DOCSLIB.ORG

High Gene Density Is Conserved at Syntenic Loci of Small and Large Grass Genomes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
High Gene Density Is Conserved at Syntenic Loci of Small and Large Grass Genomes Proc. Natl. Acad. Sci. USA Vol. 96, pp. 8265–8270, July 1999 Plant Biology High gene density is conserved at syntenic loci of small and large grass genomes CATHERINE FEUILLET AND BEAT KELLER* Institute of Plant Biology, University of Zu¨rich, Zollikerstrasse 107, CH-8008 Zu¨rich, Switzerland Communicated by Ronald L. Phillips, University of Minnesota, St. Paul, MN, April 26, 1999 (received for review December 3, 1998) ABSTRACT Comparative genomic analysis at the genetic- DNA (7). These studies suggested that the discrepancy in the map level has shown extensive conservation of the gene order size of the intergenic regions in different grasses correlated between the different grass genomes in many chromosomal with the accumulation of repeated elements between the genes regions. However, little is known about the gene organization in large genome species. Very little data are available on the in grass genomes at the microlevel. Comparison of gene- gene distribution in large and complex genomes of barley and coding regions between maize, rice, and sorghum showed that wheat. In barley, a gene density of one gene every 20 kb was the distance between the genes is correlated with the genome found in the region surrounding the mlo gene (8). In wheat, size. We have investigated the microcolinearity at Lrk gene loci Gill et al. (9) demonstrated by deletion mapping that the genes in the genomes of four grass species: wheat, barley, maize, and are distributed nonrandomly in gene-rich regions at the distal rice. The Lrk genes, which encode receptor-like kinases, were end of chromosome group 1. Recently, the analysis of a found to be consistently associated with another type of genomic fragment at a starch-branching enzyme I locus on receptor-like kinase (Tak) on chromosome groups 1 and 3 in chromosome 7D in Triticum tauschii (10) showed the presence Triticeae and on chromosomes homoeologous to Triticeae of three tandemly repeated genes within 16 kb. group 3 in the other grass genomes. On Triticeae chromosome Here, we isolated and compared genomic fragments up to 23 group 1, Tak and Lrk together with genes putatively encoding kb in size surrounding the receptor-like kinase gene Lrk10 (11) NBS͞LRR proteins form a cluster of genes possibly involved on Triticeae homoeologous chromosome groups 1 and 3 in in signal transduction. Comparison of the gene composition at wheat, barley, maize, and rice. Comparison of the gene com- orthologous Lrk loci in wheat, barley, and rice revealed a position and organization at both chromosomal locations maximal gene density of one gene per 4–5 kb, very similar to revealed at the microlevel the presence of gene-rich regions in the gene density in Arabidopsis thaliana. We conclude that the different grass genomes and indicated the emergence of small and large grass genomes contain regions that are highly different receptor-like kinase gene families during evolution. enriched in genes with very little or no repetitive DNA. The The finding of high-gene-density regions independent of the comparison of the gene organization suggested various ge- genome size is of importance for map-based cloning in large nome rearrangements during the evolution of the different genomes. grass species. MATERIALS AND METHODS The extensive contiguous genomic sequencing of the dicot model species Arabidopsis thaliana (1) has shown that the gene ␭ and Yeast Artificial Chromosome (YAC) Library Screen- density is of about one gene every 4–5 kb (2). However, A. ing. Genomic libraries from wheat (Triticum aestivum, var. thaliana has a small genome and low amount of repetitive DNA ThatcherLr10) and barley (Hordeum vulgare, var. Igri) (Strat- compared with other plant species with more complex ge- agene) were screened with the 32P-labeled pLrk10-A wheat nomes. Grass