Genetics Introduction

Total Page:16

File Type:pdf, Size:1020Kb

Genetics Introduction Genetics Introduction Inheritance Patterns Mendel was the first scientist to develop a method for predicting the outcome of inheritance patterns. He performed his work with pea plants, studying seven traits: plant height, pod shape, pod color, seed shape, seed color, flower color, and flower location. Pea plants pollinate themselves. Therefore, over many generations, pea plants develop individuals that are homozygous for particular characteristics. These populations are known as pure lines. In his work, Mendel took pure-line pea plants and cross-pollinated them with other pure-line pea plants. He called these plants the parent generation. When Mendel crossed pure-line tall plants with pure-line short plants, he discovered that all the plants resulting from this cross were tall. He called this generation the F1 generation (first filial generation). Next, Mendel crossed the offspring of the F1 generation tall plants among themselves to produce a new generation called the F2 generation (second filial generation). Among the plants in this generation, Mendel observed that three-fourths of the plants were tall and one-fourth of the plants were short. Mendel's laws of genetics Mendel conducted similar experiments with the other pea plant traits. Over many years, he formulated several principles that are known today as Mendel's laws of genetics. His laws include the following: 1. Mendel's law of dominance: When an organism has two different alleles for a trait, one allele dominates. 2. Mendel's law of segregation: During gamete formation by a diploid organism, the pair of alleles for a particular trait separate, or segregate, during the formation of gametes (as in meiosis). 3. Mendel's law of independent assortment: The members of a gene pair separate from one another independent of the members of other gene pairs. (These separations occur in the formation of gametes during meiosis.) Genetics Part - I DNA replication, transcription and translation. In very general terms, what does a chromosome contain? • Information, genetic information to carry out the characteristics of life -- precise self replication, ability to exchange energy with the environment, etc. In very general terms, what are the two related functions of DNA? • Information storage • DNA replication • Information transfer • DNA transcribed into RNA • DNA's function in information transfer What is the Central Dogma associated with information storage and retrieval? • Central Dogma: DNA-->RNA-->unfolded protein-->native, folded protein What are the three processes of the central dogma? How does DNA function as an information molecule? • replication, DNA --> DNA • transcription, DNA --> RNA • translation, RNA --> unfolded protein --> folded protein In terms of molecular conformation, what occurs through the central dogma? • Translation of linear information, a sequence of nucleotides, into 3-D information, the structure of a protein. What are the differences between DNA and RNA? • base composition: RNA = AGCU, DNA = AGCT • carbohydrate: RNA = ribose, DNA = deoxyribose • structure: RNA = single stranded, DNA = double helix RNA • usually single stranded • linear polymer of ribonucleotides. • Some secondary and tertiary structure but often ill-defined. What are the different types of RNA? What are the functions of the different types of RNA? • messenger RNA = mRNA, information transfer • transfer RNA = tRNA, information transfer • ribosomal RNA = rRNA, structural • small nuclear RNA = snRNA, ribozymes, RNA processing. What is replication? Transfer of genetic information from one generation to the next. DNA-directed DNA synthesis: replication of the genome. What is the structural basis for the precise duplication of the genome? • The Watson-Crick structure of DNA: the strands are complementary, the nucleotide sequence in one automatically specifies the other. • The enzyme, DNA polymerase III, is very accurate: it has proof reading capabilities. Is replication conservative or semi-conservative? What does that mean? • Is the parental genome of double stranded DNA fully conserved in the parental cell or is it split equally (semi- conserved) between two daughter cells? • Replication is semi-conservative. Genetics Part - II What is the evidence for semi-conservative replication? Classical experiments of Meselson and Stahl. Label DNA with *heavy isotope* N15 and allow replication in light N14: