DOCSLIB.ORG

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs In

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs In The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants Sònia Garcia, Jonathan F Wendel, Natalia Borowska-Zuchowska, Malika Ainouche, Alena Kuderova, Ales Kovarik To cite this version: Sònia Garcia, Jonathan F Wendel, Natalia Borowska-Zuchowska, Malika Ainouche, Alena Kuderova, et al.. The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants. Frontiers in Plant Science, Frontiers, 2020, 11, pp.41. 10.3389/fpls.2020.00041. hal-02498513 HAL Id: hal-02498513 https://hal-univ-rennes1.archives-ouvertes.fr/hal-02498513 Submitted on 15 Jul 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ORIGINAL RESEARCH published: 10 February 2020 doi: 10.3389/fpls.2020.00041 The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants Sònia Garcia 1,2, Jonathan F. Wendel 3, Natalia Borowska-Zuchowska 4, Malika Aïnouche 5, Alena Kuderova 2 and Ales Kovarik 2* 1 Institut Botànic de Barcelona (IBB, CSIC - Ajuntament de Barcelona), Barcelona, Spain, 2 Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia, 3 Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, United States, 4 Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland, 5 UMR CNRS 6553 ECOBIO, Université de Rennes 1, Rennes, France Introduction: Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput Edited by: sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) Hanna Weiss-Schneeweiss, pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for University of Vienna, Austria hybridogenic origin of species. Data were obtained from more than 80 plant species, Reviewed by: fi Tony Heitkam, including several well-de ned allopolyploids and homoploid hybrids of different Dresden University of evolutionary ages and from widely dispersed taxonomic groups. Technology, Germany Jelena Mlinarec, Results: (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In University of Zagreb, Croatia contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs *Correspondence: composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) Ales Kovarik [email protected] There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were Specialty section: congruent with those experimentally determined. (iv) Three-genomic comparative cluster This article was submitted to Plant analysis of reads from allopolyploids and progenitor diploids allowed identification of Systematics and Evolution, a section of the journal homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Frontiers in Plant Science Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA Received: 17 October 2019 repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally Accepted: 13 January 2020 Published: 10 February 2020 complex graph structures. Citation: Conclusion: We found that the cluster graph shapes and graph parameters (k-mer Garcia S, Wendel JF, coverage scores and connected component index) well-reflect the organization and Borowska-Zuchowska N, Aïnouche M, Kuderova A and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA Kovarik A (2020) The Utility of Graph cluster graphs computed by the RE pipeline together with the cytogenetic analysis might Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, be a reliable approach for the determination of the hybrid or allopolyploid plant species Homoploid Hybrids, and Cryptic parentage and may also be useful for detecting historical introgression events. Introgressants. Front. Plant Sci. 11:41. Keywords: 5S rRNA genes, allopolyploidy, hybridization, evolution, graph structure clustering, high-throughput doi: 10.3389/fpls.2020.00041 sequencing, repeatome Frontiers in Plant Science | www.frontiersin.org 1 February 2020 | Volume 11 | Article 41 Garcia et al. 5S rDNA Evolution in Plant Hybrids INTRODUCTION Volkov et al., 1999; Muir et al., 2001; Matyasek et al., 2003). In It is well-established that all modern plant species have contrast to 35S rDNA, the 5S rDNA loci appear to be less experienced at least one whole genome duplication and that sensitive to homogenization in some allopolyploids (Fulnecek many also have interspecific hybridization and recurrent et al., 2002; Pedrosa-Harand et al., 2006; Weiss-Schneeweiss introgression in their recent history (Wendel, 2015; Alix et al., et al., 2008; Garcia et al., 2017), retaining diagnostic capacity 2017; Nieto Feliner et al., 2017; Van De Peer et al., 2017). with respect to their parental origin. Documenting recent allopolyploidy is relatively straightforward The clustering algorithm employed by RepeatExplorer (RE) using cytogenetic analysis and genome size measurements, since (Novak et al., 2010; Novak et al., 2013) has become a tool of allopolyploids have twice as many chromosomes (or more) as the choice for the analysis of chromosome composition and genome parental species. Identification of