genomes are highly variable in size, ranging from probe (12) under high (65°C) stringency. The barley genomic diploid species with 415 Mb in rice to 16,000 Mb in the library was also screened under high stringency with a 32P- hexaploid wheat. The accumulation of repetitive sequences, labeled 610-bp HindIII͞EcoRV fragment of the wheat clone which can represent up to 80%, such as in wheat (3), raises the 3ASLrk. Genomic libraries from rice (Oryza sativa, var. IR36) question of the gene distribution in these complex genomes. and maize (Zea mays, var. B73) (CLONTECH) were screened Comparative mapping studies have established syntenic rela- with the 32P-labeled pLrk10-A probe under low (50°C) strin- tionships between the different chromosome groups in the gency. A barley (H. vulgare, var. Franka) YAC library grass genomes (4). Most of these studies have been performed (MALTAGEN) was screened by PCR by using primers (5Ј- at the genetic map level, and little is known about the GGAAGTTAGCATGCTCGG-3Ј and 5Ј-CATACCGCCAG- consequences of the evolutionary divergence on the gene GCATACAG-3Ј) designed in conserved sequences of the composition and organization at the molecular level. Recent extracellular domain of the Hv1Lrk1 and Hv1Lrk2 genes. The analysis of large, orthologous genomic fragments from maize, YAC sublibrary was constructed in ␭ZAPII (Stratagene) rice, and sorghum genomes demonstrated that the gene density according to Whittaker and Rakesh (13). The library was varies in correlation with the genome size. Indeed, at the screened with the 32P-labeled probe pLrk10-A as well as probes Sh2͞A1 region, the intergenic regions were about 7 times corresponding to the nucleotide-binding site (NBS) regions of longer in maize compared with the orthologous regions in rice HV1LRR1 and HV1LRR2. The NBS region of HV1LRR1 was and sorghum (5). At the Adh1͞u22 locus, the genes were obtained by PCR amplification on Hv1Lrr1 (AF108008) with separated by more than 120 kb in maize, whereas the ortholo- the primers 5Ј-CACTCTTGTTGATCATGTGT-3Ј and 5Ј- gous genes in sorghum were only 50 kb apart (6). Molecular analysis of 280 kb at the maize Adh1 locus demonstrated the Abbreviations: NBS, nucleotide-binding site; LRR, leucine-rich re- presence of 10 retroelement families representing 60% of the peats; YAC, yeast artificial chromosome. Data deposition: The sequences reported in this paper have been The publication costs of this article were defrayed in part by page charge deposited in the GenBank database (accession nos. U76215, U78762, AF085164–AF085169, AF100764–AF100771, and AF108008– payment. This article must therefore be hereby marked ‘‘advertisement’’ in AF108015). accordance with 18 U.S.C. §1734 solely to indicate this fact. *To whom reprint requests should be addressed. e-mail: bkeller@ PNAS is available online at www.pnas.org. botinst.unizh.ch. 8265 Downloaded by guest on September 25, 2021 8266 Plant Biology: Feuillet and Keller Proc. Natl. Acad. Sci. USA 96 (1999) AAGCTGACCTTTAGGATC-3Ј. The NBS region of nucleotide sequence level with RPM1, a resistance gene from HV1LRR2 consisted of a EcoRI͞NotI fragment of 1.4 kb A. thaliana against a bacterial disease (15). RPM1 belongs to isolated from Hv1Lrr2 (AF108010). the resistance gene class encoding intracellular NBS͞LRR Sequence Analysis. Sequencing reactions were performed types of proteins. However, ␺Lrr10 (U76215) is probably a with the Thermo Sequenase cycle sequencing kit (Amersham) pseudogene because the coding sequence for the first 70 aa at according to the instructions of the manufacturer and subse- the N-terminal sequence is lacking compared with RPM1.In quently were run on an automatic DNA sequencer. The addition, there is a frameshift mutation at position 943 and an sequences were analyzed with GCG software (Wisconsin in-frame stop codon at position 1327. Thus, within 14 kb, at the Package), BCM GENEFINDER software, and the BLAST program locus encoding the leaf rust-resistance gene Lr10 (11) on of the National Center for Biotechnology