Serveur d'exploration sur le peuplier

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Genome sequence of the palaeopolyploid soybean.

Identifieur interne : 003251 ( Main/Exploration ); précédent : 003250; suivant : 003252

Genome sequence of the palaeopolyploid soybean.

Auteurs : Jeremy Schmutz [États-Unis] ; Steven B. Cannon ; Jessica Schlueter ; Jianxin Ma ; Therese Mitros ; William Nelson ; David L. Hyten ; Qijian Song ; Jay J. Thelen ; Jianlin Cheng ; Dong Xu ; Uffe Hellsten ; Gregory D. May ; Yeisoo Yu ; Tetsuya Sakurai ; Taishi Umezawa ; Madan K. Bhattacharyya ; Devinder Sandhu ; Babu Valliyodan ; Erika Lindquist ; Myron Peto ; David Grant ; Shengqiang Shu ; David Goodstein ; Kerrie Barry ; Montona Futrell-Griggs ; Brian Abernathy ; Jianchang Du ; Zhixi Tian ; Liucun Zhu ; Navdeep Gill ; Trupti Joshi ; Marc Libault ; Anand Sethuraman ; Xue-Cheng Zhang ; Kazuo Shinozaki ; Henry T. Nguyen ; Rod A. Wing ; Perry Cregan ; James Specht ; Jane Grimwood ; Dan Rokhsar ; Gary Stacey ; Randy C. Shoemaker ; Scott A. Jackson

Source :