homoploid hybrids is more evolution (Renny-Byfield et al., 2012; Weiss-Schneeweiss et al., difficult since the chromosome number and genome size are 2015; Ribeiro et al., 2017; Mlinarec et al., 2019; Peska et al., 2019). often similar to that of the parental species (Nieto Feliner et al., The phylogenetic signal of the repeatome has also been exploited 2017). Evolutionary young allopolyploids and other hybrids tend in phylogenetic studies (Dodsworth et al., 2015; Dodsworth et al., to retain fixed polymorphisms at protein-coding and non-coding 2016; Grover et al., 2019; Vitales et al., 2019). The analysis of loci. These duplicated loci are called homoeologs (Glover et al., genomes by RE is based on an all-to-all comparison of sequence 2016) and are useful for documenting parentage as well as reads revealing their similarities. Subsequently, the data are used understanding the dynamics of polyploid genomes (Yoo et al., to build clusters of overlapping reads representing different 2014; Wendel, 2015; Bourke et al., 2018). Older allopolyploids repetitive elements. The TAREAN tool, recently introduced can have experienced episodes of intergenomic translocation, into the RepeatExplorer2 pipeline, allows repeat identification dysploidy, gene conversion, localized deletions, and other genetic and reconstruction of tandem repeats solely from sequence reads events, leading eventually to diploidization of the genome (Novak et al., 2017). Graph theory and connected component (Wendel, 2015; Wendel et al., 2018). methods lying in the heart of the computation algorithm produce Ribosomal RNA genes encoding 5S, 5.8S, 18S, and 26S graph structures reflecting genomic organization of repeats. ribosomal RNA are ubiquitous in plants and are organized Typically, tandem repeats exhibit circular (ring) shape into arrays containing hundreds to thousands of tandem topologies are characterized by high values of circularity repeats at one or more genomic loci (Hemleben and Zentgraf, parameters. Although the RepeatExplorer2/TAREAN tool was 1994; Nieto Feliner and Rosselló, 2007; Roa and Guerra, 2012; initially developed for identification of non-coding satellites, 5S Garcia et al., 2017). Due to their rapidly diverging intergenic rDNA can also be analyzed with the program. This is because 5S (IGS) and internally transcribed spacers (ITS), rDNA loci have rDNA shows many features of satellite repeats: (I) its highly become popular taxonomic markers revealing allopolyploidy and homogeneous units are tandemly arranged in a head to tail other interspecific hybridization in many plant and animal orientation, (II) it appears in high copy number, allowing systems (Alvarez and Wendel, 2003; Poczai and Hyvonen, analyses even at low coverage, and (III) the size of 5S rDNA 2010; Nieto Feliner and Rossello, 2012). The internet searches monomers (c. 200–1,000 bp) (Sastri et al., 1992; Fulnecek et al., using *ITS* and *allopolyploidy* resulted in more than 650 hits 2006) falls within the range defined for satellite DNA, allowing in Web of Science for just 2019. Most studies have used classical circularization of chains of overlapping reads. single clone sequencing approaches whereas high-throughput In this study we investigated the 5S rDNA genomic data have only rarely been employed and are limited to the 35S organization and homogeneity in more than 80 plant diploids (45S) rDNA (Matyasek et al., 2012; West et al., 2014; Boutte et al., and polyploids, exploiting high-throughput
Load more

Recommended publications
  • Stable and Widespread Structural Heteroplasmy in Chloroplast Genomes Revealed by a New Long-Read Quantification Method
    bioRxiv preprint doi: https://doi.org/10.1101/692798; this version posted July 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Classification: Biological Sciences, Evolution Title: Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method Weiwen Wang a, Robert Lanfear a a Research School of Biology, Australian National University, Canberra, ACT, Australia, 2601 Corresponding Author: Weiwen Wang, [email protected] Robert Lanfear, [email protected], +61 2 6125 2536 Keywords: Single copy inversion, flip-flop recombination, chloroplast genome structural heteroplasmy 1 bioRxiv preprint doi: https://doi.org/10.1101/692798; this version posted July 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Abstract 2 The chloroplast genome usually has a quadripartite structure consisting of a large 3 single copy region and a small single copy region separated by two long inverted 4 repeats. It has been known for some time that a single cell may contain at least two 5 structural haplotypes of this structure, which differ in the relative orientation of the 6 single copy regions. However, the methods required to detect and measure the 7 abundance of the structural haplotypes are labour-intensive, and this phenomenon 8 remains understudied.