Information (http:͞͞ chromosome 1AS, there are two genes encoding receptor-like www.ncbi.nlm.nih.gov͞). kinases and one pseudogene homologous to resistance genes. Genetic Mapping. Linkage analysis in wheat and barley was To compare the conservation of gene organization between performed as described previously (14). Mapping in maize was the Triticeae genomes, we isolated the corresponding region performed on 56 F2 plants from a cross between the inbred from barley. Under high stringency, the extracellular domain lines Tx303 and CO159 at the University of Missouri– of Lrk10 (pLrk10-A) hybridized with two unique XbaI frag- Columbia. ments that cosegregated on barley chromosome 1HS (14). We screened a barley genomic library and isolated fragments RESULTS corresponding to the two loci (XHv1.1 and XHv1.2) detected by Southern hybridization (Fig. 1b). DNA stretches of 23 and A Cluster of Receptor-Like Kinase Genes Is Located in a 5 kb were sequenced at the XHv1.1 and XHv1.2 loci, respec- Gene-Rich Region on Wheat and Barley Chromosome Group tively. At the XHv1.1 locus, we detected two genes, Hv1Lrk1 1. To investigate the gene density and gene organization at the and Hv1Tak1, homologous to Lrk10 and Tak10, respectively. Lrk10 locus (11) in wheat, a genomic fragment of 13,887 bp Similarly, two genes, Hv1Lrk2 and Hv1Tak2, were found at the (␭W1AS) containing the Lrk10 gene was isolated and char- XHv1.2 locus (Fig. 1b). The relative orientation of the Hv1Lrk acterized. Two additional genes were found upstream from and Hv1Tak genes was identical to the gene organization found Lrk10 (Fig. 1a). At a 620-bp distance from the Lrk10 transla- on wheat chromosome 1AS (Fig. 1a), i.e., Hv1Lrk and Hv1Tak tion start site, a second gene encoding another receptor-like genes were found in opposite orientation (Fig. 1b). Compar- kinase (Tak10, U78762) starts in reverse orientation. The ison of both barley Hv1LRK1͞Hv1LRK2 and Hv1TAK1͞ TAK10 protein showed high homology (68%) to LRK10 in the Hv1TAK2 proteins with the wheat LRK10 and TAK10, re- Ser͞Thr kinase domain. In addition, the Tak10 gene contains spectively, showed up to 79% homology at the amino acid level.
Load more

Recommended publications
  • Genome Sequence of the Progenitor of the Wheat D Genome Aegilops Tauschii Ming-Cheng Luo1*, Yong Q
    OPEN LETTER doi:10.1038/nature24486 Genome sequence of the progenitor of the wheat D genome Aegilops tauschii Ming-Cheng Luo1*, Yong Q. Gu2*, Daniela Puiu3*, Hao Wang4,5,6*, Sven O. Twardziok7*, Karin R. Deal1, Naxin Huo1,2, Tingting Zhu1, Le Wang1, Yi Wang1,2, Patrick E. McGuire1, Shuyang Liu1, Hai Long1, Ramesh K. Ramasamy1, Juan C. Rodriguez1, Sonny L. Van1, Luxia Yuan1, Zhenzhong Wang1,8, Zhiqiang Xia1, Lichan Xiao1, Olin D. Anderson2, Shuhong Ouyang2,8, Yong Liang2,8, Aleksey V. Zimin3, Geo Pertea3, Peng Qi4,5, Jeffrey L. Bennetzen6, Xiongtao Dai9, Matthew W. Dawson9, Hans-Georg Müller9, Karl Kugler7, Lorena Rivarola-Duarte7, Manuel Spannagl7, Klaus F. X. Mayer7,10, Fu-Hao Lu11, Michael W. Bevan11, Philippe Leroy12, Pingchuan Li13, Frank M. You13, Qixin Sun8, Zhiyong Liu8, Eric Lyons14, Thomas Wicker15, Steven L. Salzberg3,16, Katrien M. Devos4,5 & Jan Dvořák1 Aegilops tauschii is the diploid progenitor of the D genome of We conclude therefore that the size of the Ae. tauschii genome is about hexaploid wheat1 (Triticum aestivum, genomes AABBDD) and 4.3 Gb. an important genetic resource for wheat2–4. The large size and To assess the accuracy of our assembly, sequences of 195 inde- highly repetitive nature of the Ae. tauschii genome has until now pendently sequenced and assembled AL8/78 BAC clones8, which precluded the development of a reference-quality genome sequence5. contained 25,540,177 bp in 2,405 unordered contigs, were aligned to Here we use an array of advanced technologies, including ordered- Aet v3.0. Five contigs failed to align and six extended partly into gaps, clone genome sequencing, whole-genome shotgun sequencing, accounting for 0.25% of the total length of the contigs.