distinguish heavy, light and hybrid DNA by centrifugation. Results: after 1 generation, each genome contains a hybrid N15-N14 DNA; after 2 generations, there are 2 hybrid and 2 light (N14-N14) genomes. • Each strand of DNA serves as a template for the synthesis of its complement. • The strands separate and each is used as a template for the synthesis of a daughter strand. • The two new double helices each contain half the parental DNA. • This process produces a replication fork Is replication uni-directional or bi-directional? • Bi-directional • Two replication forks proceeding from the origin. DNA replication, transcription and translation. What is the major replication enzyme? DNA polymerase III, a DNA-directed DNA polymerase • Synthesis is 5'-->3' • Substrates are deoxynucleoside triphosphates (to make deoxyribonucleic acid) • Proof reading , errors removed by 3'--5' exonuclease • Processivity is very high (the ability of the enzyme to replicate a large tract of DNA before *falling* off) • Replication requires DNA unwinding by enzymes termed helicases: these enzymes unwind the DNA helix before the replication fork and wind it up again afterwards. There are large numbers of different enzymes and proteins involved at the replication fork in the replisome. DNA damage by UV radiation or chemicals is repaired by other DNA polymerases. UV-damage results in adjacent T residues in one strand becoming covaletly linked to each other, producing a thymine dimer. This causes the double helix to become distorted -- kinky. Xeroderma pigmentosa is a genetic disorder in which patients cannot carry out UV-radiation repair. They are very prone to skin cancer from an early age. What is Transcription? • Copying a gene as RNA • DNA-directed RNA synthesis from a gene What is a gene? • There is no good definition of a gene! • A sequence of DNA that is transcribed from specific start to specific stop base sequences. • Beadle and Tatum, working with the eukaryote mold Neurospora crassa, concluded that one gene codes for one protein. • But what about genes that code for RNA's like rRNA and tRNA? • A gene is a sequence of DNA that is transcribed into a single RNA as defined by specific start and stop sequences of bases. • Note the circularity of the argument! • But the single RNA may be polycistronic! What does that mean? • A cistron is synonymous with a gene. • A polycistronic RNA results from the transcription of an operon. DNA replication, transcription and translation. What's an operon? • A genetic unit containing several genes with related functions: the bacterial operon for lactose (milk sugar) metabolism contains 3 genes coding for 3 different proteins. • An operon is transcribed as a single unit, a polycistronic messenger RNA (mRNA) that codes for more than one gene product. Name 4 types of RNA. What are their functions? • mRNA, messenger RNA that is translated into protein • rRNA, ribosomal RNA that, together with ribosomal proteins, forms a structural scaffold for the translation of mRNA, the ribosome • tRNA, transfer RNA, a specific carrier of amino acids • snRNA, small nuclear RNA involved in processing of mRNA in the nucleus What is the major transcription enzyme? RNA polymerase, a DNA-directed RNA polymerase • RNA synthesis is 5'-->3' • substrates are ribonucleoside triphosphates ( to make ribonucleic acid) • begins at the promoter, 5' end of the gene • processivity is very high, proceeds to 3' end of gene without stopping or falling off the gene • proof reading by precise Watson-Crick base pairing, A=U and G=C Regulation of transcription of a gene is at the 5'-end of the gene at region(s) termed operators • Transcription of some genes is constitutive = housekeeping genes • Transcription of other genes is in response to a stimulus = inducible genes Genetics Part - III What are exons and introns? • exons are coding regions, and • introns are non-coding regions of the mRNA transcript • exons and introns are found in most, but not all, eukaryote genes • introns have to be spliced out before the mRNA is translated • splicing is by snRNA's acting as enzymes, or ribozymes, an example of the catalytic function of RNA DNA replication, transcription and translation: Translation: • Synthesis of a linear polymer of amino acids from a linear polymer of nucleotides Where does it occur? On the ribosome, a rRNA-protein complex that provides: • a scaffold for mRNA • sites for the docking of tRNA charged with a specific amino acid • an enzyme for