA. Also many base substitutions have introduced inframe stop codons.

FL HL 2 GA-9 #1 TGAGGTACCA GATCCCAA: : ::::::::: : ::::::::: : ::::::::: : FL HL 2 GA-4 #1 TGAGGTACCA GATCCCAA: : ::::::::: : ::::::::: : ::::::::: : FL HL 2 GA-5 #1 TGAGGTACCA GATCCCAA: : ::::::::: : ::::::::: : ::::::::: : FL HL 2 GA-6 #1 TGAGGTACCA GATCCCAA: : ::::::::: : ::::::::: : ::::::::: : FL HL 2 GA-3 #1 TGAGGTACCA GATCCCAA: : ::::::::: : ::::::::: : ::::::::: : FL HL 2 GA-7 #1 TGAGGTACCA GATCCCAA: : ::::::::: : ::::::::: : ::::::::: : FL HL 2 GA-8 #1 TGAGGTACCA GATCCCAA: : ::::::::: : ::::::::: : ::::::::: : FL HL 2 PA-3 #1 TGAGGTAC:C GATCCGGTCC TAATTAAGTC AGAGTTCTTT TGCTTGTTGC FL HL 2 PA-4 #1 TGTGGTATCA GATCCAGTCA CAGTTTAGTC AGAGCTCTTT TCCTGGTTGC FL HL 2 PA-6 #1 TGAGGTCA:A GATCCGGTTC CTATTTAGTC ATAGCTCTTT TCCTTGTTGC FL HL 2 PA-7 #1 TGAGGTACCA TATCTGGCCC CAATTTAGTC AGAGCTCTTT TCCTTATTGC FL HL 2 PA-9 #1 TGAGGTACTA GATCCGGTCC CAATTTATTC AAAGATCTTT TCCTTGTTGC FL HL 2 PA-ll #1 TGAGGTACTA GATCTGGTCC CAATTTAGTC AAAGCTCTTT TCCTTGTTAC FL HL 2 GA-2 #1 TGATGTACCA GATCCGGTCC CAATTTAGTC AGAGCTCTTT TCCTTGTTGC ...... #1 TGAGGTACCA GATCCCRACC CAATTTAGTC AGAGCTCTTT TCCTTGTTGC **** * ****** *** *** * ** * 87

FL HL 2 GA-9 #51 ::::::::: : ::::::::: : ::::::::: : : :TTTTGAAA FL HL 2 GA-4 #51 ::::::::: : ::::::::: : ...... ::::::::: : : :TTTTAAAA FL HL 2 GA-5 #51 ::::::::: : ::::::::: : ::::::::: : : :TTTTGAAA FL HL 2 GA-6 #51 ...... ::::::::: : ::::::::: : ::::::::: : : :TTTTGAAA FL HL 2 GA-3 #51 ...... ::::::::: : ::::::::: : ::::::::: : : :TTTTGAAA FL HL 2 GA-7 #51 ::::::::: : ::::::::: : ::::::::: : : :TTTTGAAA FL HL 2 GA-8 #51 ...... ::::::::: : ::::::::: : ::::::::: : : :TTTTGAAA FL HL 2 PA-3 #51 TATTCTATTT CAACATTGCC CTAATTTTCT AACTTATTCC GATTTTGAAA FL HL 2 PA-4 #51 TATTCTATGT CAATGTTGTT CTAATTTTCA AACTTA:CCC TATTTTGAAA FL HL 2 PA-6 #51 TATTCTATTT CGATGTTGCC CTAATTTTCT TACTTATACC CAATTTGAAA FL HL 2 PA-7 #51 TATTTTATTT CAATATTGCT CTAATTTTCT AAATTATCCC GATTTTGAAA FL HL 2 PA-9 #51 TATTCAATTT CAATGTTGCC CTAGTTTTCT AACTTATCCC GATTTGGAAA FL HL 2 PA-11 #51 TATTCAATTT CAATGTTGCC TTAGTTTTCT AACTTATCCC GATTTAGAAA FL HL 2 GA-2 #51 TATTCTATTT CAATGTTGCC CTAATTTTCT AACTTATCCC GATTTTGAAA

#51 TATTCTATTT CAATGTTGCC CTAATTTTCT AACTTATCCC GATTTTGAAA ** ** ** ** * * **

FL HL 2 GA-9 #101 TCTCAGATGA TCCGTGAGGC GATAGCGTCC CTGAAGGAGA GGATCGTGTC FL HL 2 GA-4 #101 TCTCAGATGA TCCGTGAGAC GATAGCGTCC CTGAAGGAGA GGATCGGGTC FL HL 2 GA-5 #101 TCTCAGATGA TCCGTGAGGC GATAGCGTCC CTAAAGGAGA GGATCGGGTC FL HL 2 GA-6 #101 TCTCAGATGA TCCGTGAGAC GATAGCGTCC CTGAAGGAGA GGATCGGGTC FL HL 2 GA-3 #101 TCTCAGATGA TCCGTGAGAT GATAGCGTCC CTGAAGGAGA GGATCGGGTC FL HL 2 GA-7 #101 TCACAGAGGA TCCGTGAGGC GATAGCGTCC CTGAAGGAGA GGATCGGGTC FL HL 2 GA-8 #101 TCTCAGATGA TCCGTGAGGC GATAGCGTCC CTAAAGGAGA GGATCGGGTC FL HL 2 PA-3 #101 TCTCTGATGA TCCATGAGGA GATAACATCC CTGAAGGAGA GGACCGGGTC FL HL 2 PA-4 #101 TCTCAGATGA TCCGTGAGGC AATAGCGTCC CCGAAGGAGA GGACCAGGTC FL HL 2 PA-6 #101 TCTCAGATGA TCCACGAGGC GATAGCATTC CTGAAGGAGA GGACCGGGTC FL HL 2 PA-7 #101 TCTCAGATGA TCCGTGAGGC GATAGCGTCC CTGAAGGAGA GGGCCGGGTT FL HL 2 PA-9 #101 TATCAAATGA TCCGTGAGGT GAAAGCGTCC CTGA:GGAGA GGACCGGGTC FL HL 2 PA-11 #101 TATCAAATGA TCCGTGAATT GATAGCGT:C CTGAAGAAGA GGACCGGGTC FL HL 2 GA-2 #101 TCTCAGATAT TCTGTGAGGC GATAGCATCC CTGAAGGAGA GGACCGGGTC

#101 TCTCAGATGA TCCGTGAGGC GATAGCGTCC CTGAAGGAGA GGAYCGGGTC ** ** *** *** *** * * ** * *

FL HL 2 GA-9 #151 AAGCCAGTAT GAAATCTCAA AGTTTGTTGG AGACAAGCAC AAGGGTCATC FL HL 2 GA-4 #151 AAGCCACTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGGGTCATC FL HL 2 GA-5 #151 AAGCCAGTAT GCAATCTCAG AGTTTGTTGA AGACAAGCAC AAGGGTCATC FL HL 2 GA-6 #151 AAGCCACTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGGGTCATC FL HL 2 GA-3 #151 AAGCCACTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGGGTCATC FL HL 2 GA-7 #151 AAGCCAGTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGGGTCATC FL HL 2 GA-8 #151 AAGCCAGTAT GAAATCTCAA AGTTTGTTGA AGACAAGCAC AAGGGTCATC FL HL 2 PA-3 #151 AAGAAAGTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGACTCATC FL HL 2 PA-4 #151 AAGCCAGTAT GCAATCTCAT AGTTTGATGA AGACAAGCAC AAGACACATA FL HL 2 PA-6 #151 AAGCCAGTAT GCAGTCTCAA AGTCCATTGA AGACAAGCAC AAGGGTGATC FL HL 2 PA-7 #151 AAGCCAGTAT GCAATCTCGA AATTTGTTGA AGACAAGCAT AAGGCTCACC FL HL 2 PA-9 #151 AAGCTAGTAT GAAATCTCAA AGTTTCTTGA AGACAAGCAC AAGGCTCATC FL HL 2 PA-11 #151 ATGACAGTAC GCAATCTTAA CGTCTGTTGA AGACAAGCAC AAGGCTCATC FL HL 2 GA-2 #151 AAGCCAGTAT GCAATCTCAA AGTTTGTTGC AGACAAGCAC AAGGTTCATC

#151 AAGCCAGTAT GCAATCTCAA AGTTTGTTGA AGACAAGCAC AAGGGTCATC *** *** ** **** * **** ** 88

FL HL 2 GA-9 #201 TCCCGGTAAA CTTTAAGAAG :: :TTCCTCA TCCAGCTTCG GAAGCTCAAT FL HL 2 GA-4 #201 TCCCGGTAAA CTCTAAGAAG :: :TTCCTCA TCCAGCTTCG GAAGCTCAAT FL HL 2 GA-5 #201 TCCCGGTAAA CTTTAAGAAG : ::TTCCTCA TCCAGCTTTG GAAGCTCAAT FL HL 2 GA-6 #201 TCCCGGTAAA CACTAAGAAG :: :TTCCTCA TCCAGCTTCG GAAGCTCAAT FL HL 2 GA-3 #201 TCCCGGTAAA CTCTAAGAAG :: :TTCCTCA TCCAGCTTCG GAAGTTCAAT FL HL 2 GA-7 #201 TCCTGGTAAA CTTTAAGAAG :: :TTCATCA TCCAGCTTCG GAAGCTCAAT FL HL 2 GA-8 #201 TCCCGGTAAA CTTTAAGAAG :: :TTCCTCA TCCAGCTTCG GAAGCTCAAT FL HL 2 PA-3 #201 TCCTGATAAA CTTTAAGAAG CTCCTCCTCA TCCAACTTCA GAAGCCCACT FL HL 2 PA-4 #201 TCCCGGTAAA CTTTAAAAAG CTCCACCTCA TCCAGCTTCA GAAGCTCACT FL HL 2 PA-6 #201 TCCTGGTAAA TATTAAGAAG TTCCTCCTCA TCCAGCATCG GAAGCACACT FL HL 2 PA-7 #201 TCCCGGCAAA CTATAAGAAG CTCCTCCTCA TCCAGCTTCG GAAGCTCACT FL HL 2 PA-9 #201 TCCCGGTAAA CTTTAAGAAG CTCCTCCTCG TCCAGCTTCG GAAGCTCACT FL HL 2 PA-11 #201 TCCCGGTAAA CTTTAAGAAG CTCCTCCTCG TCCAGCTTTA GAAGCTCACT FL HL 2 GA-2 #201 TCTTGGTAAA TTTTAAGAAG CTCCTCCTCA TCCCACTTAG GAAGCTCACT

#201 TCCCGGTAAA CTTTAAGAAG :TCYTCCTCA TCCAGCTTCG GAAGCTCAMT ** ** *** * ***** * ** * ** **

FL HL 2 GA-9 #251 GCTGCTCGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA FL HL 2 GA-4 #251 GCTGCTCGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA FL HL 2 GA-5 #251 GCTGCTCGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA FL HL 2 GA-6 #251 GCTGCTCGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA FL HL 2 GA-3 #251 GCTGCTCGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TACCTGCTAA FL HL 2 GA-7 #251 GCTGCTCGAA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA FI> HL 2 GA-8 #251 GCTGCTCGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TACCTGCTAA FL HL 2 PA-3 #251 GTTGCTCGCA AACTCACCAA GGTCAAGAAT TCCTATAATA TCCCTGCAAA FL HL 2 PA-4 #251 GCTGCTGGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA FL HL 2 PA-6 #251 GCTGCTGGCA AACTCACCAA GGTCAAGAAC TCTTACAAGA TCCCTGCTAA FL HL 2 PA-7 #251 GCTGCTGGCA AGCCCACAAA GGTCAAGAAC TCCTACAAGA TCCCTGCCAA FL HL 2 PA-9 #251 GCTGCTGGCA AACTCACCCA GGTCAAGAAC TCCTACAAGA TCCATGTTAA FL HL 2 PA-11 #251 ACAGCTGGCA AACTCACCAA GGTCAAGAGC TCCTACAAGA TCCCTGCTAA FL HL 2 GA-2 #251 GCTGCTGGCA AACTCACCAA GGCCAAGAAC TCCTACAAGA TCCCTGCTAA

#251 GCTGCTCGCA AACTCACCAA GGTCAAGAAC TCCTACAAGA TCCCTGCTAA *** ** ** ** ** * * **

FL HL 2 GA-9 #301 GCCCATTTCT GGTAGTATGA AAACA::::: :::::::::: GTTATCTCTG FL HL 2 GA-4 #301 GCCCATTTCT GGTAGTATGA AAACA::::: :::: :::::: GTTATCTCTG FL HL 2 GA-5 #301 GCCCATTTCT GGTAGTATGA AAACA::::: :::::::::: GTTATCTCTG FL HL 2 GA-6 #301 GCCCATTTCT GGTAGTATGA AAACA::::: :::::::::: GTTATCTCTG FL HL 2 GA-3 #301 GCCCATTTCT GGTAGTATGA AAACA::::: ::::: ::::: GTTATCTCTG FL HL 2 GA-7 #301 GCCCATTTCT GGTAGTATGA AAACA::::: :::::::::: GTTATCTCTG FL HL 2 GA-8 #301 GCCCATTTCT GGTAGTATGA AAACA::::: :::::::::: GTTATCTCTG FL HL 2 PA-3 #301 TCCCATTCTT GGTGGGATAA AAATA::::: :::::::::: GTTATCTCTG FL HL 2 PA-4 #301 GCCCGTTCAT GGTGGGATGA AAAGAGATGG GATGAAAATA GTTATCTCTG FL HL 2 PA-6 #301 GCCCGTTCTT TGTGAGATGA AAACA::::: ::::: ::::: GTTATCTCTG FL HL 2 PA-7 #301 GCCCATTGCC GGTGGGAAGA AGACA::::: :::: :::::: ACTATCTCTA FL HL 2 PA-9 #301 GCCCATTCCT GGTGGGATGA AAACA::::: ::::::: ::: GTTATCTCTG FL HL 2 PA-11 #301 GCCCGTTCCT GGTGAGATGA AAACA::::: :: :::::::: CTTATCTCTG FL HL 2 GA-2 #301 TCACATTCCT GGTGGGATGA AAAAA::::: : :::: ::::: ATTATCTCTG

#301 GCCCATTTCT GGTRGKATGA AAACAGATGG GATGAAAATA GTTATCTCTG ** * *** * *** ** ** ** * 89

FL HL 2 GA-9 #351 TGAAGCCAAA GTCTGCTGTT GTGAAACCAA ATAAGTCCAC TGCTGTTATG FL HL 2 GA-4 #351 TGACGCCAAA GTCTGCTGTT GTGAAACCAA ATAAGTCCAC TGCTGTTATG FL HL 2 GA-5 #351 TGAAGCCAAA GTCTGCAGTT GTGAAACCAA ATAAGTCAAC TGCTGTCGTG FL HL 2 GA-6 #351 TGACGCCAAA GTCTGCTGTT GTGAAACCAA ATAAGTCCAC TGCTGTTATG FL HL 2 GA-3 #351 TGACGCCAAA GTCTGCTGTT GTGAAACCAA ATAAGTCCAC TGCTGTTATG FL HL 2 GA-7 #351 TGAAGCCAAA GTCTGCTGTT GTGAAACCAA ATAAGTCCAC TGCTGTTATG FL HL 2 GA-8 #351 TGACGCCAAA GTCTGCTGTT GTGAAACCAA ATAAGTCCAC TGCTGTTATG FL HL 2 PA-3 #351 CGAATGCAAA TTCTGCTGTT GTGAAACCTA ATAAGTCCAC TAATCTTAAG FL HL 2 PA-4 #351 TGTAACCAAA GTCTGCTGTT GTGAAGCCCA ATAA: :CCAC TGCTGTTAAG FL HL 2 PA-6 #351 TAAAGCCAAA GTCTGCTGTT GTGAATCCCA ATAAGTCCAC TTCTGTTAAA FL HL 2 PA-7 #351 CCGAGCTGAA :::::::::: :::: : GCCAA A: ::GTCCAC TACTGTTATG FL HL 2 PA-9 #351 TGAAGCCAAA GTCTGCTGTT GTGAATCCCA AAAAGTCCAC TACTGTTAAG FL HL 2 PA-11 #351 TGAAGCCAAA TTCTGCTGTT GTGAATCCCA AAAAGTCCAC TGCTGTTGAG FL HL 2 GA-2 #351 TGAAGCCAAA GTCTACTGTT GTAAAGCCCA ATGAGTCCAC TGCTGTTAAG