    [Show full text]
  • Polyploidy and the Evolutionary History of Cotton
    POLYPLOIDY AND THE EVOLUTIONARY HISTORY OF COTTON Jonathan F. Wendel1 and Richard C. Cronn2 1Department of Botany, Iowa State University, Ames, Iowa 50011, USA 2Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, Oregon 97331, USA I. Introduction II. Taxonomic, Cytogenetic, and Phylogenetic Framework A. Origin and Diversification of the Gossypieae, the Cotton Tribe B. Emergence and Diversification of the Genus Gossypium C. Chromosomal Evolution and the Origin of the Polyploids D. Phylogenetic Relationships and the Temporal Scale of Divergence III. Speciation Mechanisms A. A Fondness for Trans-oceanic Voyages B. A Propensity for Interspecific Gene Exchange IV. Origin of the Allopolyploids A. Time of Formation B. Parentage of the Allopolyploids V. Polyploid Evolution A. Repeated Cycles of Genome Duplication B. Chromosomal Stabilization C. Increased Recombination in Polyploid Gossypium D. A Diverse Array of Genic and Genomic Interactions E. Differential Evolution of Cohabiting Genomes VI. Ecological Consequences of Polyploidization VII. Polyploidy and Fiber VIII. Concluding Remarks References The cotton genus (Gossypium ) includes approximately 50 species distributed in arid to semi-arid regions of the tropic and subtropics. Included are four species that have independently been domesticated for their fiber, two each in Africa–Asia and the Americas. Gossypium species exhibit extraordinary morphological variation, ranging from herbaceous perennials to small trees with a diverse array of reproductive and vegetative
    [Show full text]
  • Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants
    GBE Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants Weiwen Wang* and Robert Lanfear* Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: November 15, 2019 Downloaded from https://academic.oup.com/gbe/article/11/12/3372/5637229 by guest on 02 October 2021 Data deposition: The Herrania umbratica and Siraitia grosvenorii chloroplast genomes in this project have been deposited at NCBI under the accession MN163033 and MK279915. Abstract The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labor-intensive, and this phenomenon remains understudied. Here, we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms, and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype.
    [Show full text]
  • Variation Than Mainland Populations?
    Heredity 78 (1997) 311—327 Received 30Apr11 1996 Do island populations have less genetic variation than mainland populations? R. FRANKHAM* Key Centre for Biodiversity and Bioresources, Macquarie University, Sydney, NSW2109, Australia Islandpopulations are much more prone to extinction than mainland populations. The reasons for this remain controversial. If inbreeding and loss of genetic variation are involved, then genetic variation must be lower on average in island than mainland populations. Published data on levels of genetic variation for allozymes, nuclear DNA markers, mitochondrial DNA, inversions and quantitative characters in island and mainland populations were analysed. A large and highly significant majority of island populations have less allozyme genetic variation than their mainland counterparts (165 of 202 comparisons), the average reduction being 29 per cent. The magnitude of differences was related to dispersal ability. There were related differ- ences for all the other measures. Island endemic species showed lower genetic variation than related mainland species in 34 of 38 cases. The proportionate reduction in genetic variation was significantly greater in island endemic than in nonendemic island populations in mammals and birds, but not in insects. Genetic factors cannot be discounted as a cause of higher extinction rates of island than mainland populations. Keywords:allozymes,conservation, endemic species, extinction, genetic variation, islands. of endemic plant species as threatened on 15 islands. Introduction Human activities have been the major cause of Islandpopulations have a much higher risk of species extinctions on islands in the past 50000 years extinction than mainland populations (Diamond, (Olson, 1989) through over-exploitation, habitat loss 1984; Vitousek, 1988; Flesness, 1989; Case et al., and introduced species.