    [Show full text]
  • Genomes:Genomes: Whatwhat Wewe Knowknow …… Andand Whatwhat Wewe Don’Tdon’T Knowknow
    Genomes:Genomes: WhatWhat wewe knowknow …… andand whatwhat wewe don’tdon’t knowknow Complete draft sequence 2001 OctoberOctober 15,15, 20072007 Dr.Dr. StefanStefan Maas,Maas, BioSBioS Lehigh Lehigh U.U. © SMaas 2007 What we know Raw genome data © SMaas 2007 The range of genome sizes in the animal & plant kingdoms !! NoNo correlationcorrelation betweenbetween genomegenome sizesize andand complexitycomplexity © SMaas 2007 What accounts for the often massive and seemingly arbitrary differences in genome size observed among eukaryotic organisms? The fruit fly The mountain grasshopper Drosophila melanogaster Podisma pedestris 180 Mb 18,000 Mb The difference in genome size of a factor of 100 is difficult to explain in view of the apparently similar levels of evolutionary, developmental and behavioral complexity of these organisms. © SMaas 2007 ComplexityComplexity doesdoes notnot correlatecorrelate withwith genomegenome sizesize 3.4 × 10 9 bp 6.7 × 1011 bp Homo sapiens Amoeba dubia © SMaas 2007 ComplexityComplexity doesdoes notnot correlatecorrelate withwith genegene numbernumber ~31,000~31,000 genesgenes ~26,000~26,000 genesgenes ~50,000~50,000 genesgenes © SMaas 2007 IsIs anan ExpansionExpansion inin GeneGene NumberNumber drivingdriving EvolutionEvolution ofof HigherHigher Organisms?Organisms? Vertebrata 30,000 Urochordata 16,000 Arthropoda 14,000 Nematoda 21,000 Fungi 2,000 – 13,000 Vascular plants 25,000 – 60,000 Unicellular sps. 5,000 – 10,000 Prokaryotes 500 - 7,000 © SMaas 2007 Structure of DNA Watson and Crick in 1953 proposed that DNA is a double helix in which the 4 bases are base paired, Adenine (A) with Thymine (T) and Guanine (G) with Cytosine (C). © SMaas 2007 © SMaas 2007 © SMaas 2007 Steps in the folding of DNA to create an eukaryotic chromosome 30 nm fiber (6 nucleosomes per turn) FactorFactor ofof condensation:condensation: Ca.Ca.
    [Show full text]
  • Saccharomyces Cerevisiae
    letters to nature 19Department of Yeast Genetics, Institute of Molecular Medecine, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK The nucleotide sequence of 20L.N.C.I.B., Area Science Park, Padriciano 99, I-34012 Trieste, Italy 21GATC GmbH, Fitz-Arnold-Strasse 23, 78467 Konstanz, Germany Saccharomyces cerevisiae 22Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark chromosome IV 23AGON GmbH, Glienicker Weg 185, D-12489 Berlin, Germany 24Katholieke Universiteit Leuven, Laboratory of Gene Technology, Willem de C. Jacq1, J. Alt-Mörbe2, B. Andre3, W. Arnold4, A. Bahr5, Croylaan, 42, B-3001 Leuven, Belgium J. P. G. Ballesta6, M. Bargues7, L. Baron8, A. Becker4, N. Biteau8, 25The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge H. Blöcker9, C. Blugeon1, J. Boskovic6, P. Brandt9, M. Brückner10 , CB10 1SA, UK M. J. Buitrago11 , F. Coster12, T. Delaveau1, F. del Rey11 , B. Dujon13, 26Department of Biochemistry, Stanford University, Beckman Center, Stanford L. G. Eide14, J. M. Garcia-Cantalejo6, A. Goffeau12, A. Gomez-Peris15, CA 94305-5307, USA C. Granotier8, V. Hanemann16, T. Hankeln5, J. D. Hoheisel17, W. Jäger9, 27The Genome Sequencing Center, Department of Genetics, Washington University, A. Jimenez6, J.-L. Jonniaux12, C. Krämer5, H. Küster4, P. Laamanen18, School of Medicine, 630 S. Euclid Avenue, St Louis, Missouri 63110, USA Y. Legros8, E. Louis19, S. Möller-Rieker5, A. Monnet8, M. Moro20, 28Martinsrieder Institut für Protein Sequenzen, Max-Planck-Institut für S. Müller-Auer10 , B. Nußbaumer4, N. Paricio7, L. Paulin18, J. Perea1, Biochemie, D-82152 Martinsried bei München, Germany. M. Perez-Alonso7, J. E. Perez-Ortin15, T. M. Pohl21, H. Prydz14, B.
