Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family.
Identifieur interne : 002285 ( Main/Exploration ); précédent : 002284; suivant : 002286Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family.
Auteurs : Lianhua Guo ; Yingnan Chen ; Ning Ye ; Xiaogang Dai ; Wanxu Yang ; Tongming Yin [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2014.
Descripteurs français
- KwdFr :
- Arabidopsis (génétique), Bases de données génétiques (MeSH), Carica (génétique), Glycoprotéines (classification), Glycoprotéines (génétique), Glycoprotéines (métabolisme), Gènes de plante (MeSH), Phylogenèse (MeSH), Polyploïdie (MeSH), Populus (génétique), Protéines végétales (classification), Protéines végétales (génétique), Protéines végétales (métabolisme), Vitis (génétique).
- MESH :
- classification : Glycoprotéines, Protéines végétales.
- génétique : Arabidopsis, Carica, Glycoprotéines, Populus, Protéines végétales, Vitis.
- métabolisme : Glycoprotéines, Protéines végétales.
- Bases de données génétiques, Gènes de plante, Phylogenèse, Polyploïdie.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Carica (genetics), Databases, Genetic (MeSH), Genes, Plant (MeSH), Glycoproteins (classification), Glycoproteins (genetics), Glycoproteins (metabolism), Phylogeny (MeSH), Plant Proteins (classification), Plant Proteins (genetics), Plant Proteins (metabolism), Polyploidy (MeSH), Populus (genetics), Vitis (genetics).
- MESH :
- chemical , classification : Glycoproteins, Plant Proteins.
- genetics : Arabidopsis, Carica, Glycoproteins, Plant Proteins, Populus, Vitis.
- chemical , metabolism : Glycoproteins, Plant Proteins.
- Databases, Genetic, Genes, Plant, Phylogeny, Polyploidy.
Abstract
BACKGROUND
All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods.
RESULTS
The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene.
CONCLUSIONS
Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.
DOI: 10.1186/1471-2164-15-612
PubMed: 25047956
PubMed Central: PMC4117974
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Yin</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, 159#, Longpan Road, Nanjing 210037, China. tmyin@njfu.com.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, 159#, Longpan Road, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25047956</idno><idno type="pmid">25047956</idno><idno type="doi">10.1186/1471-2164-15-612</idno><idno type="pmc">PMC4117974</idno><idno type="wicri:Area/Main/Corpus">002083</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002083</idno><idno type="wicri:Area/Main/Curation">002083</idno><idno 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Yang</name></author><author><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name><affiliation wicri:level="1"><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, 159#, Longpan Road, Nanjing 210037, China. tmyin@njfu.com.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, 159#, Longpan Road, Nanjing 210037</wicri:regionArea><wicri:noRegion>Nanjing 210037</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Carica (genetics)</term><term>Databases, 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(génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Glycoproteins</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Glycoprotéines</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Carica</term><term>Glycoproteins</term><term>Plant Proteins</term><term>Populus</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Carica</term><term>Glycoprotéines</term><term>Populus</term><term>Protéines végétales</term><term>Vitis</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Glycoproteins</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Glycoprotéines</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Genes, Plant</term><term>Phylogeny</term><term>Polyploidy</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données génétiques</term><term>Gènes de plante</term><term>Phylogenèse</term><term>Polyploïdie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25047956</PMID><DateCompleted><Year>2015</Year><Month>03</Month><Day>12</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><PubDate><Year>2014</Year><Month>Jul</Month><Day>21</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family.</ArticleTitle><Pagination><MedlinePgn>612</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-15-612</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Lianhua</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yingnan</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Ning</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Dai</LastName><ForeName>Xiaogang</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Wanxu</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Yin</LastName><ForeName>Tongming</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, 159#, Longpan Road, Nanjing 210037, China. 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sortKey="Chen, Yingnan" sort="Chen, Yingnan" uniqKey="Chen Y" first="Yingnan" last="Chen">Yingnan Chen</name><name sortKey="Dai, Xiaogang" sort="Dai, Xiaogang" uniqKey="Dai X" first="Xiaogang" last="Dai">Xiaogang Dai</name><name sortKey="Guo, Lianhua" sort="Guo, Lianhua" uniqKey="Guo L" first="Lianhua" last="Guo">Lianhua Guo</name><name sortKey="Yang, Wanxu" sort="Yang, Wanxu" uniqKey="Yang W" first="Wanxu" last="Yang">Wanxu Yang</name><name sortKey="Ye, Ning" sort="Ye, Ning" uniqKey="Ye N" first="Ning" last="Ye">Ning Ye</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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