    [Show full text]
  • Darwin, Plants and Portugal Autor(Es): Paiva, Jorge Publicado
    Darwin, plants and Portugal Autor(es): Paiva, Jorge Publicado por: Imprensa da Universidade de Coimbra URL persistente: URI:http://hdl.handle.net/10316.2/31257 DOI: DOI:http://dx.doi.org/10.14195/978-989-26-0342-1_4 Accessed : 30-Sep-2021 22:17:11 A navegação consulta e descarregamento dos títulos inseridos nas Bibliotecas Digitais UC Digitalis, UC Pombalina e UC Impactum, pressupõem a aceitação plena e sem reservas dos Termos e Condições de Uso destas Bibliotecas Digitais, disponíveis em https://digitalis.uc.pt/pt-pt/termos. Conforme exposto nos referidos Termos e Condições de Uso, o descarregamento de títulos de acesso restrito requer uma licença válida de autorização devendo o utilizador aceder ao(s) documento(s) a partir de um endereço de IP da instituição detentora da supramencionada licença. Ao utilizador é apenas permitido o descarregamento para uso pessoal, pelo que o emprego do(s) título(s) descarregado(s) para outro fim, designadamente comercial, carece de autorização do respetivo autor ou editor da obra. Na medida em que todas as obras da UC Digitalis se encontram protegidas pelo Código do Direito de Autor e Direitos Conexos e demais legislação aplicável, toda a cópia, parcial ou total, deste documento, nos casos em que é legalmente admitida, deverá conter ou fazer-se acompanhar por este aviso. pombalina.uc.pt digitalis.uc.pt A presente colecção reúne originais de cultura científica resultantes da investigação no Ana Leonor Pereira | João Rui Pita Pedro Ricardo Fonseca Ana Leonor Pereira One hundred and fifty years ago, more precisely on the 24th of November of 1859, Darwin âmbito da história das ciências e das técnicas, da história da farmácia, da história da Darwin, introduced a new paradigm in natural history with the publication of On the origin of species medicina e de outras dimensões das práticas científicas nas diferentes interfaces com a João Rui Pita by means of natural selection, or the preservation of favoured races in the struggle for life.
    [Show full text]
  • QTL Mapping for Flowering-Time and Photoperiod Insensitivity of Cotton Gossypium Darwinii Watt
    RESEARCH ARTICLE QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt Fakhriddin N. Kushanov1☯, Zabardast T. Buriev1, Shukhrat E. Shermatov1, Ozod S. Turaev1, Tokhir M. Norov1, Alan E. Pepper2, Sukumar Saha3, Mauricio Ulloa4, John Z. Yu5, Johnie N. Jenkins3, Abdusattor Abdukarimov1, Ibrokhim Y. Abdurakhmonov1☯* 1 Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan, 2 Department of Biology, Texas A&M a1111111111 University, Colleges Station, Texas, United States of America, 3 Crop Science Research Laboratory, United a1111111111 States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of a1111111111 America, 4 Plant Stress and Germplasm Development Research, United States Department of Agriculture- a1111111111 Agricultural Research Services, Lubbock, Texas, United States of America, 5 Southern Plains Agricultural a1111111111 Research Center, United States Department of Agriculture-Agricultural Research Services, College Station, Texas, United States of America ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Kushanov FN, Buriev ZT, Shermatov SE, Abstract Turaev OS, Norov TM, Pepper AE, et al. (2017) QTL mapping for flowering-time and photoperiod Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive insensitivity of cotton Gossypium darwinii Watt. PLoS ONE 12(10): e0186240. https://doi.org/ flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement 10.1371/journal.pone.0186240 of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic Editor: Turgay Unver, Dokuz Eylul Universitesi, flowering was developed by crossing a photoperiod insensitive irradiation mutant line with TURKEY its pre-mutagenesis photoperiodic wild-type G.