peptide bond synthesis between amino acids • an enzyme for translocation of the mRNA through the ribosome What is the function of tRNA? • Carrier of a specific amino acid during translation What is the structure of tRNA? • secondary structure has some base-pairing --> cloverleaf • information transfer at the anti-codon loop, complementary to the codon • note the importance of H-bonds in the genetic code • tertiary structure is L-shaped which places the amino acid far from the codon-anticodon site • degeneracy of the code produces wobble What is the genetic code? A sequence of 3 nucleotides forms a codon • unambiguous, each codon specifies an amino acid, or start, or stop
Recommended publications
  • ROXY1, a Member of the Plant Glutaredoxin Family, Is Required for Petal Development in Arabidopsis Thaliana Shuping Xing, Mario G
    Research article 1555 ROXY1, a member of the plant glutaredoxin family, is required for petal development in Arabidopsis thaliana Shuping Xing, Mario G. Rosso and Sabine Zachgo* Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany *Author for correspondence (e-mail: [email protected]) Accepted 25 January 2005 Development 132, 1555-1565 Published by The Company of Biologists 2005 doi:10.1242/dev.01725 Summary We isolated three alleles of an Arabidopsis thaliana gene and ectopic AG expression in roxy1-3 ap1-10 double named ROXY1, which initiates a reduced number of petal mutants, as well as by enhanced first whorl carpeloidy in primordia and exhibits abnormalities during further petal double mutants of roxy1 with repressors of AG, such as ap2 development. The defects are restricted to the second whorl or lug. Glutaredoxins are oxidoreductases that oxidize or of the flower and independent of organ identity. ROXY1 reduce conserved cysteine-containing motifs. Mutagenesis belongs to a subgroup of glutaredoxins that are specific of conserved cysteines within the ROXY1 protein for higher plants and we present data on the first demonstrates the importance of cysteine 49 for its function. characterization of a mutant from this large Arabidopsis Our data demonstrate that, unexpectedly, a plant gene family for which information is scarce. ROXY1 is glutaredoxin is involved in flower development, probably predominantly expressed in tissues that give rise to new by mediating post-translational modifications of target flower primordia, including petal precursor cells and petal proteins required for normal petal organ initiation and primordia. Occasionally, filamentous organs with stigmatic morphogenesis.
    [Show full text]
  • Plant Phylogenomics: Lessons from the 1KP Project!
    Plant Phylogenomics: Lessons from the 1KP Project! Jim Leebens-Mack! Department of Plant Biology! University of Georgia! New Methods for Phylogenomics and Metagenomics Symposium ! Feb, 2013! Ancestral Angiosperm/! OneKP/MSA AToL! Amborella Genome! Collaborators! Norman Wickett! Vic Albert! MonAToL! Nam Nguyen! Raj Ayyampalayam! Claude dePamphilis! Siavash Mirarab! Brad Barbazuk! Tom Givnish ! Naim Mataci! John Bowers! Cecile Ané ! Gane Ka-Shu Wong! Jim Burnette! Raj Ayyampalayam! BGI! Srikar Chamala ! Sean Graham! Eric Carpenter! Andre Chanderbali! Dennis Stevenson! Brad Ruhfel! Josh Der! Jerry Davis! Herve Philippe.! Claude dePamphils! Alejandra Gandolfo ! Gordon Burleigh! Jamie Estill! Chris Pires ! Matt Barker! Hong Ma! Norm Wickett! Claude dePamphilis! Doug & Pam Soltis! Wendy Zomlefer! Tandy Warnow! Stephan Schuster! Michael McKain! Jamie Estill! Sue Wessler! Jill Duarte! Raj Ayyampalayam! Rod Wing! Doug & Pam Soltis! Kerr Wall! Sean Graham! Norm Wickett! Funding: NSF, iPlant, University Dennis Stevenson! Eric Wafula! of Georgia, OneKP Michael Melkonian! ……OneKP Consortium! “Nothing in biology makes sense except in the light of evolution” (Theodosius Dobzhansky, 1973)! “Nothing in evolution makes sense except in the light of phylogeny”! Darwin (1837) First Notebook on Transmutation of Species! “Phylogenomics” - Jonathan Eisen (1998; Genome Research 8:163-167)! Current Usages! 1. Using genome-scale data to resolve phylogentic relationships! 2. Genome-Scale comparisons placed within a phylogenetic context! Phylogenomics1: Plastid Genome
    [Show full text]
  • Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia Longipalpis Using Genomic and Virus–Host Interaction Signatures