RBID : pubmed:20075913

Descripteurs français

English descriptors

Abstract

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

DOI: 10.1038/nature08670
PubMed: 20075913


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name>
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<name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name>
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<name sortKey="Yu, Yeisoo" sort="Yu, Yeisoo" uniqKey="Yu Y" first="Yeisoo" last="Yu">Yeisoo Yu</name>
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<name sortKey="Sakurai, Tetsuya" sort="Sakurai, Tetsuya" uniqKey="Sakurai T" first="Tetsuya" last="Sakurai">Tetsuya Sakurai</name>
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<name sortKey="Umezawa, Taishi" sort="Umezawa, Taishi" uniqKey="Umezawa T" first="Taishi" last="Umezawa">Taishi Umezawa</name>
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<name sortKey="Bhattacharyya, Madan K" sort="Bhattacharyya, Madan K" uniqKey="Bhattacharyya M" first="Madan K" last="Bhattacharyya">Madan K. Bhattacharyya</name>
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<name sortKey="Sandhu, Devinder" sort="Sandhu, Devinder" uniqKey="Sandhu D" first="Devinder" last="Sandhu">Devinder Sandhu</name>
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<name sortKey="Valliyodan, Babu" sort="Valliyodan, Babu" uniqKey="Valliyodan B" first="Babu" last="Valliyodan">Babu Valliyodan</name>
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<name sortKey="Lindquist, Erika" sort="Lindquist, Erika" uniqKey="Lindquist E" first="Erika" last="Lindquist">Erika Lindquist</name>
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<name sortKey="Peto, Myron" sort="Peto, Myron" uniqKey="Peto M" first="Myron" last="Peto">Myron Peto</name>
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<name sortKey="Grant, David" sort="Grant, David" uniqKey="Grant D" first="David" last="Grant">David Grant</name>
</author>
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<name sortKey="Shu, Shengqiang" sort="Shu, Shengqiang" uniqKey="Shu S" first="Shengqiang" last="Shu">Shengqiang Shu</name>
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<name sortKey="Goodstein, David" sort="Goodstein, David" uniqKey="Goodstein D" first="David" last="Goodstein">David Goodstein</name>
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<name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name>
</author>
<author>
<name sortKey="Futrell Griggs, Montona" sort="Futrell Griggs, Montona" uniqKey="Futrell Griggs M" first="Montona" last="Futrell-Griggs">Montona Futrell-Griggs</name>
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<name sortKey="Abernathy, Brian" sort="Abernathy, Brian" uniqKey="Abernathy B" first="Brian" last="Abernathy">Brian Abernathy</name>
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<author>
<name sortKey="Du, Jianchang" sort="Du, Jianchang" uniqKey="Du J" first="Jianchang" last="Du">Jianchang Du</name>
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<name sortKey="Tian, Zhixi" sort="Tian, Zhixi" uniqKey="Tian Z" first="Zhixi" last="Tian">Zhixi Tian</name>
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<name sortKey="Zhu, Liucun" sort="Zhu, Liucun" uniqKey="Zhu L" first="Liucun" last="Zhu">Liucun Zhu</name>
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<name sortKey="Gill, Navdeep" sort="Gill, Navdeep" uniqKey="Gill N" first="Navdeep" last="Gill">Navdeep Gill</name>
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<name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name>
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<name sortKey="Zhang, Xue Cheng" sort="Zhang, Xue Cheng" uniqKey="Zhang X" first="Xue-Cheng" last="Zhang">Xue-Cheng Zhang</name>
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<name sortKey="Shinozaki, Kazuo" sort="Shinozaki, Kazuo" uniqKey="Shinozaki K" first="Kazuo" last="Shinozaki">Kazuo Shinozaki</name>
</author>
<author>
<name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T" last="Nguyen">Henry T. Nguyen</name>
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<name sortKey="Wing, Rod A" sort="Wing, Rod A" uniqKey="Wing R" first="Rod A" last="Wing">Rod A. Wing</name>
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<name sortKey="Cregan, Perry" sort="Cregan, Perry" uniqKey="Cregan P" first="Perry" last="Cregan">Perry Cregan</name>
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<author>
<name sortKey="Grimwood, Jane" sort="Grimwood, Jane" uniqKey="Grimwood J" first="Jane" last="Grimwood">Jane Grimwood</name>
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<name sortKey="Rokhsar, Dan" sort="Rokhsar, Dan" uniqKey="Rokhsar D" first="Dan" last="Rokhsar">Dan Rokhsar</name>
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<author>
<name sortKey="Shoemaker, Randy C" sort="Shoemaker, Randy C" uniqKey="Shoemaker R" first="Randy C" last="Shoemaker">Randy C. Shoemaker</name>
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<author>
<name sortKey="Jackson, Scott A" sort="Jackson, Scott A" uniqKey="Jackson S" first="Scott A" last="Jackson">Scott A. Jackson</name>
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<term>Arabidopsis (genetics)</term>
<term>Breeding (MeSH)</term>
<term>Chromosomes, Plant (genetics)</term>
<term>Evolution, Molecular (MeSH)</term>
<term>Gene Duplication (MeSH)</term>
<term>Genes, Duplicate (genetics)</term>
<term>Genes, Plant (genetics)</term>
<term>Genome, Plant (genetics)</term>
<term>Genomics (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Multigene Family (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Root Nodulation (genetics)</term>
<term>Polyploidy (MeSH)</term>
<term>Quantitative Trait Loci (genetics)</term>
<term>Recombination, Genetic (MeSH)</term>
<term>Repetitive Sequences, Nucleic Acid (genetics)</term>
<term>Soybean Oil (biosynthesis)</term>
<term>Soybeans (genetics)</term>
<term>Synteny (genetics)</term>
<term>Transcription Factors (genetics)</term>
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<term>Arabidopsis (génétique)</term>
<term>Chromosomes de plante (génétique)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Duplication de gène (MeSH)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Famille multigénique (génétique)</term>
<term>Gènes de plante (génétique)</term>
<term>Gènes dupliqués (génétique)</term>
<term>Génome végétal (génétique)</term>
<term>Génomique (MeSH)</term>
<term>Huile de soja (biosynthèse)</term>
<term>Locus de caractère quantitatif (génétique)</term>
<term>Nodulation racinaire (génétique)</term>
<term>Phylogenèse (MeSH)</term>
<term>Polyploïdie (MeSH)</term>
<term>Recombinaison génétique (MeSH)</term>
<term>Soja (génétique)</term>
<term>Synténie (génétique)</term>
<term>Sélection (MeSH)</term>
<term>Séquences répétées d'acides nucléiques (génétique)</term>
<term>Évolution moléculaire (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en">
<term>Soybean Oil</term>
</keywords>
<keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr">
<term>Huile de soja</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Arabidopsis</term>
<term>Chromosomes, Plant</term>
<term>Genes, Duplicate</term>
<term>Genes, Plant</term>
<term>Genome, Plant</term>
<term>Multigene Family</term>
<term>Plant Root Nodulation</term>
<term>Quantitative Trait Loci</term>
<term>Repetitive Sequences, Nucleic Acid</term>
<term>Soybeans</term>
<term>Synteny</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Arabidopsis</term>
<term>Chromosomes de plante</term>
<term>Facteurs de transcription</term>
<term>Famille multigénique</term>
<term>Gènes de plante</term>
<term>Gènes dupliqués</term>
<term>Génome végétal</term>
<term>Locus de caractère quantitatif</term>
<term>Nodulation racinaire</term>
<term>Soja</term>
<term>Synténie</term>
<term>Séquences répétées d'acides nucléiques</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Breeding</term>
<term>Evolution, Molecular</term>
<term>Gene Duplication</term>
<term>Genomics</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Polyploidy</term>
<term>Recombination, Genetic</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Données de séquences moléculaires</term>
<term>Duplication de gène</term>
<term>Génomique</term>
<term>Phylogenèse</term>
<term>Polyploïdie</term>
<term>Recombinaison génétique</term>
<term>Sélection</term>
<term>Évolution moléculaire</term>
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<div type="abstract" xml:lang="en">Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.</div>
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<ArticleTitle>Genome sequence of the palaeopolyploid soybean.</ArticleTitle>
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<AbstractText>Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.</AbstractText>
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<LastName>Schmutz</LastName>
<ForeName>Jeremy</ForeName>
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<LastName>Cannon</LastName>
<ForeName>Steven B</ForeName>
<Initials>SB</Initials>
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<Author ValidYN="Y">
<LastName>Schlueter</LastName>
<ForeName>Jessica</ForeName>
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<LastName>Ma</LastName>
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<ForeName>William</ForeName>
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<ForeName>David L</ForeName>
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<LastName>Song</LastName>
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<ForeName>Jay J</ForeName>
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<RefSource>Nature. 2010 May 6;465(7294):120</RefSource>
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