    [Show full text]
  • Cotton Genetic Resources. a Review Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, Zafar, Andrew Paterson
    Cotton genetic resources. A review Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, Zafar, Andrew Paterson To cite this version: Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, et al.. Cotton genetic re- sources. A review. Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA, 2012, 32 (2), pp.419-432. 10.1007/s13593-011-0051-z. hal-00930526 HAL Id: hal-00930526 https://hal.archives-ouvertes.fr/hal-00930526 Submitted on 1 Jan 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Agron. Sustain. Dev. (2012) 32:419–432 DOI 10.1007/s13593-011-0051-z REVIEW ARTICLE Cotton genetic resources. A review Mehboob-ur-Rahman & Tayyaba Shaheen & Nabila Tabbasam & Muhammad Atif Iqbal & Muhammad Ashraf & Yusuf Zafar & Andrew H. Paterson Accepted: 29 July 2011 /Published online: 13 October 2011 # INRA and Springer-Verlag, France 2011 Abstract Since 6000 BC, cotton has been cultivated for lint Much of the genetic diversity among G. barbadense cultivars fiber, which now dominates the natural textile industry is attributed to the introgression of G. hirsutum alleles. This worldwide. Common resources such as an integrated web process highlights the importance of introgression of new database, a microsatellite database, and comparative quantita- alleles from accessions of all the Gossypium species into tive trait loci (QTL) resources for Gossypium have accelerated cultivated cotton species.
    [Show full text]
  • Evolution and Natural History of the Cotton Genus
    Evolution and Natural History of the Cotton Genus Jonathan F. Wendel, Curt Brubaker, Ines Alvarez, Richard Cronn, and James McD. Stewart Abstract We present an overview of the evolution and diversity in Gossypium (the cotton genus). This framework facilitates insight into fundamental aspects of plant biology, provides the necessary underpinnings for effective utilization of cotton genetic resources, and guides exploration of the genomic basis of morphological diversity in the genus. More than 50 species of Gossypium are distributed in arid to semi-arid regions of the tropics and subtropics. Included are four species that independently have been domesticated for their fiber, two each in Africa-Asia and the Americas. Gossypium species exhibit extraordin- ary morphological variation, ranging from trailing herbaceous perennials to 15 m trees with a diverse array of reproductive and vegetative characteris- tics. A parallel level of cytogenetic and genomic diversity has arisen during the global radiation of the genus, leading to the evolution of eight groups of diploid (n 13) species (genome groups A through G, and K). Data implicate an origin for¼Gossypium about 5–10 million years ago and a rapid early diversification of the major genome groups. Allopolyploid cottons appear to have arisen within the last 1–2 million years, as a consequence of trans-oceanic dispersal of an A-genome taxon to the New World followed by hybridization with an indigen- ous D-genome diploid. Subsequent to formation, allopolyploids radiated into three modern lineages, two of which contain the commercially important species G. hirsutum and G. barbadense. 1 Introduction to Gossypium diversity Because the cotton genus (Gossypium L.) is so important to economies around the world, it has long attracted the attention of agricultural scientists, taxono- mists, and evolutionary biologists.
    [Show full text]
  • Downloaded from Genbank on That Full Plastid Genomes Are Not Sufficient to Reject Al- February 28, 2012
    Ruhfel et al. BMC Evolutionary Biology 2014, 14:23 http://www.biomedcentral.com/1471-2148/14/23 RESEARCH ARTICLE Open Access From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes Brad R Ruhfel1*, Matthew A Gitzendanner2,3,4, Pamela S Soltis3,4, Douglas E Soltis2,3,4 and J Gordon Burleigh2,4 Abstract Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. Results: We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa.