    viruses Article Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus–Host Interaction Signatures Paula Fonseca 1 , Flavia Ferreira 2, Felipe da Silva 3, Liliane Santana Oliveira 4,5 , João Trindade Marques 2,3,6 , Aristóteles Goes-Neto 1,3, Eric Aguiar 3,7,*,† and Arthur Gruber 4,5,8,*,† 1 Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil; [email protected] (P.F.); [email protected] (A.G-N.) 2 Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil; [email protected] (F.F.); [email protected] (J.T.M.) 3 Bioinformatics Postgraduate Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 30270-901, Brazil; [email protected] 4 Bioinformatics Postgraduate Program, Universidade de São Paulo, São Paulo 05508-000, Brazil; [email protected] 5 Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil 6 CNRS UPR9022, Inserm U1257, Université de Strasbourg, 67084 Strasbourg, France 7 Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), State University of Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16, Ilhéus 45652-900, Brazil 8 European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany * Correspondence: [email protected] (E.A.); [email protected] (A.G.) † Both corresponding authors contributed equally to this work. Citation: Fonseca, P.; Ferreira, F.; da Silva, F.; Oliveira, L.S.; Marques, J.T.; Goes-Neto, A.; Aguiar, E.; Gruber, Abstract: Hematophagous insects act as the major reservoirs of infectious agents due to their intimate A.
    [Show full text]
  • Comparative Analysis of Chloroplast Genomes Indicated Diferent Origin for Indian Tea (Camellia Assamica Cv TV1) As Compared to Chinese Tea Hukam C
    www.nature.com/scientificreports OPEN Comparative analysis of chloroplast genomes indicated diferent origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea Hukam C. Rawal1, Sangeeta Borchetia2, Biswajit Bera3, S. Soundararajan3, R. Victor J. Ilango4, Anoop Kumar Barooah2, Tilak Raj Sharma1, Nagendra Kumar Singh1 & Tapan Kumar Mondal1* Based upon the morphological characteristics, tea is classifed botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specifc origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of diferent chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a diferent group from that of China tea, indicating that TV1 might have undergone diferent domestications and hence owe diferent origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree. Tea is natural morning drink consumed by majority of the world population. Tea is a woody, perennial and highly cross-pollinated crop, so the genus is very dynamic as indicated with the recent discovery of several new species 1. At present, more than 350 species are available in this genus Camellia 2.
    [Show full text]
  • The Phylogenetic Significance of Vestured Pits in Boraginaceae
    Rabaey & al. • Vestured pits in Boraginaceae TAXON 59 (2) • April 2010: 510–516 WOOD ANATOMY The phylogenetic significance of vestured pits in Boraginaceae David Rabaey,1 Frederic Lens,1 Erik Smets1,2 & Steven Jansen3,4 1 Laboratory of Plant Systematics, Institute of Botany and Microbiology, Kasteelpark Arenberg 31, P.O. Box 2437, 3001 Leuven, Belgium 2 Netherlands Centre for Biodiversity Naturalis (section NHN), Leiden University, P.O.Box 9514, 2300 RA Leiden, The Netherlands 3 Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, Richmond, Surrey, U.K. 4 Institute of Systematic Botany and Ecology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany Author for correspondence: David Rabaey, [email protected] Abstract The bordered pit structure in tracheary elements of 105 Boraginaceae species is studied using scanning electron microscopy to examine the systematic distribution of vestured pits. Forty-three species out of 16 genera show a uniform pres- ence of this feature throughout their secondary xylem. Most vestures are small, unbranched and associated with the outer pit aperture of bordered intervessel pits. The feature is likely to have originated independently in the distantly related subfamilies Boraginoideae (tribe Lithospermeae) and Ehretioideae. The distribution of vestures in Ehretia agrees with recent molecular phylogenies: (1) species with vestured pits characterise the Ehretia I group (incl. Rotula), and (2) species with non-vestured pits belong to the Ehretia II group (incl. Carmona). The occurrence of vestured pits in Hydrolea provides additional support for excluding this genus from Hydrophylloideae, since Hydrolea is the only species of this subfamily with vestured pits. Functional advantages of vestured pits promoting parallel evolution of this conservative feature are suggested.