    [Show full text]
  • Improved Maize Reference Genome with Single-Molecule Technologies Yinping Jiao1, Paul Peluso2, Jinghua Shi3, Tiffany Liang3, Michelle C
    OPEN LETTER doi:10.1038/nature22971 Improved maize reference genome with single-molecule technologies Yinping Jiao1, Paul Peluso2, Jinghua Shi3, Tiffany Liang3, Michelle C. Stitzer4, Bo Wang1, Michael S. Campbell1, Joshua C. Stein1, Xuehong Wei1, Chen-Shan Chin2, Katherine Guill5, Michael Regulski1, Sunita Kumari1, Andrew Olson1, Jonathan Gent6, Kevin L. Schneider7, Thomas K. Wolfgruber7, Michael R. May8, Nathan M. Springer9, Eric Antoniou1, W. Richard McCombie1, Gernot G. Presting7, Michael McMullen5, Jeffrey Ross-Ibarra10, R. Kelly Dawe6, Alex Hastie3, David R. Rank2 & Doreen Ware1,11 Complete and accurate reference genomes and annotations provide research, which will enable increases in yield to feed the growing world fundamental tools for characterization of genetic and functional population. The current assembly of the maize genome, based on variation1. These resources facilitate the determination of biological Sanger sequencing, was first published in 2009 (ref. 3). Although this processes and support translation of research findings into initial reference enabled rapid progress in maize genomics1, the origi- improved and sustainable agricultural technologies. Many reference nal assembly is composed of more than 100,000 small contigs, many genomes for crop plants have been generated over the past decade, of which are arbitrarily ordered and oriented, markedly complicating but these genomes are often fragmented and missing complex detailed analysis of individual loci6 and impeding investigation of inter- repeat regions2. Here we report the assembly and annotation of a genic regions crucial to our understanding of phenotypic variation7,8 reference genome of maize, a genetic and agricultural model species, and genome evolution9,10. using single-molecule real-time sequencing and high-resolution Here we report a vastly improved de novo assembly and annotation optical mapping.
    [Show full text]
  • Apis Mellifera)
    COMPUTATIONAL ANALYSIS OF DIFFICULT-TO-PREDICT GENES AND DETECTION OF LINEAGE-SPECIFIC GENES IN HONEY BEE (APIS MELLIFERA) A Dissertation submitted to the Faculty of the Graduate School of Arts and Sciences of Georgetown University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology. By Anna K. Bennett, M.S. Washington, DC July 29, 2013 Copyright 2013 by Anna K. Bennett All Rights Reserved ii COMPUTATIONAL ANALYSIS OF DIFFICULT-TO-PREDICT GENES AND DETECTION OF LINEAGE-SPECIFIC GENES IN HONEY BEE (APIS MELLIFERA) Anna K. Bennett, M.S. Thesis Advisor: Christine G. Elsik, Ph.D. ABSTRACT Honey bees are key agricultural pollinators and a research model for social behavior and the evolution of eusociality. Generation of reliable gene predictions is critical to the success of laboratory experiments and comparative analyses for sequenced genomes. The honey bee genome, published in 2006 by the Honey Bee Genome Sequencing Consortium, had fewer predicted genes than expected, partially due to a lack of transcriptome data and protein homologs from closely related species. As part of ongoing Consortium efforts, genomes of two closely related taxa were sequenced, dwarf honey bee (Apis florea) and buff-tailed bumble bee (Bombus terrestris), the draft A. mellifera genome was improved with additional sequence, and multiple A. mellifera tissue transcriptomes were sequenced. The Consortium predicted genes using seven methods and used these data to produce an improved official gene set (OGSv3.2) with ~5000 more protein-coding genes than the first set (OGSv1.0). We present our approach to detect previously unknown genes in A.
    [Show full text]
  • Genome-Wide Analysis of Admixture and Adaptation in the Africanized Honeybee
    Nelson, R. M., Wallberg, A., Simões, Z. L. P., Lawson, D. J., & Webster, M. T. (2017). Genome-wide analysis of admixture and adaptation in the Africanized honeybee. Molecular Ecology, 26(14), 3603-3617. https://doi.org/10.1111/mec.14122 Peer reviewed version License (if available): CC BY-NC Link to published version (if available): 10.1111/mec.14122 Link to publication record in Explore Bristol Research PDF-document This is the author accepted manuscript (AAM). The final published version (version of record) is available online via Wiley at https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14122 . Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ Genome-wide analysis of admixture and adaptation in the Africanized honeybee Ronald M. Nelson1, Andreas Wallberg1, Zilá Luz Paulino Simões2, Daniel J. Lawson3, Matthew T. Webster1* 1. Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. 2. Department of Biology, University of São Paulo, São Paulo, Brazil. 3. Department of Mathematics, University of Bristol, Bristol, United Kingdom. Keywords: Africanized honeybee, admixture, introgression, adaptation, biological invasion, natural selection *[email protected] Running title: Adaptation in Africanized honeybees 1 Abstract Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments.