#351 TGAAGCCAAA GTCTGCTGTT GTGAAACCAA ATAAGTCCAC TGCTGTTATG ******** * *** ***** * ** * ****

FL HL 2 GA-9 #401 CCAGATAAGG TGGCTGCGAA GCCGAATCCA AAATCAACTG TTGCAAAGCT FL HL 2 GA-4 #401 CCAGATAAGG TGGCTGTGAA GCCGAATAAA AAATCAACTG TTGCAAAGCC FL HL 2 GA-5 #401 CCAGATAAGG TGGCTGTGAA GCCGAATCCA AAATCAACTG TTGCAAAGCC FL HL 2 GA-6 #401 CCAGATAAGG TGGCTGTGAA GCCGAATAAA AAATCAACTG TTGCAAAGCC FL HL 2 GA-3 #401 CCAGATAAGG TGGCTGTGAA GCCGAATCAA AAATCAACTG TTGCAAAGCC FL HL 2 GA-7 #401 CCAGATAAGG TGGCTGTGAA GCCGAATCAA AAATCAACTG TTGCAAAGCC FL HL 2 GA-8 #401 CCAGATAAGG TGGCTGTGAA GCCGAATCAA AAATCAACTG TTGCAAAGCC FL HL 2 Pk-3 #401 CCAAATAAGG TTGCCGTGAA GCCGAAGCCA AAAGCATCTC CTGTAAAGCC FL HL 2 PA-4 #401 ACAAAAAAGG TGGCTGTGAA GCCAAAGCCA AAAGCATCTG CTGCAAATCA FL HL 2 PA-6 #401 CCAAATAAGT TGCATGTGAA GCCGAAGCCA AAAGCATCTG CTACAAATCC FL HL 2 PA-7 #401 CCAAAGAAGG TGGCTGTGAA GCCGAAGCCA AAATCATATA CTGCAAAACC FL HL 2 PA-9 #401 CCAAATAAGG TGGTTGTGAA GCCGAAGCCA AAAGCATCTG CTGCAAAACC FL HL 2 PA-11 #401 TCAAATAAGG TGTCTGTGAA GCCGAAGCCA AAAGCATCTG CTGCAAAACC FL HL 2 GA-2 #401 CCAAATAAGT TGGCCGTGAA GCCGAAGCCA AAAGCATCTG CTGCAAAGCC

#401 CCARATAAGG TGGCTGTGAA GCCGAAKCCA AAATCAWCTG YTGCAAAGCC ** **** * * *** ** ** ** **

FL HL 2 GA-9 #451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GATCGCAGTG AAGTCGAAAC FL HL 2 GA-4 #451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GATTGCAGTG AAGTCGATAC FL HL 2 GA-5 #451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GATCGCAGTG AAGTCGAAAC FL HL 2 GA-6 #451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GATTGCAGTG AAGTCGATAC FL HL 2 GA-3 #451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GATTGCAGTG AAGTCGAAAC FL HL 2 GA-7 #451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GATTGCAGTG AAGTCGAAAC FL HL 2 GA-8 #451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GATTGCAGTG AAGTCGAAAC FL HL 2 PA-3 #451 TAAATCCAAG CCAGCTGTTG TGAACCCAAA GACAGCAGCG AAGTCAAAAT FL HL 2 PA-4 #451 TAAATCCAAA TCTGCTGCTG CAAAGACAAA GACTGCAGTG AAGTCGGAAT FL HL 2 PA-6 #451 TAAATCCAAG TCTGCTGCTG TGATGCCAAA GACCGCAGCA AAGTCGAAAT FL HL 2 PA-7 #451 TAAAGCCAAG TCTACTGCTG CGAAGCCAGA GACAGCAGCA AAATTGAAAT FL HL 2 PA-9 #451 TAAATTCGAG TCTGCTGCTC CGAATCCCAA GACAGCAGCG AAGTCAAAAT FL HL 2 PA-11 #451 TAAATCCAAG TCTGCTGCTC CGAAGCCAAA GACCGCAGCG AAGTCGAAAT FL HL 2 GA-2 #451 TAAATCCAAG TCTGCTGCTG CGAAGCCAAA GACCGCAGCG AAGTCAAAAT

#451 TAAATCCAAG TCTGCTGCTG TGAAGCCAAA GAYTGCAGTG AAGTCGAAAY ** *** ** * * ** *** ** ** ** * **** * 90

FL HL 2 GA-9 #501 CTGTTGCACC AATGTCTAAA ACATCCGGTG GACTGGCAAA GGTAAAAAAG FL HL 2 GA-4 #501 CTGTTGCACC TATGTCTAAA ACATCCGGTG GACTGGCAAA GGTAAAAAAG FL HL 2 GA-5 #501 CTGTTGCACC TATGTCTAAA ACATCCGGTG GACTGGCAAA GGTAACAAAG FL HL 2 GA-6 #501 CTGTTGCACC TATGTCTAAA ACATCCGGTG GACTGGCAAA GGTAAAAAAG FL HL 2 GA-3 #501 CTGTTGCACC TATGTCTAAA ACATCCGGTG GACTGGCAAA GGTAAAAAAG FL HL 2 GA-7 #501 CTGTTGCACC TATGTCTAAA ACATCCGGTG GACTGGCAAA GGTAAAAAAG FL HL 2 GA-8 #501 CTGTTGCACC TATGTCTAAA ACATCCGGTG GACTGGCAAA GGTAAAAAAG FL HL 2 PA-3 #501 ATATTGCACC TAAGTTTAAA GCTTATGGTG GACTGGAAAA GGCAGCAAAG FL HL 2 PA-4 #501 CTGTTGCACC TAAGTCTAAA GCTACTGGTG GACTGGCAAA GGCAGCAAAG FL HL 2 PA-6 #501 CCGTTGCACC TAACTCTAAA GCTTCTAATG GACTGGCAAA GGCAGCAAAG FL HL 2 PA-7 #501 CTGTTGCGCC TAAGCTTAAA ACTGCTGGTG GATCGGGGAA GGCAGCAAAG FL HL 2 PA-9 #501 CTGTTGCACC TAAATCTAAA GCTTCGGGTT GACTGGCAAA GACAGCAAAG FL HL 2 PA-11 #501 ATGTTGCACC TAAATCTAAA GCTTCTGGTT GACTGGCAAA GGCAGCAAAG FL HL 2 GA-2 #501 CTGTTGCACC TAAGTCTAAA GCTTCTGGTG GACTGACAAA GGCAGCAAAG ...... #501 CTGTTGCACC TAWGTCTAAA ACWTCCGGTG GACTGGCAAA GGYARCAAAG *** ** **** * ****** * ** **

FL HL 2 GA-9 #551 ACCC:CAGTC AATGTCACTC CTTCCACCAA GCTGAAGATG TCTGCTCCAG FL HL 2 GA-4 #551 ACCC:CAGTC AATGTCACTC CTTCCACCAA GCCGAAGATG GCTGCTCCAG FL HL 2 GA-5 #551 ACCT:CAGTC AATGTTACTC CTTCCACCAG GCCGAAGATG GCTGCTCCAG FL HL 2 GA-6 #551 ACCC:CAGTC AATGTCACTC CTTCCACCAA GCCGAAGATG GCTGCTCCAG FL HL 2 GA-3 #551 A:CCCCAGTC AGTGTCACTC CTTCCACCAA GCCGAAGATG GCTGCTCCAG FL HL 2 GA-7 #551 ACCCC:AGTC AATGTCACTC CTTCCACCAA GCCGAAGATG GCTGCTCCAG FL HL 2 GA-8 #551 GCCC:CAGTC AATGTCACTC CTTCCACCAA GCTGAAGATG GCTGCTCCAG FL HL 2 PA-3 #551 A:CCTTAGTC AATGTCACTC CTTCTGCCAA GCA FL HL 2 PA-4 #551 A: TCTCAGTC AATGTCACTC CTTCCGC FL HL 2 PA-6 #551 ACCCTCAGTC AATGTCACTC CATCCGCTAA GCT FL HL 2 PA-7 #551 A:CCTCAGCC AAAGCCACTC C: : :TGTCAA GCT FL HL 2 PA-9 #551 A:CCACAGTC AATGTCACTC CCACCGCCAA GTAGAAGAAG ACTGCTCTAG FL HL 2 PA-11 #551 A:CCACAGTC AATGTCACTC CTACCGCCAA GTAGAAGAAG GCTGCTCCAG FL HL 2 GA-2 #551 A:CCTCAATC AATGTCACTC CCTCCGCCAA GCT ...... #551 ACCCTCAGTC AATGTCACTC CTTCCRCCAA GCYGAAGATG GCTGCTCCAG ****** ** ******* * ***** **

FL HL 2 GA-9 #601 TTGCTGCCAA GAAGCCGAAG ATTGTGAATA AGTCCCCT FL HL 2 GA-4 #601 TTGCTGCCAA GAAGCCGAAG ATTGTGAATA AGTCCCCT FL HL 2 GA-5 #601 TTGCTGCAAA GAAGCTGAAG ATTGTGAATA AATCCCCT FL HL 2 GA-6 #601 TTGCTGCCAA GAAGCCGAAG ATTGTGAATA AGTCCCCT FL HL 2 GA-3 #601 TTGCGGCCGA GAAGCCGAAG ATTGTGAATA AGTCCCCT FL HL 2 GA-7 #601 TTGCTGCCAA GAAGCCGAAG ATTGTGAATA AGTCCCCT FL HL 2 GA-8 #601 TTGCTGCCAA GAAGCCGAAG ATTGTGAATA AGTCCCCT FL HL 2 PA-9 #601 TTACTGCCAA AAAGCTGAAG ATTGCGAATG AGGCCCCT FL HL 2 PA-11 #601 TTGCTGCCAA AAAGCAGAAG ATTGTGAATG AGGACCCA ...... #601 TTGCTGCCAA GAAGCCGAAG ATTGTGAATA AGTCCCCT

Fig 24- Multiple alignment of new histone-like gene family. Group 1, group 2 and group 3 clones of new histone-like protein family from Fritillaria liliacea. *- Nucleotide difference in the alignment, :-. Gap in he sequence 91

Phylogenetic Analysis of new histone-like gene family

Phylogenetic analysis of a new histone-like gene family was performed using maximum parsimony, which chooses the tree that requires fewest evolutionary changes.

Fig-25 is an unrooted phylogram ofthe new histone-like gene family. There are two main groups present, group 2 genes are separated from group-1 and group-3 genes with

100% bootstrap support. In the group 2 cluster, FL HL 2 GA-6 and FL HL GA-4 are nearly identical and could represent identical clones. Sequence variation found between these two clones, might represent a peR error. Also, each member ofthis group has few apomorphic characters as can be seen by the short branch lengths among them. Group 1 and group 3 genes have a 73 bp insertion in the intron and form a distinct group separate from group 2 genes that is supported by a 100% bootstrap value. Group 1 and group 3 pseudogenes do not form a distinct groupswith any bootstrap value. 92

R.H..2G\6 R.H..2G\4 90 R.H..2G\3 R.H..2G\7 R.H..2G\ R.H..2G\5

R.H..2G\9

R.H..2PA 11 100

R.H..2PA9 R. H..2 PA 7 ---_v R.H..2PA4

R.H..2PA6 R.H..2G\2

-- 5changes

Fig. 25. Phylogenetic tree of new histone-like protein gene family from Fr;tillar;a Iiliacea. Phylogenetic tree was constructed using maximum parsimony. Numbers on each branch indicate the percent ofbootstrap replicates supporting that node. 93

Discussion

Histone-like Gene Family in Fritillaria liIiacea

In Fritillaria liliacea the histone-like gene family consists oftwo functional genomic sequences and 12 processed pseudogenes, which can be classified into 3 groups. The genomic clones contain two exons and one intron. The presence ofan intervening intron in the histone-like protein ofFritillaria liliacea and the presence ofpoly A tail in the

Fritillaria agrestis eDNA, suggests that the histone-like protein might be a replacement variant histone. According to Tanaka et al. (1999), the histone variant from Lilium logiflorum is a nucleolar protein and might be involved in ribosomal DNA organization.

Based on sequence similarity, the histone-like protein from Fritillaria liliacea might also be a nucleolar replacement histone variant. In most ofthe eukaryotes, two classes of histone genes are found, the replication-dependant histone genes and rep1ication­ independent or replacement variant histone genes (Osley, 1991). The expression of replication-dependant histones is correlated with the S phase ofthe cell cycle and with

DNA replication. These genes are devoid ofintrons; their mRNAs are not po1yade1ny1ated and have a stem-loop structure the end ofa short 3' untrans1ated region

(Mancini, 2001). In contrast to replication-dependant histones, replacement variant histones are expressed constitutively throughout the cell cycle and these genes contain introns, produce po1yade1ny1ated mRNAs with long 3' untrans1ated regions and do not have a 3' stem-loop structure (Wells, 1985). 94

Two functional genomic sequences from the histone-like gene family ofFritillaria liliacea could represent two different genes or could be allelic variants. Also, variants within each genomic and pseudogene group could represent different genes, be allelic variants or result from PCR errors.

PCR error rate or PCR fidelity depends in part on the DNA polymerase used in the amplification reaction (Cline, 1996). The enzyme used for PCR amplification was Taq

DNA polymerase. Since this enzyme lacks 3'-5' exonuclease/proofreading activity, the bases misincorporated during PCR are not corrected. The in-vitro error rate ofTaq DNA

5 polymerase varies from ~ 2 x 10 -5 to < 1 x 10- (Hansen, 2001), while the error rate of proofreading enzyme like Pfu is 2.0 x 10 -6 to 6.5 x 10 -7 (Andre et aI., 1997). PCR

fidelity can also be affected by other factors such as Mg+2 concentration, dNTP

concentration, annealing temperature and pH. In a study on PCR error rates no PCR

errors were observed in 10,000 bp under the conditions used in this study (Baysdorfer,

pers comm.).

In this work I have set the cut-offto 3 errors/lOOO bases, that is, clones having more

than 3 substitutions from the consensus sequence are classified as distinct genes rather

than the same gene with the difference due to PCR error. Using this criteria there are 12

pseudogenes in this gene family. The high percentage ofprocessed pseudogenes in this

gene family could be the result ofan active reverse transcriptase in Fritillaria (Rao, pers.

comm.). Since the histone-like protein may be replacement variant, it is constitutive and

expressed at low but constant level throughout the cell cycle (Alvelo-Ceron, 2000).

Availability ofhistone like protein mRNA in meiotic tissue, where reverse transcriptase 95

is active (Kidwell & Lisch, 2001), can explain the high percentage ofprocessed pseudogenes in this gene family.