    [Show full text]
  • Evolution of the Insects
    CY501-C01[001-041].qxd 2/14/05 4:05 PM Page 1 quark11 Quark11:Desktop Folder: 1 DiDiversityversity and Evolution and Evolution cockroaches, but this also brings up a very important aspect INTRODUCTION about fossils, which is their proper interpretation. Evolution begets diversity, and insects are the most diverse Fossil “roachoids” from 320 MYA to 150 MYA were actually organisms in the history of life, so insects should provide pro- early, primitive relatives of living roaches that retained a found insight into evolution. By most measures of evolution- large, external ovipositor and other primitive features of ary success, insects are unmatched: the longevity of their lin- insects (though they did have a shield-like pronotum and eage, their species numbers, the diversity of their forewings similar to modern roaches). To interpret roachoids adaptations, their biomass, and their ecological impact. The or any other fossil properly, indeed the origin and extinction challenge is to reconstruct that existence and explain the of whole lineages, it is crucial to understand phylogenetic unprecedented success of insects, knowing that just the relationships. The incompleteness of fossils in space, time, veneer of a 400 MY sphere of insect existence has been peeled and structure imposes challenges to understanding them, away. which is why most entomologists have avoided studying fos- sil insects, even beautifully preserved ones. Fortunately, there Age. Insects have been in existence for at least 400 MY, and if has never been more attention paid to the phylogenetic rela- they were winged for this amount of time (as evidence sug- tionships of insects than at present (Kristensen, 1975, 1991, gests), insects arguably arose in the Late Silurian about 420 1999a; Boudreaux, 1979; Hennig, 1981; Klass, 2003), includ- MYA.
    [Show full text]
  • BORAGINACEAE the Genus Codon Was Formally Established
    78 Bothalia 35,1 (2005) Omalycus (1814) predates Calvatia Fr. (1849) by 35 years, DOMINGUEZ DE TOLEDO, L. 1993. Gasteromycetes (Eumycota) del and its adoption to cover species of Calvatia would require centra y oeste de la Argentina. I. Analisis critico de los caracteres taxonomicos, clave de los generos y orden Podaxales. Dar- a considerable number of new combinations, something winiana 32: 195-235. which is highly undesirable. Since Calvatia is already a DURIEU DE MAISONNEUVE, M.C. 1848. Exploration scientifique nomen consen’andum, it would be logical to add Omalycus de I 'Algerie 1,10. Imprimerie royale, Paris. to the list of rejected names against it, which would not pre­ FARR, E.R., LEUSSINK, J.A. & STAFLEU, F.A. (eds). 1979. Index nominum genericorum (Plantarum), vol. II. Regnum vegetabile clude the use of Omalycus for a segregate including C. 101. Bohn, Scheltema & Holkema. Utrecht. cyathiformis. A formal proposal to that effect has been sub­ GREUTER, W„ MCNEILL. J„ BARRIE. F.R., BURDET. H.M., mitted to the journal Taxon. DEMOULIN, V., FILGUEIRAS, T.S., NICOLSON. D.H., SILVA. PC., SKOG, J.E., TREHANE, P.. TURLAND, N.J. & HAWKSWORTH. D.L. 2000. International Code of Botanical AC KNO WLEDGEMENTS Nomenclature (Saint Louis Code) Regnum Vegetabile 138. Koeltz Scientific Books, Konigstein. HAWKSWORTH. D.L.. KIRK. P.M., SUTTON. B.C. & PEGLER. The first author wishes to express his gratitude to Dr D.N. 1995. Ainsworth and Bisby’s dictionary of the Fungi, edn B. Hein (B); Dr M. Pignal and Prof. P. Morat (P); and 8. CAB International, Wallingford. Dr B.