    [Show full text]
  • Recombination in Diverse Maize Is Stable, Predictable, and Associated with Genetic Load
    Recombination in diverse maize is stable, predictable, and associated with genetic load Eli Rodgers-Melnicka,1, Peter J. Bradburya,b,1, Robert J. Elshirea, Jeffrey C. Glaubitza, Charlotte B. Acharyaa, Sharon E. Mitchella, Chunhui Lic, Yongxiang Lic, and Edward S. Bucklera,b aInstitute for Genomic Diversity, Cornell University, Ithaca, NY 14853; bUS Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and cInstitute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China Edited by Qifa Zhang, Huazhong Agricultural University, Wuhan, China, and approved February 6, 2015 (received for review July 21, 2014) Among the fundamental evolutionary forces, recombination ar- On a molecular level, chromatin structure heavily influences guably has the largest impact on the practical work of plant the cross-over rate in plants. Not only are heterochromatic breeders. Varying over 1,000-fold across the maize genome, the regions generally depleted of cross-overs (11), but KO of cytosine- local meiotic recombination rate limits the resolving power of DNA-methyl-transferase (MET1)inArabidopsis thaliana leads quantitative trait mapping and the precision of favorable allele to both genome-wide CpG hypomethylation and a relative in- introgression. The consequences of low recombination also theo- crease in the proportion of cross-overs within the euchromatic – retically extend to the species-wide scale by decreasing the power chromosomal arms (12 14). Nucleotide content may also be as- of selection relative to genetic drift, and thereby hindering the sociated with the local frequency of recombination, potentially purging of deleterious mutations. In this study, we used genotyp- due to the effect of GC-biased gene conversion (bGC) during res- ing-by-sequencing (GBS) to identify 136,000 recombination break- olution of heteroduplexes that form at cross-over junctions (15).
    [Show full text]
  • Co-Expression of Neighboring Genes in the Zebrafish (Danio Rerio) Genome
    Int. J. Mol. Sci. 2009, 10, 3658-3670; doi:10.3390/ijms10083658 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome Huai-Kuang Tsai 1, Pei-Ying Huang 2, Cheng-Yan Kao 2 and Daryi Wang 3,* 1 Institute of Information Science, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, 115, Taipei, Taiwan; E-Mail: [email protected] (H.-K.T.) 2 Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan; E-Mails: [email protected] (P.-Y.H.); [email protected] (C.-Y.K.) 3 Biodiversity Research Center, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, 115, Taipei, Taiwan * Author to whom correspondence should be addressed; E-Mail: [email protected] (D.W.); Tel. +886-2-27890159; Fax: +886-2-27829624. Received: 14 July 2009; in revised form: 11 August 2009 / Accepted: 20 August 2009 / Published: 21 August 2009 Abstract: Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson’s correlation coefficient R>0.7) is low (0.24% ~ 0.67%); however, it is still significantly higher than that of random pairs.
    [Show full text]
  • Ceranae, an Emergent Pathogen of Honey Bees
    Genomic Analyses of the Microsporidian Nosema ceranae, an Emergent Pathogen of Honey Bees R. Scott Cornman1, Yan Ping Chen1, Michael C. Schatz2, Craig Street3, Yan Zhao4, Brian Desany5, Michael Egholm5, Stephen Hutchison5, Jeffery S. Pettis1, W. Ian Lipkin3, Jay D. Evans1* 1 USDA-ARS Bee Research Lab, Beltsville, Maryland, United States of America, 2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America, 3 Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America, 4 USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America, 5 454 Life Sciences/Roche Applied Sciences, Branford, Connecticut, United States of America Abstract Recent steep declines in honey bee health have severely impacted the beekeeping industry, presenting new risks for agricultural commodities that depend on insect pollination. Honey bee declines could reflect increased pressures from parasites and pathogens. The incidence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we present a draft assembly (7.86 MB) of the N. ceranae genome derived from pyrosequence data, including initial gene models and genomic comparisons with other members of this highly derived fungal lineage. N. ceranae has a strongly AT-biased genome (74% A+T) and a diversity of repetitive elements, complicating the assembly. Of 2,614 predicted protein-coding sequences, we conservatively estimate that 1,366 have homologs in the microsporidian Encephalitozoon cuniculi, the most closely related published genome sequence. We identify genes conserved among microsporidia that lack clear homology outside this group, which are of special interest as potential virulence factors in this group of obligate parasites.