In a protein database search at NCBI, the histone-like protein from Fritillaria liliacea showed a high similarity to Fritillaria agrestis and Lilium longiflorum histone-like protein (Fig.6). The search also showed some similarity to the ribosomal-sedimenting protein from Pisum sativum and to histone HI WHIRl from Triticum aestivum. During this search, a homologue ofthe histone-like protein from Arabidopsis (gb accession #

AF360211.1) was found. Although this putative HI histone variant showed only 55 % amino acid similarity (data not shown) and 60 % nucleotide similariry to Fritillaria agrestis and Fritillaria liliacea, it has the same intron exon position and the start and stop codon structure (Fig. 26). Since the Arabidopsis genome is fully sequenced and contains no other homologues, it can be assumed that the Arabidopsis genome contains only one copy ofthe histone-like protein gene.

Arabidopsis genomic sequence x Fritillaria agrestis cDNA sequence

Arabidopsis 1 ctcctcatcacaaaattctccgacgcattacattttcttccgatcaatac 50 III 111I11 IIII II II II I II I F agrestis 1 .. GCTCCTCACAACCGCAACAGTCTCTTTCCTTCTT ....TGTTCTCTGT 44

Arabidopsis 51 agagagatcagtttctgagagagaagaagatgtctatagaggaagaaaac 100 I III III III 1I111 II II II I F agrestis 45 TCCCTCTTTTATTTTTGATTCCCCTGAA.ATGTCGGCAGCCGTTGCAATC 93 --r ~ Start Arabidopsis 101 gttccaacgactgttgactcaggagctgccgatacaacggtgaaatctcc 150 Codon IIII III II III I II F agrestis 94 GAGACTCCCGCCTTTGCTCCGGTCCCTG TTGCC 126

Arabidopsis 151 ggagaagaaaccggcggcgaaaggtggtaaatctaagaagacgacgacgg 200 1111 I 1111I1 11I111 II II I 1111 IIII F agrestis 127 AGAGATG.AACCGGTGGCGAAGCCGGGCAAGGTGACGAAGGCCAAGGCCC 175 96

Arabidopsis 201 ctaaagcaacgaagaagcctgtgaaagctgctgctccaacgaagaagaaa 250 1111 II 11I1 II I 1I111111 F agrestis 176 CTAAGGAGAAGAAG GCCTCCGTCGCGAAGAAG 207

Arabidopsis 251 acaacttcctctcaccctacctatgaagaggtcaatattcgatctaaact 300 II I II 111111111 I F agrestis 208 CCTGCTCTCCATCCTACCTATCTCGAG 228

Intron Splice sites

Arabidopsis 351 tttgaattcgatgcagatgattaaagatgcgattgtaacgttgaaggaga 400 11111 I II 11111 I II 11111111 F agrestis 229 ATGATCAGTGAAGCGATCGCTTCGCTGAAGGAGC 268

Arabidopsis 401 gaactggatctagtcaatacgcgattcagaaattcatagaggagaaacat 450 I II111111 II II 11111 III III II I II II II II F agrestis 269 GGACTGGATCGAGCCAGTACGCTATTGCGAAGTTTGTTGAAGACAAGCAC 318

Arabidopsis 451 aaatc ...actgcctcctacttttaggaagcttttgcttgtgaatctcaa 497 II II II II 1 I II I 1111111 I 11111 III F agrestis 319 AAGTCTCATCTCCCGGCGAACTTCAAGAAGCTTCTCCTTGTCCAGTTGCA 368

Arabidopsis 498 gagacttgttgcttctgagaaattggttaaagtcaaagcttcttttaaga 547 II III 1111 III III I II II II III I 1111 F agrestis 369 GAAACTCACTGCTGCTGGCAAACTCACGAAGGTGAAGAATTCCTACAAGA 418

Arabidopsis 548 ttccttctgctagatccgcagcaacacctaaaccggctgctccggttaag 597 I II II I III I II 11111 III F agrestis 419 T CTCTGCCAAACCAACCCCTGCTGC GAAG 447

Arabidopsis 598 aagaaggcaactgtagtagctaaacctaagggtaaggttgctgctgctgt 647 II I III II III III 1111I11 II F agrestis 448 CCTAAATCCGCTGCTGT GAAGCCAAAGTCTGCTGCTACTAA 488

Arabidopsis 648 tgctcctgctaaagctaaagcggcggctaaaggaactaagaagcctgcgg 697 I II II II I 1111 I II 1111I1 I F agrestis 489 ACTCAAGTCCGCTGCCAAGAAGGTGAAGAAAGCAGCTGTGAAGCCAAAGC 538

Arabidopsis 698 ctaaagttgttgc... taaggctaaggttactgc ..taaacct.aaggct 741 II111 II III III I II I 111I I III I II I F agrestis 539 CTAAATCTGCTGCCGTGAAGCCAAAAGCCCCTGCCGTGAACATGAAATCC 588

Arabidopsis 742 aaggttactgctgctaaacctaagtctaagtctgttgctgctgtttccaa 791 III I I111 II II II I 1 II I II F agrestis 589 AAGCCTGCTGCCCTGAAGCCAAA TACAGTGACAAA 623

Arabidopsis 792 gactaaagctgttgctgctaagcctaaggctaaggagagaccagctaaag 841 I II 1I11 III III III II II 11111 II I F agrestis 624 ATCAAAGACTGTAGCTCTGAAGGGGAAGACTGCTGGCCGTCCAGCAAAGG 673

Arabidopsis 842 cttctaggacttcgactagaacatctccagggaaaaaagttgctgctcct 891 III III II III 1I11 111111 III 11I11111 F agrestis 674 CGGCAAAGACATCCGTCAAAGCTGCTCC.GGGAAAGAAG ..GCTGCTCC. 719

Arabidopsis 892 gctaagaaagtggctgtgactaagaaggctccggctaagagtgtgaaggt 941 1111111 II 111111111 1111 II 111111 F agrestis 720 AGTGGCTCTG AAGAAGGCTAAGGCTGGGA AGAAGGT 755

Arabidopsis 942 gaagtctccggcgaagagagcttcgac~gaaggctaagaagtgaagaa991 I III I 1111 III II II II I II I F agrestis 756 AACAACTC ... CCAAGAAGGCTAAGAAATAGATGGGATGGGTTTGGATTG 802 Stop ~ Codon Arabidopsis 992 gattggtttaggataggttttggggggagattgaatacatggtggtggtt 1041 II IIIII II III III II I II I F agrestis 803 GAGGGATGCATGCTGTAAATTTGATGAACTATGA .... GTGCTTATGTTA 848 97

Arabidopsis 1042 agcttctatagggtagtcttgtataattgaatcatccttgaaggagcttg 1091 II IIII I II II II I III I II II F agrestis 849 AGGTTCTTGTGTCTACTGTGGTTTTGTTG TGAAATGGAACAG 890

Arabidopsis 1092 ctttccaaagttttttacttgtttctttggtttcttcttgaaac 1135 II I III III II 1III II III F agrestis 891 AACTCGTCATTTTCTTAATGGCGAATTTGATATGCCGAAAAAAAAAAAAA 940

Fig. 26. Intron exon structure of histone-like protein cDNA sequence of Fritillaria agrestis and Arabidopsis putative histone gene sequence. Sequence alignment was obtained using GAP at SeqWeb GCG sequence Analysis software. GAP program uses the Needleman and Wunsch algorithm to find the alignment of two complete sequences that maximizes the number ofmatches and minimizes the number of gaps.

The results ofa Fluorescent In-Situ Hybridization (FISH) analysis (Hanley, pers. comm.) ofFritillaria agrestis using a histone-like protein gene specific probe support the hypothesis that there are 1-2 copies offunctional histone-like genes and approximately 12 pseudogenes in Fritillaria. In this study, using a histone-like protein specific genomic

probe (includes intron) under high stringency, two distinct spots are visible in the diploid

cell preparation, while under low stringency additional spots are observed.

In contrast to the histone like gene family from Fritillaria liliacea, the ribulose-I, 5-

biphosphate carboxylase (rbcS) gene family in Fritillaria agrestis has undergone

considerable expansion (Baysdorfer, pers. comm.). In other plants there are 6-12 family

members while the rbcS gene family from Fritillaria agrestis has considerably more

functional genes. Also, this family has a number ofconventional pseudogenes, but no

processed pseudogenes. These results suggest that segmental duplication might be

responsible for the expansion ofthis gene family in Fritillaria. The lack ofprocessed 98

pseudogenes could be the result ofleafspecific expression ofrbcS and its lack of expression in meiotic cells.

New Histone-like Gene Family from Fritillaria liliacea.

The new histone-like genes are also part ofa multigene family, with two functional gene groups and four pseudogenes identified. All pseudogenes from this family are classical pseudogenes. Since all members ofthis gene family have not been amplified, the exact number and types cannot be predicted. The presence ofan intron, and a histone linker domain suggest that this protein might also be a constitutive HI histone variant.

Characterization ofthis new gene family is the subj ect offuture work. 99

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Appendix

1. Raw Sequence Data

Clone FL HL 1GA-l

LOCUS AF394112 827 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GA-1. ACCESSION AF394112 SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State university, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA COMMENT Bankit Comment: Fritillaria liliacea is a member of the Liliaceae family, and is a close relative of Fritillaria agrestis, which is in the database. FEATURES Location/Qualifiers source 1. .827 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGA-1" /note="closely related to Fritillaria agrestis" mRNA join«1. .135,321. .>827) /product="histone-like protein" CDS join(<1 .. 135,321.. >827) /codon_start=l /product="histone-like protein" /translation="PAFAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYL EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVK NSYKISAKPTAAVKPRSAAVKPKSAVAKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVK PKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKAK" BASE COUNT 226 a 208 c 194 9 199 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg tggcgaagcc ggccaaggtg 61 acgaaggcca aggcccctaa ggagaagaag gcctccattg cgaagaagcc tgctctccat 121 cctacctatc ttgaggtctg atccagccac tatttcctct agatttgtta atttatcgaa 181 tttgtgcagt ccaaatttgt gtacttccac cagatctgtt aatttattga atttatgcag 241 tccaattttg tgtacttcct ctagatttgt taatttatga aattaatgta gtctaatttg 301 gtctactttc taaatctcag atgatcagtg aagcgattgc ttcgctgaag gagcggactg 3.61 gatcgagcca gtacgctatt gcaaagtttg ttgaagacaa gcacaagtct catctcccgg 421 cgaacttcaa gaagcttctc cttgtccagt tgcggaaact cactgctgct ggcaaactca 481 cgaaggtgaa gaactcctac aagatctctg ccaaaccaac cgctgctgtg aagcctagat 541 ccgctgctgt gaagccaaag tctgctgttg ctaagctcaa gtccgctgcc aagaaggtga 601 agaaagcagc tgtgaagcca aagcctaaat ctgctgccgt gaagccaaaa gcccctgccg 661 tgaaaccgaa atccaagcct gctgccctga agccaaatac agtgacaaaa tcaaagactg 721 tagctctgaa gggaaagact gctggccgtc cagcaaaggc ggcaaagaca tccgtcaaag 781 ctgctccggg aaagaaggct gctccagtgg ctctgaagaa ggctaag 113

Clone FL HL 1GA-2

LOCUS AF394113 827 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GA-2. ACCESSION AF394113 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families from Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .827 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGA-2" /note="closely related to Fritillaria agrestis" mRNA join«1. .135,321. . >827) /product="histone-like protein" CDS join (<1 .. 135,321. . >827) /codon_start=l /product="histone-like protein" /translation="PAFAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYL EMISGAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVK TSYKISAKPTAAVKPRSAAVKPKSAVAKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVK PKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKAK" BASE COUNT 224 a 209 c 195 9 199 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg tggcgaagcc ggccaaggtg 61 acgaaggcca aggcccctaa ggagaagaag gcctccattg cgaagaagcc tgctctccat 121 cctacctatc ttgaggtctg atccagccac tatttcctct agatttgtta atttatcgaa 181 tttgtgcagt ccaaatttgt gtacttccac cagatctgtt aatttattga atttatgcag 241 tccaattttg tgtacttcct ctagatttgt taatttatga aattaatgta gtctaatttg 301 gtctactttc taaatctcag atgatcagtg gagcgattgc ttcgctgaag gagcggactg 361 gatcgagcca gtacgctatt gcaaagtttg ttgaagacaa gcacaagtct catctcccgg 421 cgaacttcaa gaagcttctc cttgtccagt tgcggaaact cactgctgct ggcaaactca 481 cgaaggtgaa gacctcctac aagatctctg ccaaaccaac cgctgctgtg aagcctagat 541 ccgctgctgt gaagccaaag tctgctgttg ctaagctcaa gtccgctgcc aagaaggtga 601 agaaagcagc tgtgaagcca aagcctaaat ctgctgccgt gaagccaaaa gcccctgccg 661 tgaaaccgaa atccaagcct gctgccctga agccaaatac agtgacaaaa tcaaagactg 721 tagctctgaa gggaaagact gctggccgtc cagcaaaggc ggcaaagaca tccgtcaaag 781 ctgctccggg aaagaaggct gctccagtgg ctctgaagaa ggctaag 114

Clone FL HL 1GA-3

LOCUS AF394114 827 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GA-3. ACCESSION AF394114 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd., Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .827 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGA-3" /note="closely related to Fritillaria agrestis" mRNA join(<1 .. 135,321.. >827) /product="histone-like protein" CDS join«1. .135,321. .>827) /codon_start=l /product="histone-like protein" /translation="PAFAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYL EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVK NSYKISAKPTAAVKPRSAAVKPKSAVAKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVK PKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKAK" BASE COUNT 227 a 208 c 193 9 199 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg tggcgaagcc ggccaaggtg 61 acgaaggcca aggcccctaa ggagaagaag gcctccattg cgaagaagcc tgctctccat 121 cctacctatc ttgaggtctg atccagccac tatttcctct agatttgtta atttatcgaa 181 tttgtgcagt ccaaatttgt gtacttccac cagatctgtt aatttattga atttatgcag 241 tccaattttg tgtacttcct ctagatttgt taatttatga aattaatgta gtctaatttg 301 gtctactttc taaatctcag atgatcagtg aagcgattgc ttcgctgaag gagcggactg 361 gatcgagcca gtacgctatt gcaaagtttg ttgaagacaa gcacaagtct catctcccgg 421 cgaacttcaa gaagcttctc cttgtccagt tgcggaaact cactgctgct ggcaaactca 481 cgaaggtgaa gaactcctac aagatctctg ccaaaccaac cgctgctgtg aagcctagat 541 ccgctgctgt gaagccaaag tctgctgttg ctaagctcaa gtccgctgcc aagaaggtga 601 agaaagcagc tgtgaagcca aagcctaaat ctgctgccgt gaagccaaaa gcccctgccg 661 tgaaaccgaa atccaagcct gctgccctga agccaaatac agtgacaaaa tcaaagactg 721 tagctctgaa gggaaagact gctggccgtc cagcaaaggc ggcaaagaca tccgtcaaag 781 ctgctccggg aaagaaggct gctccagtgg ctctaaagaa ggctaag 115