    [Show full text]
  • Complete Chloroplast Genome of Novel Adrinandra
    www.nature.com/scientificreports OPEN Complete chloroplast genome of novel Adrinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis Huu Quan Nguyen1, Thi Ngoc Lan Nguyen 1*, Thi Nhung Doan2, Thi Thu Nga Nguyen1, Mai Huong Phạm2, Tung Lam Le2, Danh Thuong Sy1, Hoang Ha Chu2 & Hoang Mau Chu 1* Adrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra genus, which is well- known for its potential health benefts due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adrinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the frst report for the chloroplast genome of the A.
    [Show full text]
  • 3 Secondary Structure of the ITS1 Transcript and Its Application in a Reconstruction of the Phylogeny of Boraginales 2
    3 Secondary Structure of the ITS1 Transcript 3 Secondary Structure of the ITS1 Transcript and its Application in a Reconstruction of the Phylogeny of Boraginales 2 Abstract In this study, we present the possibilities for calculating systematic relationships on higher taxonomical levels based exclusively on ITS1. This is demonstrated for Boraginales (Boraginaceae s.str., Cordiaceae, Ehretiaceae, Heliotropiaceae, Hydrophyllaceae s.str., and Lennoaceae). Secondary structure of the ITS1 region is more conserved than the primary structure (i.e., sequence itself) and is therefore a tool for optimising alignments. It increases the number of structural characters. Information inferred from the secondary structure enables us to construct well-resolved phylogenetic trees at higher taxonomical levels. A general secondary structure of ITS1 for Boraginales, with four major helices, is here proposed. In each subtaxon, derivations from this structure are found. The paraphyly of Boraginaceae s.l. is evident both from a comparison of secondary structures and from bootstrap analysis. Boraginaceae s.str. are the sister group of a clade formed by Hydrophyllaceae s.str., Cordiaceae, Ehretiaceae, Heliotropiaceae, and Lennoaceae. The last four taxa constitute a monophyletic group (primarily woody Boraginales), which is the sister group of Hydrophyllaceae s.str. Lennoaceae are closely related to Ehretiaceae, and these two taxa in turn are the sister group of Cordiaceae. 3.1 Introduction The highly variable First Internal Transcribed Spacer (ITS1) lies between the 18S and the 5.8S genes of the nucleus. It was initially proposed for use at lower taxonomical levels (BALDWIN 1992) and has been extensively employed in phylogenetic studies. It has been recently argued that the secondary structure of the ITS1 region is conserved at higher taxonomical levels, while the primary sequence is highly variable (NUES et al.
    [Show full text]
  • Phylogenetic Analysis of 83 Plastid Genes Further Resolves the Early Diversification of Eudicots
    Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots Michael J. Moorea,1, Pamela S. Soltisb, Charles D. Bellc, J. Gordon Burleighd, and Douglas E. Soltisd aBiology Department, Oberlin College, Oberlin, OH 44074; bFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; cDepartment of Biological Sciences, University of New Orleans, New Orleans, LA 70148; and dDepartment of Biology, University of Florida, Gainesville, FL 32611 Edited* by Michael J. Donoghue, Yale University, New Haven, CT, and approved January 26, 2010 (received for review July 14, 2009) Although Pentapetalae (comprising all core eudicots except Gun- (BS) values regardless of the partitioning strategy (Fig. 1 and Figs. nerales) include ≈70% of all angiosperms, the origin of and rela- S1–S3). The ML topologies were also similar to the maximum tionships among the major lineages of this clade have remained parsimony (MP) topology (Fig. S4). Relationships among early- largely unresolved. Phylogenetic analyses of 83 protein-coding diverging angiosperms and among many clades of Mesangio- and rRNA genes from the plastid genome for 86 species of seed spermae agree with those from the largest previous plastid genome plants, including new sequences from 25 eudicots, indicate that analyses (12, 15). Below, we focus on results regarding relation- soon after its origin, Pentapetalae diverged into three clades: (i) ships within the eudicots, with an emphasis on the ML topologies. a “superrosid” clade consisting of Rosidae, Vitaceae, and Saxifra- Within Eudicotyledoneae, a basal grade emerged, with most gales; (ii)a“superasterid” clade consisting of Berberidopsidales, nodes receiving 100% ML BS support. In all ML analyses, Santalales, Caryophyllales, and Asteridae; and (iii) Dilleniaceae.