    [Show full text]
  • Genetics and Genomics of Cotton (Plant Genetics and Genomics
    Plant Genetics and Genomics: Crops and Models Volume 3 Plant Genetics and Genomics: Crops and Models Series Editor: Richard A. Jorgensen Forthcoming and planned volumes Vol. 1 Genomics of Tropical Crop Plants (eds: Paul Moore/Ray Ming) Vol. 2 Genetics and Genomics of Soybean (ed: Gary Stacey) Vol. 3 Genetics and Genomics of Cotton (ed: Andrew Paterson) Vol. 4 Plant Cytogenetics: Genome Structure and Chromosome Function (eds: Hank Bass/Jim Birchler) Vol. 5 Plant Cytogenetics: Methods and Instruction (eds: Hank Bass/Jim Birchler) Vol. 6 Genetics and Genomics of the Rosaceae (eds: Kevin Folta/Sue Gardiner) Vol. 7 Genetics and Genomics of the Triticeae (ed: Catherine Feuillet/Gary Muehlbauer) Vol. 8 Genomics of Poplar (ed: Stefan Janssen et al.) Andrew H. Paterson Editor Genetics and Genomics of Cotton 13 Editor Andrew H. Paterson University of Georgia Plant Genome Mapping Laboratory 111 Riverbend Road Athens, GA 30602 USA [email protected] ISBN 978-0-387-70809-6 e-ISBN 978-0-387-70810-2 DOI 10.1007/978-0-387-70810-2 Library of Congress Control Number: 2008941164 # Springer ScienceþBusiness Media, LLC 2009 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer ScienceþBusiness Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.
    [Show full text]
  • The Status of the Endemic Flora of Galapagos: the Number of Threatened Species Is Increasing Alan Tye Charles Darwin Foundation
    BIODIVERSITY AND BIOPHYSICAL RESOURSES The status of the endemic flora of Galapagos: the number of threatened species is increasing Alan Tye Charles Darwin Foundation The endemic species of Galapagos are of the greatest Results conservation interest because their future depends entirely on their continued existence in the islands. A The new evaluations cover 180 species, compared complete evaluation of the threat status of the endemic with 175 in 2002, eight of which were Not Evaluated vascular plants (flowering plants and ferns) of (IUCN category NE) 1. Of the 180 evaluated in 2006, Galapagos was published in the last Galapagos nine species were placed in the IUCN category Data Report 1. A re-evaluation of their threat status at full Deficient (DD) owing to uncertainties regarding the species level was carried out during 2006, as a contri - limits of the taxon and therefore its distribution. For bution to the Ecuadorian national plant Red Data the 171 species that were fully evaluated, Table 1 Book 2. The present report summarises the results of summarizes the results of the latest re-evaluation and this re-evaluation and assesses changes since 2002. the previous full evaluation in 2002 1. No species were As in the last report 1, all species have been evaluated classified as EW (Extinct in the Wild). Table 1 gives the under the IUCN criteria 3, using the same methods as numbers and percentages of species in each category, by Tye 4,5 . These threat evaluations are carried out and reveals that 100 of the 168 extant species that under the auspices of the Galapagos Plant Specialist were evaluated (excluding the three extinct and the Group of IUCN, and become the official evaluations nine DD species) are threatened (60%).
    [Show full text]
  • Comparative Genomics of Gossypium Spp
    COMPARATIVE GENOMICS OF GOSSYPIUM SPP. THROUGH GBS AND CANDIDATE GENES – DELVING INTO THE CONTROLLING FACTORS BEHIND PHOTOPERIODIC FLOWERING A Dissertation by CARLA JO LOGAN YOUNG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Alan E. Pepper Committee Members, Konstantin V. Krutovsky John Z. Yu Keerti S. Rathore Wayne K. Versaw Head of Department, U. J. McMahan August 2013 Major Subject: Biology Copyright 2013 Carla Jo Logan Young ABSTRACT Cotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas.
    [Show full text]