Clone FL HL 1GA-4

LOCUS AF394115 827 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GA-4. ACCESSION AF394115 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Frit illaria. REFERENCE 1 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 827) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd., Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .827 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGA-4" /note="closely related to Fritillaria agrestis" mRNA join(<1 .. 135,321. .>827) /product="histone-like protein" CDS join «1. .135,321. . >827) /codon_start=l /product="histone-like protein" /translation="PAFAPVPVARDEPVAKPAKVTKAKAPKEKKASIAKKPALHPTYL EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVK NSYKISAKPTAAVKPRSAAVKPKSAVAKLKSAVKKVKKAAVKPKPKSAAVKPKAPAVK PKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKAK" BASE COUNT 226 a 207 c 194 9 200 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg tggcgaagcc ggccaaggtg 61 acgaaggcca aggcccctaa ggagaagaag gcctccattg cgaagaagcc tgctctccat 121 cctacctatc ttgaggtctg atccagccac tatttcctct agatttgtta atttatcgaa 181 tttgtgcagt ccaaatttgt gtacttccac cagatctgtt aatttattga atttatgcag 241 tccaattttg tgtacttcct ctagatttgt taatttatga aattaatgta gtctaatttg 301 gtctactttc taaatctcag atgatcagtg aagcgattgc ttcgctgaag gagcggactg 361 gatcgagcca gtacgctatt gcaaagtttg ttgaagacaa gcacaagtct catctcccgg 421 cgaacttcaa gaagcttctc cttgtccagt tgcggaaact cactgctgct ggcaaactca 481 cgaaggtgaa gaactcctac aagatctctg ccaaaccaac cgctgctgtg aagcctagat 541 ccgctgctgt gaagccaaag tctgctgttg ctaagctcaa gtccgctgtc aagaaggtga 601 agaaagcagc tgtgaagcca aagcctaaat ctgctgccgt gaagccaaaa gcccctgccg 661 tgaaaccgaa atccaagcct gctgccctga agccaaatac agtgacaaaa tcaaagactg 721 tagctctgaa gggaaagact gctggccgtc cagcaaaggc ggcaaagaca tccgtcaaag 781 ctgctccggg aaagaaggct gctccagtgg ctctgaagaa ggctaag 116

Clone FL HL 1GA-5

LOCUS AF394116 659 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GA-5. ACCESSION AF394116 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .659 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGA-5" /note="closely related to Fritillaria agrestis" mRNA join(<1 .. 4,190 .. >659) /product="histone-like protein" CDS join(<1 .. 4,190 .. >659) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTAAVKPRSAAVKPKSAVAKLKSAAKKVKKAAVKPK PKSAAVKPKAPAVKPKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPG" BASE COUNT 185 a 158 c 146 9 170 t ORIGIN 1 tgaggtctga tccagccact atttcctcta gatttgttaa tttatcgaat ttgtgcagtc 61 caaatttgtg tacttccacc agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgattgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaaactc actgctgctg gcaaactcac gaaggtgaag 361 aactcctaca agatctctgc caaaccaacc gctgctgtga agcctagatc cgctgctgtg 421 aagccaaagt ctgctgttgc taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aagccaaaag cccctgccgt gaaaccgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtgacaaaat caaagactgt agctctgaag 601 ggaaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggg 117

Clone FL HL 1GB-l

LOCUS AF394117 818 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-1. ACCESSION AF394117 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 818) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 818) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .818 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-1" /note="closely related to Fritillaria agrestis" mRNA join (d .. 126,312 .. >818) /product="histone-like protein" CDS join(d .. 126,312 .. >818) /codon_start=l /product="histone-like protein" /translation="PAFAPVPVARDEPAAKPAKAKAPKEKKASVAKKPALHPTYLEMI SEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSY KISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVNMKS KPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKAK" BASE COUNT 222 a 207 c 191 9 198 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg cggcgaagcc ggccaaggcc 61 aaggccccta aggagaagaa ggcctccgtt gcgaagaagc ctgctctcca tcctacctat 121 ctcgaggtct gatccagcca ctatttcctc tagatttgtt aatttattga atttgtgcag 181 tccaaatttg tgtacttcct ctagatctgt taatttattg aatttatgca gtccaatttt 241 gtgtacttcc tctagatttg ttaatttatg aaattaatgt agtctaattt ggtctacttt 301 ctaaatctca gatgatcagt gaagcgatcg cttcgctgaa ggagcggact ggatcgagcc 361 agtacgctat tgcaaagttt gttgaagaca agcacaagtc tcatctcccg gcgaacttca 421 agaagcttct ccttgtccag ttgcggaagc tcactgctgc tggcaagctc acaaaggtga 481 agaattccta caagatctct gccaaaccga cccctgctgc gaagcctaaa tcagctgctg 541 tgaagccaaa gtctactgct agtaagctca agtccgctgc caagaaggtg aagaaagcag 601 ctgtgaagcc aaagcctaaa tctgctgccg tgaagccaaa agcccctgcc gtgaacatga 661 aatccaagcc tgctgccctg aagccaaata cagtgacaaa atcaaagact gtagctctga 721 aggggaagac tgctggccgt ccagcaaagg cggcaaagac atccgtcaaa gctgctccgg 781 gaaagaaggc tgctccagtg gctctgaaga aggctaag 118

Clone FL HL 1GB-2

LOCUS AF394118 659 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-2. ACCESSION AF394118 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .659 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-2" /note="closely related to Fritillaria agrestis" mRNA join (<1 .. 4,190 .. >659) /product="histone-like protein" CDS join(<1 .. 4, 190 .. >659) /codon_start=2 /product="histone-like protein" /translation="EMISEAIAPLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPK PKSAAVKPKAPAVNMKSKPAALKPNTVAKSKTVALKGKTAGRPAKAAKTSVKAAPG" BASE COUNT 184 a 158 c 147 9 170 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttattgaat ttgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct ccgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaagctc actgctgctg gcaagctcac aaaggtgaag 361 aattcctaca agatctctgc caaaccgacc cctgctgcga agcctaaatc agctgctgtg 421 aagccaaagt ctactgctag taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aagccaaaag cccctgccgt gaacatgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtggcaaaat caaagactgt agctctgaag 601 gggaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggg 119

Clone FL HL 1GB-3

LOCUS AF394119 659 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-3. ACCESSION AF394119 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridip1antae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Bilogical Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .659 /organism="Friti1Iaria 1iliacea" /db_xref="taxon:167482" /clone="lGB-3" /note="closely related to Fritillaria agrestis" mRNA join«l .. 4,190 .. >659) /product="histone-like protein" CDS join (<1 .. 4,190 .. >659) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPK PKSAAVKPKAPAVNMKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPG" BASE COUNT 185 a 157 c 146 9 171 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttattgaat ttgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaagctc actgctgctg gcaagctcac aaaggtgaag 361 aattcctaca agatctctgc caaaccgacc cctgctgcga agcctaaatc agctgctgtg 421 aagccaaagt ctactgctag taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aagccaaaag cccctgccgt gaacatgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtgacaaaat caaagactgt agctctgaag 601 gggaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggg 120

Clone FL HL 1GB-4

LOCUS AF394120 781 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-4. ACCESSION AF394120 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 781) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 781) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .781 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-4" /note="closely related to Fritillaria agrestis" mRNA join(<1 .. 126,312 .. >781) /product="histone-like protein" CDS join(<1 .. 126,312 .. >781) /codon_start=l /product="histone-like protein" !translation="PAFAPVPVARDEPAAKPAKAKAPKEKKASVAKKPALHPTYLEMI SEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSY KISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVNMKS KPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPG" BASE COUNT 210 a 200 c 179 9 192 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg cggcgaagcc ggccaaggcc 61 aaggccccta aggagaagaa ggcctccgtt gcgaagaagc ctgctctcca tcctacctat 121 ctcgaggtct gatccagcca ctatttcctc tagatttgtt aatttattga atttgtgcag 181 tccaaatttg tgtacttcct ctagatctgt taatttattg aatttatgca gtccaatttt 241 gtgtacttcc tctagatttg ttaatttatg aaattaatgt agtctaattt ggtctacttt 301 ctaaatctca gatgatcagt gaagcgatcg cttcgctgaa ggagcggact ggatcgagcc 361 agtacgctat tgcaaagttt gttgaagaca agcacaagtc tcatctcccg gcgaacttca 421 agaagcttct ccttgtccag ttgcggaagc tcactgctgc tggcaagctc acaaaggtga 481 agaattccta caagatctct gccaaaccga cccctgctgc gaagcctaaa tcagctgctg 541 tgaagccaaa gtctactgct agtaagctca agtccgctgc caagaaggtg aagaaagcag 601 ctgtgaagcc aaagcctaaa tctgctgccg tgaagccaaa agcccctgcc gtgaacatga 661 aatccaagcc tgctgccctg aagccaaata cagtgacaaa atcaaagact gtagctctga 721 aggggaagac tgctggccgt ccagcaaagg cggcaaagac atccgtcaaa gctgctccgg 781 9 121

Clone FL HL 1GB-5

LOCUS AF394121 696 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-5. ACCESSION AF394121 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Bilogical Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .696 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-5" /note="closely related to Fritillaria agrestis" mRNA join(<1 .. 4, 190 .. >696) /product="histone-like protein" CDS join(<1 .. 4,190 .. >696) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPK PKSAAVKPKAPAVNMKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKK AAPVALKKAK" BASE COUNT 197 a 164 c 158 9 177 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttattgaat ttgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaagctc actgctgctg gcaagctcac aaaggtgaag 361 aattcctaca agatctctgc caaaccgacc cctgctgcga agcctaaatc agctgctgtg 421 aagccaaagt ctactgctag taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aagccaaaag cccctgccgt gaacatgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtgacaaaat caaagactgt agctctgaag 601 gggaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggga 661 aagaaggctg ctccagtggc tctgaagaag gctaag 122

Clone FL HL 1GB-6

LOCUS AF394122 818 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-6. ACCESSION AF394122 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 818) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 818) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1 .. 818 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-6" /note="closely related to Fritillaria agrestis" mRNA join«l .. 126,312 .. >818) /product="histone-like protein" CDS join (<1 .. 126, 312 .. >818 ) /codon_start=l /product="histone-like protein" /translation="PAFAPVPVARDEPAAKPAKAKAPKEKKASVAKKPALHPTYLEMI SEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQLRKLTAAGKLTKVKNSY KISAKPTPAAKPKSAAVKPKSTXSKLKSAAKKVKKAAVKPKPKSAAVKPKAPAVNMKS KPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKKAAPVALKKAK" BASE COUNT 222 a 205 c 191 9 197 t 3 others ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg cggcgaagcc ggccaaggcc 61 aaggccccta aggagaagaa ggcctccgtt gcgaagaagc ctgctctcca tcctacctat 121 ctcgaggtct gatccagcca ctatttcctc tagatttgtt aatttattga atttgtgcag 181 tccaaatttg tgtacttcct ctagatctgt taatttactg aatttatgca gtccaatttt 241 gtgtacttcc tctagatttg ttaatttatg aaattaatgt agtctaattt ggtctacttt 301 ctaaatctca gatgatcagt gaagcgatcg cttcgctgaa ggagcggact ggatcgagcc 361 agtacgctat tgcaaagttt gttgaagaca agcacaagtc tcatctcccg gcgaacttca 421 agaagcttct ccttgtccag ttgcggaagc tcactgctgc tggcaagctc acaaaggtga 481 agaattcyta caagatmtct gccaaaccga cccctgctgc gaagcctaaa tcagctgctg 541 tgaagccaaa gtctactgyt agtaagctca agtccgctgc caagaaggtg aagaaagcag 601 ctgtgaagcc aaagcctaaa tctgctgccg tgaagccaaa agcccctgcc gtgaacatga 661 aatccaagcc tgctgccctg aagccaaata cagtgacaaa atcaaagact gtagctctga 721 aggggaagac tgctggccgt ccagcaaagg cggcaaagac atccgtcaaa gctgctccgg 781 gaaagaaggc tgctccagtg gctctgaaga aggctaag 123

Clone FL HL 1GB-7

LOCUS AF394123 659 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-7. ACCESSION AF394123 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL unpublished REFERENCE 2 (bases 1 to 659) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-200l) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1 . . 659 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="IGB-7" /note="closely related to Fritillaria agrestis" mRNA join(<1 .. 4,190 .. >659) /product="histone-like protein" CDS join(<1 .. 4,190 .. >659) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPK PKSAAVKPKAPAVNMKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPG" BASE COUNT 185 a 158 c 146 9 170 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttattgaat ttgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaagctc actgctgctg gcaagctcac aaaggtgaag 361 aattcctaca agatctctgc caaaccgacc cctgctgcga agcctaaatc agctgctgtg 421 aagccaaagt ctactgccag taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aagccaaaag cccctgccgt gaacatgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtgacaaaat caaagactgt agctctgaag 601 gggaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggg 124

Clone FL HL 1GB-8

LOCUS AF394124 696 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-8. ACCESSION AF394124 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .696 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-8" /note="closely related to Fritillaria agrestis" mRNA join (<1 .. 4,190 .. >696) /product="histone-like protein" CDS join (<1 .. 4,190 .. >696) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPK PKSAAVKPKAPAVNMKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKK AAPVALKKAK" BASE COUNT 197 a 165 c 158 9 176 t ORIGIN 1 cgaggtctga tccagccacc atttcctcta gatttgttaa tttattgaat ttgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaagctc actgctgctg gcaagctcac aaaggtgaag 361 aattcctaca agatctctgc caaaccgacc cctgctgcga agcctaaatc agctgctgtg 421 aagccaaagt ctactgctag taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aagccaaaag cccctgccgt gaacatgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtgacaaaat caaagactgt agctctgaag 601 gggaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggga 661 aagaaggctg ctccagtggc tctgaagaag gctaag 125

Clone FL HL 1GB-9

LOCUS AF394125 696 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-9. ACCESSION AF394125 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .696 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-9" /note="closely related to Fritillaria agrestis" exon <1 .. 4 CDS join(<1 .. 4,190 .. >696) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPK PKSAAVKLKAPAVNMKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKK VAPVALKKAK" mRNA join(<1 .. 4,190 .. >696) /product="histone-like protein" exon 190 .. >696 BASE COUNT 197 a 162 c 158 9 179 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttattgaat ttgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaagctc actgctgctg gcaagctcac aaaggtgaag 361 aattcctaca agatctctgc caaaccgacc cctgctgcga agcctaaatc agctgctgtg 421 aagccaaagt ctactgctag taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aagctaaaag cccctgccgt gaacatgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtgacaaaat caaagactgt agctctgaag 601 gggaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggga 661 aagaaggttg ctccagtggc tctgaagaag gctaag 126

Clone FL HL IGB-I0

LOCUS AF394126 696 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GB-10. ACCESSION AF394126 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 696) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1..696 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGB-10" /note="closely related to Fritillaria agrestis" exon <1 .. 4 CDS join(<1 .. 4,190 .. >696) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKKLLLVQ LRKLTAAGKLTKVKNSYKISAKPTPAAKPKSAAVKPKSTASKLKSAAKKVKKAAVKPK PKSAAVNPKAPAVNMKSKPAALKPNTVTKSKTVALKGKTAGRPAKAAKTSVKAAPGKK AAPVALKKAK" mRNA join «1. .4,190 .. >696) /product="histone-like protein" exon 190 .. >696 BASE COUNT 197 a 164 c 157 9 178 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttattgaat ttgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aagcttctcc ttgtccagtt gcggaagctc actgctgctg gcaagctcac aaaggtgaag 361 aattcctaca agatctctgc caaaccgacc cctgctgcga agcctaaatc agctgctgtg 421 aagccaaagt ctactgctag taagctcaag tccgctgcca agaaggtgaa gaaagcagct 481 gtgaagccaa agcctaaatc tgctgccgtg aatccaaaag cccctgccgt gaacatgaaa 541 tccaagcctg ctgccctgaa gccaaataca gtgacaaaat caaagactgt agctctgaag 601 gggaagactg ctggccgtcc agcaaaggcg gcaaagacat ccgtcaaagc tgctccggga 661 aagaaggctg ctccagtggc tctgaagaag gctaag 127