    [Show full text]
  • RABBIT EARS, Encoding a SUPERMAN-Like Zinc Finger Protein, Regulates Petal Development in Arabidopsis Thaliana Seiji Takeda, Noritaka Matsumoto and Kiyotaka Okada
    CORRIGENDUM Development 138, 3591 (2011) doi:10.1242/dev.072058 © 2011. Published by The Company of Biologists Ltd RABBIT EARS, encoding a SUPERMAN-like zinc finger protein, regulates petal development in Arabidopsis thaliana Seiji Takeda, Noritaka Matsumoto and Kiyotaka Okada There was an error published in Development 131, 425-434. On page 428, the description of the rbe-1 mutation and its position as depicted in Fig. 2B were incorrect. The correct description is as follows. In rbe-1, a C to T transversion at nucleotide position 241 in the cDNA sequence results in the replacement of an arginine with a stop codon at amino acid 81 in the RBE protein. The authors apologise to readers for this mistake. Research article 425 RABBIT EARS, encoding a SUPERMAN-like zinc finger protein, regulates petal development in Arabidopsis thaliana Seiji Takeda, Noritaka Matsumoto* and Kiyotaka Okada†,‡ Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan *Present address: Department of Biology, Duke University, Durham, NC 27708, USA †CREST Research Project ‡Author for correspondence (e-mail: [email protected]) Accepted 21 October 2003 Development 131, 425-434 Published by The Company of Biologists 2004 doi:10.1242/dev.00938 Summary Floral organs usually initiate at fixed positions in thus may be a transcription factor. RBE transcripts are concentric whorls within a flower. Although it is expressed in petal primordia and their precursor cells, and understood that floral homeotic genes determine the disappeared at later stages. When cells that express RBE identity of floral organs, the mechanisms of position are ablated genetically, no petal primordia arise.
    [Show full text]
  • Fruit Development and Ripening
    PP64CH10-Seymour ARI 23 March 2013 14:57 Fruit Development and Ripening Graham B. Seymour,1 Lars Østergaard,2 Natalie H. Chapman,1 Sandra Knapp,4 and Cathie Martin3 1Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom; email: [email protected], [email protected] 2Department of Crop Genetics and 3Department of Metabolic Biology, John Innes Center, Norwich NR4 7UH, United Kingdom; email: [email protected], [email protected] 4Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom; email: [email protected] Annu. Rev. Plant Biol. 2013. 64:219–41 Keywords First published online as a Review in Advance on Arabidopsis, tomato, diet, gene regulation, epigenetics February 4, 2013 The Annual Review of Plant Biology is online at Abstract plant.annualreviews.org Fruiting structures in the angiosperms range from completely dry to This article’s doi: highly fleshy organs and provide many of our major crop products, by Universidad Veracruzana on 01/08/14. For personal use only. 10.1146/annurev-arplant-050312-120057 including grains. In the model plant Arabidopsis, which has dry fruits, Copyright c 2013 by Annual Reviews. a high-level regulatory network of transcription factors controlling All rights reserved Annu. Rev. Plant Biol. 2013.64:219-241. Downloaded from www.annualreviews.org fruit development has been revealed. Studies on rare nonripening mutations in tomato, a model for fleshy fruits, have provided new insights into the networks responsible for the control of ripening. It is apparent that there are strong similarities between dry and fleshy fruits in the molecular circuits governing development and maturation.
    [Show full text]