    [Show full text]
  • Genome-Wide Analysis of Local Chromatin Packing in Arabidopsis Thaliana
    Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Research Genome-wide analysis of local chromatin packing in Arabidopsis thaliana Congmao Wang,1,3 Chang Liu,1,3 Damian Roqueiro,2 Dominik Grimm,2 Rebecca Schwab,1 Claude Becker,1 Christa Lanz,1 and Detlef Weigel1 1Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen,€ Germany; 2Machine Learning and Computational Biology Research Group, Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tubingen,€ Germany The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs.
    [Show full text]
  • Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts
    International Journal of Molecular Sciences Article Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts 1,2, 1, 1 1,2 1 Neetika Nath y , Lisa Hagenau y , Stefan Weiss , Ana Tzvetkova , Lars R. Jensen , Lars Kaderali 2 , Matthias Port 3, Harry Scherthan 3 and Andreas W. Kuss 1,* 1 Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; [email protected] (N.N.); [email protected] (L.H.); [email protected] (S.W.); [email protected] (A.T.); [email protected] (L.R.J.) 2 Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany; [email protected] 3 Bundeswehr Institute for Radiobiology Affiliated to the University of Ulm, 80937 München, Germany; [email protected] (M.P.); [email protected] (H.S.) * Correspondence: [email protected]; Tel.: +49-3834-420-5814 These authors contributed equally. y Received: 8 July 2020; Accepted: 31 July 2020; Published: 12 August 2020 Abstract: While ionizing radiation (IR) is a powerful tool in medical diagnostics, nuclear medicine, and radiology, it also is a serious threat to the integrity of genetic material. Mutagenic effects of IR to the human genome have long been the subject of research, yet still comparatively little is known about the genome-wide effects of IR exposure on the DNA-sequence level. In this study, we employed high throughput sequencing technologies to investigate IR-induced DNA alterations in human gingiva fibroblasts (HGF) that were acutely exposed to 0.5, 2, and 10 Gy of 240 kV X-radiation followed by repair times of 16 h or 7 days before whole-genome sequencing (WGS).
    [Show full text]
  • Saccharomyces Cerevisiae HOWARD BUSSEY*T, DAVID B
    Proc. Natl. Acad. Sci. USA Vol. 92, pp. 3809-3813, April 1995 Genetics The nucleotide sequence of chromosome I from Saccharomyces cerevisiae HOWARD BUSSEY*t, DAVID B. KABACKI, WUWEI ZHONG*, DAHN T. Vo*, MICHAEL W. CLARK*, NATHALIE FORTIN*, JOHN HALL*, B. F. FRANCIs OUELLETTE*, TERESA KENG§, ARNOLD B. BARTONI, YUPING SUt, CHRIS J. DAVIESt, AND REG K. STORMS*II *Yeast Chromosome I Project, Biology Department, McGill University, Montreal, QC, Canada H3A lB1; *Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey-New Jersey Medical School, Newark, NJ 07103; §Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada H3A 2B4; 1Department of Biology, University of North Carolina, Chapel Hill, NC 27599; and I1Biology Department, Concordia University, Montreal, QC, Canada H3G 1M8 Communicated by Phillips W Robbins, Massachusetts Institute of Technology, Cambridge, MA, January 12, 1995 ABSTRACT Chromosome I from the yeast Saccharomyces plates for DNA sequencing. These were the library of Riles et cerevisiae contains a DNA molecule of -231 kbp and is the aL (8), a cosmid from the collection of Dujon (9), chromosome smallest naturally occurring functional eukaryotic nuclear walking (10), and PCR amplified fragments of genomic DNA. chromosome so far characterized. The nucleotide sequence of DNA fragments, except those generated by PCR which were this chromosome has been determined as part of an interna- used directly, were subcloned into the Bluescript KS(+) plas- tional collaboration to sequence the entire yeast genome. The mid from Stratagene prior to sequencing. All DNA sequencing chromosome contains 89 open reading frames and 4 tRNA was performed using double-stranded DNA templates.
    [Show full text]