Clone FL HL IGC-l

LOCUS AF394127 705 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1GC-1. ACCESSION AF394127 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 705) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 705) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .705 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lGC-1" /note="closely related to Fritillaria agrestis" exon <1. .4 CDS join«1. .4,190 .. >705) /codon_start=2 /product="histone-like protein" /translation="EMISEAIASLKERTGSSQYAIAKFVEDKHKSHLPANFKRLLLVQ LRKLTAARKLTKVKNSYKIPAKPISGSMKTVISVKPKSAVVKPNKSTAVVPDKVAVKP NPKSTVAKPKSKSAAVKPKIAVKSKPVAPMSKTSGGLAKVTKTSVNVTPSTRPKMAAP VAAKKLKIVNKSP" mRNA join(<1 .. 4,190 .. >705) /product="histone-like protein" exon 190 .. >705 BASE COUNT 198 a 160 c 147 9 200 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttattgaat tcgtgcagtc 61 caaatttgtg tacttcctct agatctgtta atttattgaa tttatgcagt ccaattttgt 121 gtacttcctc tagatttgtt aatttatgaa attaatgtag tctaatttgg tctactttct 181 aaatctcaga tgatcagtga agcgatcgct tcgctgaagg agcggactgg atcgagccag 241 tacgctattg caaagtttgt tgaagacaag cacaagtctc atctcccggc gaacttcaag 301 aggcttctcc ttgtccagtt gcggaagctc actgctgctc gcaaactcac caaggtcaag 361 aactcctaca agatccctgc taagcccatt tctggtagta tgaaaacagt tatctctgtg 421 aagccaaagt ctgcagttgt gaaaccaaat aagtcaactg ctgtcgtgcc agataaggtg 481 gctgtgaagc cgaatccaaa atcaactgtt gcaaagccta aatccaagtc tgctgctgtg 541 aagccaaaga tcgcagtgaa gtcgaaacct gttgcaccta tgtctaaaac atccggtgga 601 ctggcaaagg taacaaagac ctcagtcaat gttactcctt ccaccaggcc gaagatggct 661 gctccagttg ctgcaaagaa gctgaagatt gtgaataaat cccct 128

Clone FL HL IPA-l

LOCUS AF394128 642 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PA-1. ACCESSION AF394128 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 642) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 642) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .642 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPA-1" /note="closely related to Fritillaria agrestis" BASE COUNT 180 a 179 c 167 9 116 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg tggcgaagcc gggcaaggtg 61 acgaaggcca aggcccctaa ggagaagaag gcctccgtcg cgaagaagcc tgctctccat 121 cctacctatc tcgagatgat cagtgaagcg atcgcttcgc tgaaggagcg gactggatcg 181 agccagtacg ctattgcgaa gtttgttgaa gacaagcaca agtctcatct cccggcgaac 241 ttcaagaagc ttctccttgt ccagttgcag aaactcactg ctgctggcaa actcacgaag 301 gtgaagaatt cctacaagat ctctgccaaa ccaacccctg ctgcgaagcc taaatccgct 361 gctgtgaagc caaagtctgc tgctactaaa ctcaagtccg ctgccaagaa ggtgaagaaa 421 gcagctgtga agccaaagcc taaatctgct gccgtgaagc caaaagcccc tgccgtgaac 481 atgaaatcca agcctgctgc cctgaagcca aatacagtga caaaatcaaa gactgtagct 541 ctgaagggga agactgctgg ccgtccagca aaggcggcaa agacatccgt caaagctgct 601 ccgggaaaga aggctgctcc agtggctctg aagaaggcta ag 129

Clone FL HL IPA-2

LOCUS AF394129 642 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PA-2. ACCESSION AF394129 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 642) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 642) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .642 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPA-2" /note="closely related to Fritillaria agrestis" BASE COUNT 181 a 180 c 166 9 115 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg tggcgaagcc gggcaaggtg 61 acgaaggcca aggcccctaa ggagaagaag gcctccgtcg cgaagaagcc tgctctccat 121 cctacctatc tcgagatgat cagtgaagcg atcgcttcgc tgaaggagcg gactggatcg 181 agccagtacg ctattgcgaa gtttgttgaa gacaagcaca agtctcatct cccggcgaac 241 ttcaagaagc ttctccttgt ccagttgcag aaactcactg ctgctggcaa actcacgaag 301 gtgaagaatt cctacaagat ctctgccaaa ccaacccctg ctgcgaagcc taaatccgct 361 gctgtgaagc caaagtctgc tgctactaaa ctcaagtccg ctgccaagaa ggtgaagaaa 421 gcagctgtga agccaaagcc taaatctgct gccgtgaagc caaaagcccc tgccgtgaaa 481 ccgaaatcca agcctgctgc cctgaagcca aatacagtga caaaatcaaa gactgtagct 541 ctgaagggaa agactgctgg ccgtccagca aaggcggcaa agacatccgt caaagctgct 601 ccgggaaaga aggctgctcc agtggctctg aagaaggcta ag 130

Clone FL HL IPA-3

LOCUS AF394130 642 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PA-3. ACCESSION AF394130 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 642) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 642) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .642 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPA-3" /note="closely related to Fritillaria agrestis" BASE COUNT 178 a 177 c 170 9 117 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccaga gatgaaccgg tggcgaagcc gggcaaggtg 61 acgaaggcca aggcccctaa ggagaagaag gcctccgtcg cgaagaagcc tgctctccat 121 cctacctatc tcgagatgat cagtgaagcg atcgcttcgc tgaaggagcg gactggatcg 181 agccagtacg ctattgcgaa gtttgttgaa gacaagcaca agtctcatct cccggcgaac 241 ttcaagaagc ttctccttgt ccagttgcag aaactcactg ctgctggcaa actcacgaag 301 gtgaagaatt cctacaagat ctctgccaaa ccaaccgctg ctgtgaagcc tagatccgct 361 gctgtgaagc caaagtctgc tgttgctaag ctcaagtccg ctgccaagaa ggtgaagaaa 421 gcagctgtga agccaaagcc taaatctgct gccgtgaagc caaaagcccc tgccgtgaaa 481 ccgaaatcca agcctgctgc cctgaagcca aatacagtga caaaatcaaa gactgtagct 541 ctgaagggaa agactgctgg ccgtccagca aaggcggcaa agacatccgt caaagctgct 601 ccgggaaaga aggctgctcc agtggctctg aagaaggcta ag 131

Clone FL HL IPA-4

LOCUS AF394131 510 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PA-4. ACCESSION AF394131 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 510) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 510) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State university, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .510 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPA-4" /note="closely related to Fritillaria agrestis" BASE COUNT 162 a 122 c 115 9 111 t ORIGIN 1 cgagatgatt agtgaagcga tcgctttgct gaaggagcag actggatcaa accagtacga 61 tattgtaaag tttgttgaaa acaagcataa gtcccatctc ccgacgaact tcaagaagct 121 tcctcttgtc cagttgtgga aactcactgt tgctggcaaa ctcaccaaga tcaagaattc 181 tacatgatct ctgccaaacc aacccctact gtgaagccca agtccgccgc tgtggagccg 241 aagtctgctg ctaccaagcc catgtctact gccaagaagg tgaagaaagc agctgtgaag 301 ccgaagtcta aatctgctgc cgtgaaacta aatgctccta ctgtgaagct gaaatccaag 361 actactgccc cgaagccaaa gacagtgata aaatcaaagg ttgtagctct aaagccaaag 421 actgctggcc gtccagcaaa gtcgatgaag acatatgtta aagctgcttt gggaaagaag 481 gtcactctag cggctctgaa gaaatataaa 132

Clone FL HL IPB-l

LOCUS AF394132 593 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PB-1. ACCESSION AF394132 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 593) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 593) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .593 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPB-1" /note="closely related to Fritillaria agrestis" BASE COUNT 163 a 160 c 154 9 116 t ORIGIN 1 cccgcctttg ctccggtccc tgtttgccgg agatgatcta gcggcaaagc cgaccaaggt 61 gacgaaggcc aaggtcccta aggagaagaa ggcctctatt gcgaagaagc ctgctctcca 121 tcctacctat ctcgagatga ttagtgaagc gatcgctttg ctgaaggagc agactggatc 181 gagccagtac gctattgcaa agtttgttga aacaagcata agtcccatct cccggcgaac 241 ttcaagaagc ttcccttgtc cagttgcgga aactcactgt tgctggcaaa ctcaccaagg 301 tcaagaattc tacgtgatct ctgccaaacc aacccctgct gtgaagccca agtccgccgc 361 tgtggagccg atgtctgctg ctaccaagcc caagtctgct gccaagaagg tgtagaaagt 421 agctgtgaag ccgaaatcca agcctgctgc cccgaagaca aagacagtga caaaatcaaa 481 ggcagtagct ctgaagacaa agaccgttgg ccgtccagca aaggcggcga agatatctgt 541 taaagctgct ccgagaaaga aggtcggctc cagtggccct gaaggaagct aag 133

Clone FL HL IPB-2

LOCUS AF394133 593 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PB-2. ACCESSION AF394133 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 593) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 593) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .593 /organism="Fritillaria liliacea" / db..xref= "taxon: 167482" /clone="lPB-2" /note="closely related to Fritillaria agrestis" BASE COUNT 164 a 162 c 153 9 114 t ORIGIN 1 cccgcctttg ctccggtccc tgttgccgga gatgatctag cggcaaagcc gaccaaggtg 61 acgaaggcca aggtccctaa ggagaagaag gcctctattg cgaagaagcc tgctctccat 121 cctacctatc tcgagatgat tagtgaagcg atcgctttgc tgaaggagca gactggatcg 181 agccagtacg ctattgcaaa gtttgttgaa aacaagcata agtcccatct cccggcgaac 241 ttcaagaagc ttccccttgt ccagttgcgg aaactcactg ttgctggcaa actcaccaag 301 gtcaagaatt ctacgtgatc tctgccaaac caacccctgc tgtgaagccc aagtccgccg 361 ctgtggagcc gatgtctgct gctaccaagc ccaagtctgc tgccaagaag gtgtagaaag 421 cagctgtgaa gccgaaatcc aagcctgctg ccccgaagac aaagacagtg acaaaatcaa 481 aggcagtagc tctgaagaca aagaccgttg gccgtccagc aaaggcggcg aagatatctg 541 ttaaagctgc tccgagaaag aaggtcgctc cagtggccct gaaggaagct aag 134

Clone FL HL clone IPB-3

LOCUS AF394134 626 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PB-3. ACCESSION AF394134 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 626) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 626) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .626 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPB-3" /note="closely related to Fritillaria agrestis" BASE COUNT 165 a 169 c 150 9 142 t ORIGIN 1 ttatttgttc tattttccct cttttacttt taatttcctt gaaatgtccg cagccgttgc 61 aattgagact cccgcctttg ctccggtccc tgttgccgga gatgatctag cggcaaagcc 121 gaccaaggtg acgaaggcca aggtccctaa ggagaagaag gcctctattg cgaagaagcc 181 tgctctccat cctacctatc tcgagatgat tagtgaagcg atcgctttgc tgaaggagca 241 gactggatcg agccagtacg ctattgcaaa gtttgttgaa aacaagcata agtcccatct 301 cccggcgaac ttcaagaagc ttccccttgt ccagttgcgg aaactcactg ttgctggcaa 361 actcaccaag gtcaagaatt ctacgtgatc tctgccaaac caacccctgc tgtgaagccc 421 aagtccgccg ctgtggagcc gatgtctgct gctaccaagc ccaagtctgc tgccaagaag 481 gtgtagaaag cagctgtgaa gccgaaatcc aagcctgctg ccccgaagac aaagacagtg 541 acaaaaccaa aggcagtagc tctgaagaca aagactgttg gccgtccagc aaaggcggcg 601 aagatatctg ttaaagctgc tccgag 135

Clone FL HL IPB-4

LOCUS AF394135 425 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PB-4. ACCESSION AF394135 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 425) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 425) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .425 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPB-4" /note="closely related to Fritillaria agrestis" BASE COUNT 122 a 110 c 107 9 86 t ORIGIN 1 cgagatgatt agtgaagtga tcgctttgct gaaggagtag actggatcga gccagtacgc 61 tattgcaaag tttgttgaaa acaagcataa gtcccatctc ccggcgaact tcaagaagtt 121 tccccttgtc cagttgcgga aactcactgt tgctggcaaa ctcaccaagg tcaagaattc 181 tacgtgatct ctgccaaacc aacccctgct gtgaagccca agtccgccgc tgtggagccg 241 atgtctgctg ctaccaagcc caagtctgct gccaagaagg tgtagaaagc agctgtgaag 301 ccgaaatcca agcctgctgc cccgaagaca aagacagtga caaaatcaaa ggcagtagct 361 ctgaagacaa agaccgttgg ccgtccagca aaggcggcga agatatctgt taaagctgct 421 ccgag 136

Clone FL HL IPB-5

LOCUS AF394136 425 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PB-5. ACCESSION AF394136 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 425) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 425) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .425 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPB-5" /note="closely related to Fritillaria agrestis" BASE COUNT 122 a 113 c 107 9 83 t ORIGIN 1 cgagatgatt agtgaagcga tcgctttgct gaaggagcag actggatcga gccagtacgc 61 tattgcaaag tttgttgaaa acaagcataa gtcccatctc ccggcgaact tcaagaagct 121 tccccttgtc cagttgcgga aactcactgt tgctggcaaa ctcaccaagg tcaagaattc 181 tacgtgatct ctgccaaacc aacccctgct gtgaagccca agtccgccgc tgtggagccg 241 atgtctgctg ctaccaagcc caagtctgct gccaagaagg tgtagaaagc agctgtgaag 301 ccgaaatcca agcctgctgc cccgaagaca aagacagtga caaaaccaaa ggcagtagct 361 ctgaagacaa agactgttgg ccgtccagca aaggcggcga agatatctgt taaagctgct 421 ccgag 137

Clone FL HL IPB-6

LOCUS AF394137 424 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PB-6. ACCESSION AF394137 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 424) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 424) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .424 /organism="Fritillaria liliacea" /db_xref=" taxon: 167482" /clone="lPB-6" /note="closely related to Fritillaria agrestis" BASE COUNT 121 a 107 c 107 9 89 t ORIGIN 1 cgagatgatt agtgaagtga tcgctttgct gaaggagtag actggatcga gccagtacgc 61 tattgcaaag tttgttgaaa acaagcataa gccccatctc ccggcgaact tcaagaagtt 121 tccccttgtc cagttacgga aactcactgt tgctggcaaa ctcaccgagg tcaagaattc 181 tacatgatct ctgccaaacc aacccctgct gtgaagccca agtctgccgc tgtggagccg 241 aagtctgctg ctaccaagcc caagtctgct gccaagaagg tgtagaaagc agctgtgaag 301 ccgaaatcca agcctgctgc cctgaagtca aagacagtga taaaatcaag gcagtagctc 361 tgaagccaaa gactggtggc tgtccagcaa aggcggcgaa gatatctgtt aaagctgctc 421 cgag 138

Clone FL HL IPB-7

LOCUS AF394138 425 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PB-7. ACCESSION AF394138 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 425) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 425) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .425 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPB-7" /note="closely related to Fritillaria agrestis" BASE COUNT 120 a 107 c 107 9 91 t ORIGIN 1 cgagatgatt agtgaagtga tcgctttgct tgaaggagta gcctggatcg agccagtacg 61 ctattgcaaa gtttgttgaa aacaagcata agtcccatct cccggcgaac ttcaagaagt 121 ttccccttgt ccagttacgg aaactcactg ttgctggcaa actcaccgag gtcaagaatt 181 ctacatgatc tctgccaaac caacccctgc tgtgaagccc aagtctgccg ctgtggagcc 241 gaagtctgct gctaccaagc ccaagtctgc tgccaagaag gtgtagaaag cagctgtgaa 301 gccgaaatcc aagcctgctg ccctgaagtc aaagacagtg ataaaatcaa ggcagtagct 361 ctgaagccaa agactggtgg ctgtccagca aaggcggcga agatatctgt taaagctgct 421 ccgag 139

Clone FL HL IPC-l

LOCUS AF394139 491 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PC-1. ACCESSION AF394139 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 491) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 491) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .491 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPC-1" /note="closely related to Fritillaria agrestis" BASE COUNT 161 a 119 c 104 9 107 t ORIGIN 1 cgagatgatt agtaaagcga tcactttgct gaaggagcag actggataga gccagtacgc 61 tattgcaaag tttgttaaaa ataagcataa gtcccatctc ccgacaaact tcaagaaact 121 tctccttgtt cagttgcaga aactcactgt tgctgaaaaa ctcactaagg tcaagaattc 181 ctacaagatc tctgccaaac caacccctgc tgtgaaaccc aattctgccg ctgcagagct 241 gaagtctgtt gctaccaagc ccaagtcagt agcaagccca agtcttctgc catgaaggtg 301 aagaaagcaa ctatgaagtc gaagcctaaa tctgctgccg taaaaccaaa agctcatgct 361 gtgaagccga aatccaagac tactgccccg aagccaaaga cagtgacaaa atcaaagggt 421 gtagctctaa atccaaagac tgctggctgt ccagcaaagt cggtgaagac atatgttaaa 481 gctgctttgg 9 140

Clone FL HL IPC-2

LOCUS AF394140 491 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PC-2. ACCESSION AF394140 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 491) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 491) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .491 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPC-2" /note="closely related to Fritillaria agrestis" BASE COUNT 162 a 118 c 103 9 108 t ORIGIN 1 caagatgatt agtaaagcga tcactttgct gaaggagcag actggataga gccagtacgc 61 tattgcaaag tttgttaaaa ataagcataa gtcccatctc ccgacaaact tcaagaaact 121 tctccttgtt cagttgcaga aactcactgt tgctgaaaaa ctcactaagg tcaagaattt 181 ctacaagatc tctgccaaac caacccctgc tgtgaaaccc aattctgccg ctgcagagct 241 gaagtctgtt gctaccaagc ccaagtcagt agcaagccca agtcttctgc catgaaggtg 301 aagaaagcaa ctatgaagtc gaagcctaaa tctgctgccg taaaaccaaa agctcatgct 361 gtgaagccga aatccaagac tactgccccg aagccaaaga cagtgacaaa atcaaagggt 421 gtagctctaa atccaaagac tgctggctgt ccagcaaagt cggtgaagac atatgttaaa 481 gctgctttgg 9 141

Clone FL HL IPC-3

LOCUS AF394141 490 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PC-3. ACCESSION AF394141 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 490) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 490) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .490 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPC-3" /note="closely related to Fritillaria agrestis" BASE COUNT 160 a 113 c 105 9 112 t ORIGIN 1 caagatgatt agtgatgcga tcactttgct gaaggagcag actggataga gccagtacgc 61 tattgcaaag tttgttgaaa ttaagcataa gtcccatctc ccaatgaact tcaagaaatt 121 ctccttattc agttgcggaa actcactttt gctggaaaag taactaaggt caagaatttc 181 tacaagatct ctgccaaccc aacccctgct gtgaaaccca agtctgtcac tgcagagctg 241 aagtctgttg ctaccaagct caagtcagca gcaagcccaa gtcttctgcc aagaaggtga 301 agaaagcagc tataaagttg aagtctaaat ctactgccgt gaaaccaaaa gctcacgctg 361 tgaagccaaa atccaagact actgccccga agccaaagac agtgacaaaa tcaaagggtg 421 tatctctaaa gccaaagact gctggctgtc cagcaaagtt ggcgaagaca tatgttaaag 481 ctgctttggg 142

Clone FL HL IPD-l

LOCUS AF394142 495 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PD-1. ACCESSION AF394142 KEYI'VORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 495) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 495) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .495 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPD-1" /note="closely related to Fritillaria agrestis" BASE COUNT 162 a 115 c 105 9 113 t ORIGIN 1 caagatgatt agtgatgcga tcactttgct gaaggagcag actggataga gccagtacgc 61 tattgcaaag tttgttgaaa ttaagcataa gtcccatctc ccaatgaact tcaagaaatt 121 ctccttattc agttgcggaa actcactttt gctggaaaag taactaaggt caagaatttc 181 tacaagatct ctgccaaccc aacccaaccc ctgctgtgaa acccaagtct gtcactgcag 241 agctgaagtc tgttgctacc aagctcaagt cagcagcaag cccaagtctt ctgccaagaa 301 ggtgaagaaa gcagctataa agttgaagtc taaatctact gccgtgaaac caaaagctca 361 tgctgtgaag ccaaaatcca agactactgc cccgaagcca aagacagtga caaaatcaaa 421 gggtgtatct ctaaagccaa agactgctgg ctgtccagca aagttggcga agacatatgt 481 taaagctgct ttggg 143

Clone FL HL IPE-l

LOCUS AF394143 537 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PE-1. ACCESSION AF394143 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 537) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Friti11aria JOURNAL unpublished REFERENCE 2 (bases 1 to 537) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State university, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .537 /organism="Fritillaria 1iliacea" /db_xref=ltaxon:167482" /clone=llPE-1" /note="closely related to Fritillaria agrestis" BASE COUNT 162 a 124 c 134 9 117 t ORIGIN 1 tgagataatt agtgaaggga tagatttgct gaaggagcag actggatcga gcacctatct 61 gagatgatta gtgaagcgat aaatttgctg aaggagcaga ctggattggg ccagtacgct 121 atggcaaagt ttgttgaaaa caagtataag tcccatctcc cggcaaactt caagaagctt 181 ctccttgtcc agttacggaa actcactgtt gctgacaaac tcaccaaggt caagaattct 241 acatgatctc tgccaaacca agatctctgc caaaccaacc cctgctgtga agcccaagtc 301 cgtcactgtg gagctgaatt ctgctactat caagcccaag tctgctgcca agaaggtgta 361 gaaagcagtt gtgaagccga aatccaagcc tgctgtcccg aggccaaaga cagtgacaaa 421 atccaaggca gtagctctga agccaaatat tgttggccgt ccggcaaagg cggtgaagac 481 atctgttaaa gctgctccgg gaaaaaggtc gcttcagtgg ccctgaagga agctaag 144

Clone FL HL IPF-l

LOCUS AF394144 731 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 1PF-1. ACCESSION AF394144 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 731) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 731) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-20011 Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .731 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="lPF-1" /note="closely related to Fritillaria agrestis" BASE COUNT 216 a 179 c 183 9 153 t ORIGIN 1 ctcacctttg cttcggtccc tgtcgccaga gatgatctga cggaaaagcc gaccaaggtg 61 acgaaggcca aggtccctaa gaagaagaag gcctctgtta cgaagaagcc tgctctccat 121 tctacctatc tcgagatgat tagtgaagcg atcgctttgc tgaaggagca gactggatca 181 aaccagtacg atattgtaaa gtttgttgaa aacaagcata agtcccatct cccgacgaac 241 ttcaagaagc ttcctcttgt ccagttgtgg aaactcactg ttgctggcaa actcaccaag 301 atcaagaatt ctacatgatc tctgccaaac caacccctac tgtgaagccc aagtccgccg 361 ctgtggagcc gaagtctgct gctaccaagc ccatgtctac tgccaagaag gtgtagaaag 421 cagctgtgaa accgaaatcc aagcctgttg ccccgaagct aaagacagtg acaaaatcaa 481 aggcagtagc tctgaagcca aagactgctg gccgtctagc aaagatggcg aagatatctg 541 ttaaagctgc tccgagaaag aaggtcgctc cagtggccct gaaggaagct aaggctggga 601 aggtggtact cagagtcaat catatttctg ggaagaagtt gatgcttcat cggccagcaa 661 agatggcgaa gatatctgtt aaagctgctc cgagaaagaa ggtcgctcca gtggccctga 721 aggaagctaa 9 145

Clone FL HL 2GA-l

LOCUS AF394145 225 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-1. ACCESSION AF394145 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 225) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 225) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .225 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-1" /note="closely related to Fritillaria agrestis" BASE COUNT 77 a 69 c 40 9 39 t ORIGIN 1 caagatgttg aagacaagca caaagctcaa agctcagctt ccggctaacg tcaagaagct 61 ccttctcaac cagctgagga aactaactgc caccggcaaa gtcaccaagc tcaagaaatc 121 caataaatta tcccctatca agcccagcat tgcccccaag tcaaagtctg ccatgccaaa 181 gccaaagtca gttactgcaa agtccaagtc cacatctggg aagcc 146

Clone FL HL 2GA-2

LOCUS AF394146 567 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-2. ACCESSION AF394146 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 567) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 567) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .567 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-2" /note="closely related to Fritillaria agrestis" BASE COUNT 164 a 145 c 113 9 144 t 1 others ORIGIN 1 tgatgtacca gatccggtcc caatttagtc agagctcttt tccttgntgc tattctattt 61 caatgttgcc ctaattttct aacttatccc gattttgaaa tctcagatat tctgtgaggc 121 gatagcatcc ctgaaggaga ggaccgggtc aagccagtat gcaatctcaa agtttgttgc 181 agacaagcac aaggttcatc tcttggtaaa ttttaagaag ctcctcctca tcccacttag 241 gaagctcact gctgctggca aactcaccaa ggccaagaac tcctacaaga tccctgctaa 301 tcacattcct ggtgggatga aaaaaattat ctctgtgaag ccaaagtcta ctgttgtaaa 361 gcccaatgag tccactgctg ttaagccaaa taagttggcc gtgaagccga agccaaaagc 421 atctgctgca aagcctaaat ccaagtctgc tgctgcgaag ccaaagaccg cagcgaagtc 481 aaaatctgtt gcacctaagt ctaaagcttc tggtggactg acaaaggcag caaagacctc 541 aatcaatgtc actccctccg ccaagct 147

Clone FL HL 2GA-3

LOCUS AF394147 545 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-3. ACCESSION AF394147 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL unpublished REFERENCE 2 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1 .. 545 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-3" /note="closely related to Fritillaria agrestis" BASE COUNT 165 a 132 c 123 9 125 t ORIGIN 1 tgaggtacca gatcccaatt ttgaaatctc agatgatccg tgagatgata gcgtccctga 61 aggagaggat cgggtcaagc cactatgcaa tctcaaagtt tgttgaagac aagcacaagg 121 gtcatctccc ggtaaactct aagaagttcc tcatccagct tcggaagttc aatgctgctc 181 gcaaactcac caaggtcaag aactcctaca agatacctgc taagcccatt tctggtagta 241 tgaaaacagt tatctctgtg acgccaaagt ctgctgttgt gaaaccaaat aagtccactg 301 ctgttatgcc agataaggtg gctgtgaagc cgaatcaaaa atcaactgtt gcaaagccta 361 aatccaagtc tgctgctgtg aagccaaaga ttgcagtgaa gtcgaaacct gttgcaccta 421 tgtctaaaac atccggtgga ctggcaaagg taaaaaagac cccagtcagt gtcactcctt 481 ccaccaagcc gaagatggct gctccagttg cggccgagaa gccgaagatt gtgaataagt 541 cccct 148

Clone FL HL 2GA-4

LOCUS AF394148 545 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-4. ACCESSION AF394148 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Frit illaria. REFERENCE 1 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State university, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .545 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone=12GA-4" /note="closely related to Fritillaria agrestis" BASE COUNT 167 a 134 c 119 9 125 t ORIGIN 1 tgaggtacca gatcccaatt ttaaaatctc agatgatccg tgagacgata gcgtccctga 61 aggagaggat cgggtcaagc cactatgcaa tctcaaagtt tgttgaagac aagcacaagg 121 gtcatctccc ggtaaactct aagaagttcc tcatccagct tcggaagctc aatgctgctc 181 gcaaactcac caaggtcaag aactcctaca agatccctgc taagcccatt tctggtagta 241 tgaaaacagt tatctctgtg acgccaaagt ctgctgttgt gaaaccaaat aagtccactg 301 ctgttatgcc agataaggtg gctgtgaagc cgaataaaaa atcaactgtt gcaaagccta 361 aatccaagtc tgctgctgtg aagccaaaga ttgcagtgaa gtcgatacct gttgcaccta 421 tgtctaaaac atccggtgga ctggcaaagg taaaaaagac cccagtcaat gtcactcctt 481 ccaccaagcc gaagatggct gctccagttg ctgccaagaa gccgaagatt gtgaataagt 541 cccct 149

Clone FL HL 2GA-S

LOCUS AF394149 545 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-5. ACCESSION AF394149 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .545 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-5" /note="closely related to Fritillaria agrestis" BASE COUNT 166 a 130 c 123 9 126 t ORIGIN 1 tgaggtacca gatcccaatt ttgaaatctc agatgatccg tgaggcgata gcgtccctaa 61 aggagaggat cgggtcaagc cagtatgcaa tctcagagtt tgttgaagac aagcacaagg 121 gtcatctccc ggtaaacttt aagaagttcc tcatccagct ttggaagctc aatgctgctc 181 gcaaactcac caaggtcaag aactcctaca agatccctgc taagcccatt tctggtagta 241 tgaaaacagt tatctctgtg aagccaaagt ctgcagttgt gaaaccaaat aagtcaactg 301 ctgtcgtgcc agataaggtg gctgtgaagc cgaatccaaa atcaactgtt gcaaagccta 361 aatccaagtc tgctgctgtg aagccaaaga tcgcagtgaa gtcgaaacct gttgcaccta 421 tgtctaaaac atccggtgga ctggcaaagg taacaaagac ctcagtcaat gttactcctt 481 ccaccaggcc gaagatggct gctccagttg ctgcaaagaa gctgaagatt gtgaataaat 541 cccct 150

Clone FL HL 2GA-6

LOCUS AF394150 545 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-6. ACCESSION AF394150 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Frit illaria. REFERENCE 1 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .545 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-6" /note="closely related to Fritillaria agrestis" BASE COUNT 167 a 134 c 120 9 124 t ORIGIN 1 tgaggtacca gatcccaatt ttgaaatctc agatgatccg tgagacgata gcgtccctga 61 aggagaggat cgggtcaagc cactatgcaa tctcaaagtt tgttgaagac aagcacaagg 121 gtcatctccc ggtaaacact aagaagttcc tcatccagct tcggaagctc aatgctgctc 181 gcaaactcac caaggtcaag aactcctaca agatccctgc taagcccatt tctggtagta 241 tgaaaacagt tatctctgtg acgccaaagt ctgctgttgt gaaaccaaat aagtccactg 301 ctgttatgcc agataaggtg gctgtgaagc cgaataaaaa atcaactgtt gcaaagccta 361 aatccaagtc tgctgctgtg aagccaaaga ttgcagtgaa gtcgatacct gttgcaccta 421 tgtctaaaac atccggtgga ctggcaaagg taaaaaagac cccagtcaat gtcactcctt 481 ccaccaagcc gaagatggct gctccagttg ctgccaagaa gccgaagatt gtgaataagt 541 cccct 151

Clone FL HL 2GA-7

LOCUS AF394151 545 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-7. ACCESSION AF394151 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases I to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 28500 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .545 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-7" /note="closely related to Fritillaria agrestis" BASE COUNT 169 a 129 c 123 9 124 t ORIGIN 1 tgaggtacca gatcccaatt ttgaaatcac agaggatccg tgaggcgata gcgtccctga 61 aggagaggat cgggtcaagc cagtatgcaa tctcaaagtt tgttgaagac aagcacaagg 121 gtcatctcct ggtaaacttt aagaagttca tcatccagct tcggaagctc aatgctgctc 181 gaaaactcac caaggtcaag aactcctaca agatccctgc taagcccatt tctggtagta 241 tgaaaacagt tatctctgtg aagccaaagt ctgctgttgt gaaaccaaat aagtccactg 301 ctgttatgcc agataaggtg gctgtgaagc cgaatcaaaa atcaactgtt gcaaagccta 361 aatccaagtc tgctgctgtg aagccaaaga ttgcagtgaa gtcgaaacct gttgcaccta 421 tgtctaaaac atccggtgga ctggcaaagg taaaaaagac cccagtcaat gtcactcctt 481 ccaccaagcc gaagatggct gctccagttg ctgccaagaa gccgaagatt gtgaataagt 541 cccct 152

Clone FL HL 2GA-8

LOCUS AF394152 545 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-8. ACCESSION AF394152 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .545 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-8" /note="closely related to Fritillaria agrestis" BASE COUNT 167 a 130 c 122 9 126 t ORIGIN 1 tgaggtacca gatcccaatt ttgaaatctc agatgatccg tgaggcgata gcgtccctaa 61 aggagaggat cgggtcaagc cagtatgaaa tctcaaagtt tgttgaagac aagcacaagg 121 gtcatctccc ggtaaacttt aagaagttcc tcatccagct tcggaagctc aatgctgctc 181 gcaaactcac caaggtcaag aactcctaca agatacctgc taagcccatt tctggtagta 241 tgaaaacagt tatctctgtg acgccaaagt ctgctgttgt gaaaccaaat aagtccactg 301 ctgttatgcc agataaggtg gctgtgaagc cgaatcaaaa atcaactgtt gcaaagccta 361 aatccaagtc tgctgctgtg aagccaaaga ttgcagtgaa gtcgaaacct gttgcaccta 421 tgtctaaaac atccggtgga ctggcaaagg taaaaaaggc cccagtcaat gtcactcctt 481 ccaccaagct gaagatggct gctccagttg ctgccaagaa gccgaagatt gtgaataagt 541 cccct 153

Clone FL HL 2GA-9

LOCUS AF394153 545 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2GA-9. ACCESSION AF394153 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 545) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .545 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2GA-9" /note="closely related to Fritillaria agrestis" BASE COUNT 166 a 132 c 121 9 126 t ORIGIN 1 tgaggtacca gatcccaatt ttgaaatctc agatgatccg tgaggcgata gcgtccctga 61 aggagaggat cgtgtcaagc cagtatgaaa tctcaaagtt tgttggagac aagcacaagg 121 gtcatctccc ggtaaacttt aagaagttcc tcatccagct tcggaagctc aatgctgctc 181 gcaaactcac caaggtcaag aactcctaca agatccctgc taagcccatt tctggtagta 241 tgaaaacagt tatctctgtg aagccaaagt ctgctgttgt gaaaccaaat aagtccactg 301 ctgttatgcc agataaggtg gctgcgaagc cgaatccaaa atcaactgtt gcaaagctta 361 aatccaagtc tgctgctgtg aagccaaaga tcgcagtgaa gtcgaaacct gttgcaccaa 421 tgtctaaaac atccggtgga ctggcaaagg taaaaaagac cccagtcaat gtcactcctt 481 ccaccaagct gaagatgtct gctccagttg ctgccaagaa gccgaagatt gtgaataagt 541 cccct 154

Clone FL HL 2PA-I

LOCUS AF394154 292 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-1. ACCESSION AF394154 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 292) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 292) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .292 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-1" /note="closely related to Fritillaria agrestis" BASE COUNT 96 a 85 c 59 9 52 t ORIGIN 1 caagatgatc aaggaggcaa tcacctcgct gaaggagcga actggatcga gccagtacgt 61 aatctcgaag tttgttgaag acaagcacaa agctcaaagc tcagcttccg gctaacatca 121 agaagctcct tctcaaccag ctgaggaaac taactgccac cggcaaagtc accaagctca 181 agaactccaa taaattatcc cctatcaagc ccagcattgc ccccaagtca aagtctgccg 241 tgccaaagcc aaagtcagtt actgcaaagt ccaattccac agctgggaag cc 155

Clone FL HL 2PA-2

LOCUS AF394155 292 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-2. ACCESSION AF394155 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 292) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE [email protected] JOURNAL Unpublished REFERENCE 2 (bases 1 to 292) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .292 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-2" /note="closely related to Fritillaria agrestis" BASE COUNT 96 a 85 c 59 9 52 t ORIGIN 1 caagatgatc aaggaggcaa tcacctcgct gaaggagcga actggatcga gccagtacgt 61 aatctcgaag tttgttgaag acaagcacaa agctcaaagc tcagcttccg gctaacatca 121 agaagctcct tctcaaccag ctgaggaaac taactgccac cggcaaagtc accaagctca 181 agaactccaa taaattatcc cctatcaagc ccagcattgc ccccaagtca aagtctgccg 241 tgccaaagcc aaagtcagtt actgcaaagt ccaagtccac atctgggaag cc 156

Clone FL HL 2PA-3

LOCUS AF394156 566 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-3. ACCESSION AF394156 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 566) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 566) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State university, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .566 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-3" /note="closely related to Fritillaria agrestis" BASE COUNT 179 a 131 c 104 9 152 t ORIGIN 1 tgaggtaccg atccggtcct aattaagtca gagttctttt gcttgttgct attctatttc 61 aacattgccc taattttcta acttattccg attttgaaat ctctgatgat ccatgaggag 121 ataacatccc tgaaggagag gaccgggtca agaaagtatg caatctcaaa gtttgttgaa 181 gacaagcaca agactcatct cctgataaac tttaagaagc tcctcctcat ccaacttcag 241 aagcccactg ttgctcgcaa actcaccaag gtcaagaatt cctataatat ccctgcaaat 301 cccattcttg gtgggataaa aatagttatc tctgcgaagt caaattctgc tgttgtgaaa 361 cctaataagt ccactaatct taagccaaat aaggttgccg tgaagccgaa gccaaaagca 421 tctcctgtaa agcctaaatc caagccagct gttgtgaacc caaagacagc agcgaagtca 481 aaatatattg cacctaagtt taaagcttat ggtggactgg aaaaggcagc aaagacctta 541 gtcaatgtca ctccttctgc caagca 157

Clone FL HL 2PA-4

LOCUS AF394157 574 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-4. ACCESSION AF394157 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 574) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 574) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .574 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-4" /note="closely related to Fritillaria agrestis" BASE COUNT 177 a 134 c 121 9 142 t ORIGIN 1 tgtggtatca gatccagtca cagtttagtc agagctcttt tcctggttgc tattctatgt 61 caatgttgtt ctaattttca aacttaccct attttgaaat ctcagatgat ccgtgaggca 121 atagcgtccc cgaaggagag gaccaggtca agccagtatg caatctcata gtttgatgaa 181 gacaagcaca agacacatat cccggtaaac tttaaaaagc tccacctcat ccagcttcag 241 aagctcactg ctgctggcaa actcaccaag gtcaagaact cctacaagat ccctgctaag 301 cccgttcatg gtgggatgaa aagagatggg atgaaaatag ttatctctgt gtaaccaaag 361 tctgctgttg tgaagcccaa taatccactg ctgttaagac aaaaaaggtg gctgtgaagc 421 caaagccaaa agcatctgct gcaaatcata aatccaaatc tgctgctgca aagacaaaga 481 ctgcagtgaa gtcggaatct gttgcaccta agtctaaagc tactggtgga ctggcaaagg 541 cagcaaagat ctcagtcaat gtcactcctt ccgc 158

Clone FL HL 2PA-5

LOCUS AF394158 424 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-5. ACCESSION AF394158 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 424) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 424) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State university, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .424 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-5" /note="closely related to Fritillaria agrestis" BASE COUNT 121 a 107 c 107 9 89 t ORIGIN 1 cgagatgatt agtgaagtga tcgctttgct gaaggagtag actggatcga gccagtacgc 61 tattgcaaag tttgttgaaa acaagcataa gccccatctc ccggcgaact tcaagaagtt 121 tccccttgtc cagttacgga aactcactgt tgctggcaaa ctcaccgagg tcaagaattc 181 tacatgatct ctgccaaacc aacccctgct gtgaagccca agtctgccgc tgtggagccg 241 aagtctgctg ctaccaagcc caagtctgct gccaagaagg tgtagaaagc agctgtgaag 301 ccgaaatcca agcctgctgc cctgaagtca aagacagtga taaaatcaag gcagtagctc 361 tgaagccaaa gactggtggc tgtccagcaa aggcggcgaa gatatctgtt aaagctgctc 421 cgag 159

Clone FL HL 2PA-6

LOCUS AF394159 567 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-6. ACCESSION AF394159 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 567) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 567) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, Calofornia State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .567 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-6" /note="closely related to Fritillaria agrestis" BASE COUNT 167 a 142 clIO 9 148 t ORIGIN 1 tgaggtcaag atccggttcc tatttagtca tagctctttt ccttgttgct attctatttc 61 gatgttgccc taattttctt acttataccc aatttgaaat ctcagatgat ccacgaggcg 121 atagcattcc tgaaggagag gaccgggtca agccagtatg cagtctcaaa gtccattgaa 181 gacaagcaca agggtgatct cctggtaaat attaagaagt tcctcctcat ccagcatcgg 241 aagcacactg ctgctggcaa actcaccaag gtcaagaact cttacaagat ccctgctaag 301 cccgttcttt gtgagatgaa aacagttatc tctgtaaagc caaagtctgc tgttgtgaat 361 cccaataagt ccacttctgt taaaccaaat aagttgcatg tgaagccgaa gccaaaagca 421 tctgctacaa atcctaaatc caagtctgct gctgtgatgc caaagaccgc agcaaagtcg 481 aaatccgttg cacctaactc taaagcttct aatggactgg caaaggcagc aaagaccctc 541 agtcaatgtc actccatccg ctaagct 160

Clone FL HL 2PA-7

LOCUS AF394160 546 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-7. ACCESSION AF394160 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 546) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 546) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .546 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-7" /note="closely related to Fritillaria agrestis" BASE COUNT 162 a 140 c 118 9 126 t ORIGIN 1 tgaggtacca tatctggccc caatttagtc agagctcttt tccttattgc tattttattt 61 caatattgct ctaattttct aaattatccc gattttgaaa tctcagatga tccgtgaggc 121 gatagcgtcc ctgaaggaga gggccgggtt aagccagtat gcaatctcga aatttgttga 181 agacaagcat aaggctcacc tcccggcaaa ctataagaag ctcctcctca tccagcttcg 241 gaagctcact gctgctggca agcccacaaa ggtcaagaac tcctacaaga tccctgccaa 301 gcccattgcc ggtgggaaga agacaactat ctctaccgag ctgaagccaa agtccactac 361 tgttatgcca aagaaggtgg ctgtgaagcc gaagccaaaa tcatatactg caaaacctaa 421 agccaagtct actgctgcga agccagagac agcagcaaaa ttgaaatctg ttgcgcctaa 481 gcttaaaact gctggtggat cggggaaggc agcaaagacc tcagccaaag ccactcctgt 541 caagct 161

Clone FL HL2PA-8

LOCUS AF394161 500 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-8. ACCESSION AF394161 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 500) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 500) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .500 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-8" /note="closely related to Fritillaria agrestis" BASE COUNT 146 a 125 c 113 9 116 t ORIGIN 1 cgaggtctga tccagccact atttcctcta gatttgttaa tttatgaaat taatgtagtc 61 taatttggtc tactttctaa atctcagatg atcagtgaag cgatcgcttc gctgaaggag 121 cggactggat cgagccagta cgctattgca aagtttgttg aagacaagca caagtctcat 181 ctcccggcga acttcaagaa gcttctcctt gtccagttgc ggaagctcac tgctgctggc 241 aagctcacaa aggtgaagaa ttcctacaag atctctgcca aaccgacccc tgctgcgaag 301 cctaaatcag ctgctgtgaa gccaaagtct actgctagta agctcaagtc cgctgccaag 361 aaggtgaaga aagcagctgt gaagccaaag cctaaatctg ctgccgtgaa gccaaaagcc 421 cctgccgtga acatgaaatc caagcctgct gccctgaagc caaatacagt gacaaaatca 481 aagactgtag ctctgaaggg 162

Clone FL HL 2PA-9

LOCUS AF394162 621 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-9. ACCESSION AF394162 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Frit illaria. REFERENCE 1 (bases 1 to 621) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 621) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .621 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-9" /note="closely related to Fritillaria agrestis" BASE COUNT 186 a 153 c 130 9 152 t ORIGIN 1 tgaggtacta gatccggtcc caatttattc aaagatcttt tccttgttgc tattcaattt 61 caatgttgcc ctagttttct aacttatccc gatttggaaa tatcaaatga tccgtgaggt 121 gaaagcgtcc ctgaggagag gaccgggtca agctagtatg aaatctcaaa gtttcttgaa 181 gacaagcaca aggctcatct cccggtaaac tttaagaagc tcctcctcgt ccagcttcgg 241 aagctcactg ctgctggcaa actcacccag gtcaagaact cctacaagat ccatgttaag 301 cccattcctg gtgggatgaa aacagttatc tctgtgaagc caaagtctgc tgttgtgaat 361 cccaaaaagt ccactactgt taagccaaat aaggtggttg tgaagccgaa gccaaaagca 421 tctgctgcaa aacctaaatt cgagtctgct gctccgaatc ccaagacagc agcgaagtca 481 aaatctgttg cacctaaatc taaagcttcg ggttgactgg caaagacagc aaagaccaca 541 gtcaatgtca ctcccaccgc caagtagaag aagactgctc tagttactgc caaaaagctg 601 aagattgcga atgaggcccc t 163

Clone FL HL 2PA-IO

LOCUS AF394163 295 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-10. ACCESSION AF394163 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 295) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 295) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .295 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-10" /note="close1y related to Friti11aria agrestis" BASE COUNT 103 a 71 c 35 9 86 t ORIGIN 1 accccaaaca agataaatac atcttgtgag aaatagttca cactatttct tactcttcac 61 ctctccttag tttcttcaat aacaaaatat acccttgact acttcagcgt gaggaagtca 121 taagttaggg gaaaaggcta cacccacctt tgtatcttac acccaatatc taggaactat 181 cagtaccata catgagcata ccactaaaac tcatgttcca aattacctaa ctctctaata 241 atcccatact tggtaaatat atgactacca agtacctaag ttcttaatga ggaat 164

Clone FL HL 2PA-ll

LOCUS AF394164 621 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-11. ACCESSION AF394164 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 621) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 621) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .621 /organism="Fritillaria liliacea" /db_xref="taxon:167482" /clone="2PA-11" /note="closely related to Fritillaria agrestis" BASE COUNT 188 a 152 c 128 9 153 t ORIGIN 1 tgaggtacta gatctggtcc caatttagtc aaagctcttt tccttgttac tattcaattt 61 caatgttgcc ttagttttct aacttatccc gatttagaaa tatcaaatga tccgtgaatt 121 gatagcgtcc tgaagaagag gaccgggtca tgacagtacg caatcttaac gtctgttgaa 181 gacaagcaca aggctcatct cccggtaaac tttaagaagc tcctcctcgt ccagctttag 241 aagctcacta cagctggcaa actcaccaag gtcaagagct cctacaagat ccctgctaag 301 cccgttcctg gtgagatgaa aacacttatc tctgtgaagc caaattctgc tgttgtgaat 361 cccaaaaagt ccactgctgt tgagtcaaat aaggtgtctg tgaagccgaa gccaaaagca 421 tctgctgcaa aacctaaatc caagtctgct gctccgaagc caaagaccgc agcgaagtcg 481 aaatatgttg cacctaaatc taaagcttct ggttgactgg caaaggcagc aaagaccaca 541 gtcaatgtca ctcctaccgc caagtagaag aaggctgctc cagttgctgc caaaaagcag 601 aagattgtga atgaggaccc a 165

Clone FL HL 2PA-12

LOCUS AF394165 184 bp DNA PLN 23-JUL-2001 DEFINITION Fritillaria liliacea histone-like gene, clone 2PA-12. ACCESSION AF394165 KEYWORDS SOURCE Fritillaria liliacea. ORGANISM Fritillaria liliacea Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Liliales; Liliaceae; Fritillaria. REFERENCE 1 (bases 1 to 184) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE rbcS and histone-like gene families in Fritillaria JOURNAL Unpublished REFERENCE 2 (bases 1 to 184) AUTHORS Gadkari,R. and Baysdorfer,C. TITLE Direct Submission JOURNAL Submitted (22-JUN-2001) Biological Sciences, California State University, 25800 Carlos Bee Blvd, Hayward, CA 94542, USA FEATURES Location/Qualifiers source 1. .184 !organism="Fritillaria liliacea" !db_xref="taxon:167482" !clone="2PA-12" !note="closely related to Fritillaria agrestis" BASE COUNT 51 a 49 c 38 g 46 t ORIGIN 1 cgtatgtgtc tcctccacca ttgatagcaa cccccacttc cccttcgatt aagccctaga 61 agactccgga tgctgatgga gaatgtcaag actgccctca agaagtggct ataagaagaa 121 gatgcacccc ctgaagaaaa tctctccctc tagttcatac atttagaatc ggattggagt 181 gtgt 166

2. BLAST N database search of histone-like protein genomic clones from Fritillaria liliacea.

(Query: The histone-like protein genomic clone from Fritillaria liliacea. Subject: Matching sequence from the database. Score: The alignment score. Expect: This value represents the probability ofa match appearing by chance. Identities: Total number of identical residues in common.)

gi126412101gb1AF031547.11AF031547 Fritillaria agrestis histone-like protein mRNA, complete cds Length = 956

Score = 898 bits (453), Expect 0.0 Identities = 495/509 (97%) Strand = Plus / Plus

Query: 319 agatgatcagtgaagcgattgcttcgctgaaggagcggactggatcgagccagtacgcta 378 I11I1I1111111111111 11I1111111111111111111111111111111111111 Sbjct: 233 agatgatcagtgaagcgatcgcttcgctgaaggagcggactggatcgagccagtacgcta 292

Query: 379 ttgcaaagtttgttgaagacaagcacaagtctcatctcccggcgaacttcaagaagcttc 438 1111 111I11111111111111111111111111111111111111111111111111I Sbjct: 293 ttgcgaagtttgttgaagacaagcacaagtctcatctcccggcgaacttcaagaagcttc 352

Query: 439 tccttgtccagttgcggaaactcactgctgctggcaaactcacgaaggtgaagaactcct 498 1I1111111111111 11I111111111111111111111111111111111111 1I11 Sbjct: 353 tccttgtccagttgcagaaactcactgctgctggcaaactcacgaaggtgaagaattcct 412

Query: 499 acaagatctctgccaaaccaaccgctgctgtgaagcctagatccgctgctgtgaagccaa 558 11111111111111111111111 111111 111I1111 11111111111111111111 Sbjct: 413 acaagatctctgccaaaccaacccctgctgcgaagcctaaatccgctgctgtgaagccaa 472

Query: 559 agtctgctgttgctaagctcaagtccgctgccaagaaggtgaagaaagcagctgtgaagc 618 111111111 I 1111 1111111111111111111111111111111111111111111 Sbjct: 473 agtctgctgctactaaactcaagtccgctgccaagaaggtgaagaaagcagctgtgaagc 532

Query: 619 caaagcctaaatctgctgccgtgaagccaaaagcccctgccgtgaaaccgaaatccaagc 678 1111111111111111111111111111111111111111111111 11111111111 Sbjct: 533 caaagcctaaatctgctgccgtgaagccaaaagcccctgccgtgaacatgaaatccaagc 592

Query: 679 ctgctgccctgaagccaaatacagtgacaaaatcaaagactgtagctctgaagggaaaga 738 1II111111111111111111111111111111111111111111111111111I 1111 Sbjct: 593 ctgctgccctgaagccaaatacagtgacaaaatcaaagactgtagctctgaaggggaaga 652

Query: 739 ctgctggccgtccagcaaaggcggcaaagacatccgtcaaagctgctccgggaaagaagg 798 111111111111111111111111111111111111111111111111111111111111 Sbjct: 653 ctgctggccgtccagcaaaggcggcaaagacatccgtcaaagctgctccgggaaagaagg 712 167

Query: 799 ctgctccagtggctctgaagaaggctaag 827 11I11111111111111111111111111 Sbjct: 713 ctgctccagtggctctgaagaaggctaag 741

Score = 236 bits (119), Expect 2e-59 Identities = 128/131 (97%) Strand = Plus / Plus

Query: 1 cccgcctttgctccggtccctgttgccagagatgaaccggtggcgaagccggccaaggtg 60 11111111111I1111111111111111111111111111111111111111 II II II I Sbjct: 100 cccgcctttgctccggtccctgttgccagagatgaaccggtggcgaagccgggcaaggtg 159

Query: 61 acgaaggccaaggcccctaaggagaagaaggcctccattgcgaagaagcctgctctccat 120 II II II IIIIIIIIII II IIIIIIIIIII1IIIIII I 111111111111111111111 Sbjct: 160 acgaaggccaaggcccctaaggagaagaaggcctccgtcgcgaagaagcctgctctccat 219

Query: 121 cctacctatct 131 II II 111I11 I Sbjct: 220 cctacctatct 230

>gi164749491dbj IAB012694.11AB012694 Lilium longiflorum p35 mRNA for variant of histone HI, complete cds Length = 980

Score = 216 bits (109), Expect 2e-53 Identities = 184/209 (88%) Strand = Plus / Plus

Query: 319 agatgatcagtgaagcgattgcttcgctgaaggagcggactggatcgagccagtacgcta 378 1111111111111 11111 11111 11111111111 II 111111111111 11111 Sbjct: 200 agatgatcagtgaggcgatcgcttcactgaaggagcgaaccggatcgagccagatcgcta 259

Query: 379 ttgcaaagtttgttgaagacaagcacaagtctcatctcccggcgaacttcaagaagcttc 438 II 111111111111 I 111111111 1111 II 11111 11111111111111 I Sbjct: 260 tctcgaagtttgttgaaaataagcacaaggctcacctgccggccaacttcaagaagctcc 319

Query: 439 tccttgtccagttgcggaaactcactgctgctggcaaactcacgaaggtgaagaactcct 498 I 11111111111111111111111 11111111 11111111111111 11111 1111 Sbjct: 320 tacttgtccagttgcggaaactcaccgctgctggtaaactcacgaaggttaagaattcct 379

Query: 499 acaagatctctgccaaaccaaccgctgct 527 1111111111111111 II III 11111 Sbjct: 380 acaagatctctgccaagcccaccactgct 408

Score = 105 bits (53), Expect 5e-20 Identities = 89/101 (88%) Strand = Plus / Plus

Query: 552 aagccaaagtctgctgttgctaagctcaagtccgctgccaagaaggtgaagaaagcagct 611 I1II1 II 1111111 III 1111 1111111 11111 1111111111111111111 Sbjct: 451 aagcccaaatctgctgctgccaagcccaagtccactgccgcgaaggtgaagaaagcagct 510 168

Query: 612 gtgaagccaaagcctaaatctgctgccgtgaagccaaaagc 652 II 1I111 111111111111 t 1111 11111111 III t 1 Sbjct: 511 gtaaagccgaagcctaaatctgctgctgtgaagcccaaagc 551

Score ~ 85.7 bits (43), Expect 5e-14 Identities ~ 81/93 (87%), Gaps 3/93 (3%) Strand ~ Plus / Plus

Query: 43 gcgaagccggccaaggtgacgaaggccaaggcccctaaggagaagaaggcctccattgcg 102 1111111 t 11111111 II 111111 1111 III 111I11111111111111 I II Sbjct: 112 gcgaagccggccaaggcgaagaaggcaaaggtcccaaaggagaagaaggcctccgtcgc- 170 Query: 103 aagaagcctgctctccatcctacctatcttgag 135 111111 lilt 1111111111111 111111 Sbjct: 171 --gaagcccgctctccatcctacctaccttgag 201

Score ~ 42.1 bits (21), Expect ~ 0.63 Identities ~ 33/37 (89%) Strand ~ Plus / Plus

Query: 791 aaagaaggctgctccagtggctctgaagaaggctaag 827 111111111 II t II 111111 II t 1111111111 Sbjct: 666 aaagaaggcggctccggtggcttcgaagaaggctaag 702

Score ~ 38.2 bits (19), Expect 9.8 Identities ~ 25/27 (92%) Strand ~ Plus / Plus

Query: 530 gaagcctagatccgctgctgtgaagcc 556 t 1111111 III 11111111111111 Sbjct: 519 gaagcctaaatctgctgctgtgaagcc 545 169

3. BLAST N database search with processed pseudogene clones from Fritillaria liliacea.

(Query: The histone-like protein pseudogene clone from Fritillaria liliacea. Subject: Matching sequence from the database. Score: The alignment score. Expect: This value represents the probability ofa match appearing by chance. Identities: Total number of identical residues in common.)

>giI2641210IgbIAF031547.1IAF031547 Fritillaria agrestis histone-like protein mRNA, complete cds Length = 956

Score = 1241 bits (626), Expect 0.0 Identities = 638/642 (99%) Strand = Plus / Plus

Query: 1 cccgcctttgctccggtccctgttgccagagatgaaccggtggcgaagccgggcaaggtg 60 111111111111111111111111111111111111111111111111111111111111 Sbjct: 100 cccgcctttgctccggtccctgttgccagagatgaaccggtggcgaagccgggcaaggtg 159

Query: 61 acgaaggccaaggcccctaaggagaagaaggcctccgtcgcgaagaagcctgctctccat 120 111111111111111111111111111111111111111111111111111111111111 Sbjct: 160 acgaaggccaaggcccctaaggagaagaaggcctccgtcgcgaagaagcctgctctccat 219

Query: 121 cctacctatctcgagatgatcagtgaagcgatcgcttcgctgaaggagcggactggatcg 180 II II IIIIIIIIII i II IIIIIII1IIIIIIIIIIIIIIIIIIIIII1IIIII II I I I 1 I Sbjct: 220 cctacctatctcgagatgatcagtgaagcgatcgcttcgctgaaggagcggactggatcg 279

Query: 181 agccagtacgctattgcgaagtttgttgaagacaagcacaagtctcatctcccggcgaac 240 111111111111111111111111111111111111111111111111111111111111 Sbjct: 280 agccagtacgctattgcgaagtttgttgaagacaagcacaagtctcatctcccggcgaac 339

Query: 241 ttcaagaagcttctccttgtccagttgcagaaactcactgctgctggcaaactcacgaag 300 111111111111111111111111111111111111111111111111111111111111 Sbjct: 340 ttcaagaagcttctccttgtccagttgcagaaactcactgctgctggcaaactcacgaag 399

Query: 301 gtgaagaattcctacaagatctctgccaaaccaacccctgctgcgaagcctaaatccgct 360 111111111111111111111111111111111111111111111111111111111111 Sbjct: 400 gtgaagaattcctacaagatctctgccaaaccaacccctgctgcgaagcctaaatccgct 459

Query: 361 gctgtgaagccaaagtctgctgctactaaactcaagtccgctgccaagaaggtgaagaaa 420 11111111111111111111111111111111111111111111111111111111I111 Sbjct: 460 gctgtgaagccaaagtctgctgctactaaactcaagtccgctgccaagaaggtgaagaaa 519

Query: 421 gcagctgtgaagccaaagcctaaatctgctgccgtgaagccaaaagcccctgccgtgaaa 480 111111 i 1111111111111111111111111111111111111111111111111111 Sbjct: 520 gcagctgtgaagccaaagcctaaatctgctgccgtgaagccaaaagcccctgccgtgaac 579 170

Query: 481 ccgaaatccaagcctgctgccctgaagccaaatacagtgacaaaatcaaagactgtagct 540 1111111111111111111111111111111111111111111111111111111111 Sbjct: 580 atgaaatccaagcctgctgccctgaagccaaatacagtgacaaaatcaaagactgtagct 639

Query: 541 ctgaagggaaagactgctggccgtccagcaaaggcggcaaagacatccgtcaaagctgct 600 111I1111 1I1111111111111111111111111111111111111111111111111 Sbjct: 640 ctgaaggggaagactgctggccgtccagcaaaggcggcaaagacatccgtcaaagctgct 699

Query: 601 ccgggaaagaaggctgctccagtggctctgaagaaggctaag 642 111111111111111111111111111111111111111111 Sbjct: 700 ccgggaaagaaggctgctccagtggctctgaagaaggctaag 741 171

4. Intron Exon Structure of histone-like gene and new histone-like gene from Fritillaria liliacea.

(Section in bold represents the intron.)

Histone-like protein #101 CGAAGAAGCC TGCTCTCCAT CCTACCTATC TYGAGGTCTG ATCCAGCCAC

Histone-like protein #151 TATTTCCTCT AGATTTGTTA ATTTATYGAA TTTGTGCAGT CCAAATTTGT

Histone-like protein #201 GTACTTCCWC YAGATCTGTT AATTTATTGA ATTTATGCAG TCCAATTTTG

Histone-like protein #251 TGTACTTCCT CTAGATTTGT TAATTTATGA AATTAATGTA GTCTAATTTG

New histone-like protein #1 TGA GGTACCAGAT CCCAATTTGA AATCTCAGAT

Histone-like protein #301 GTCTACTTTC TAAATCTCAG ATGATCAGTG AAGCGATYGC TTCGCTGAAG

New histone-like protein #34 GATCCGTGAG ATGATATGAG ATGATAGCGT CCCTGAAGGA GAGGATCGGG

Histone-like protein #351 GAGCGGACTG GATCGAGCCA GTACGCTATT GCAAAGTTTG TTGAAGACAA

New histone-like protein #84 TCAAGCCACT ATGCAATCTC AAAGTT......

Histone-like protein #401 GCACAAGTCT CATCTCCCGG CGAACTTCAA GAAGCTTCTC CTTGTCCAGT

Histone-like protein #451 TGCGGAARCT CACTGCTGCT GGCAARCTCA CRAAGGTGAA GAAYTCCTAC