Analyses of the oligopeptide transporter gene family in poplar and grape.
Identifieur interne : 002F96 ( Main/Exploration ); précédent : 002F95; suivant : 002F97Analyses of the oligopeptide transporter gene family in poplar and grape.
Auteurs : Jun Cao [République populaire de Chine] ; Jinling Huang ; Yongping Yang ; Xiangyang HuSource :
- BMC genomics [ 1471-2164 ] ; 2011.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de profil d'expression de gènes (MeSH), Analyse de séquence d'ADN (MeSH), Arabidopsis (génétique), Duplication de gène (MeSH), Famille multigénique (MeSH), Gènes de plante (MeSH), Génome végétal (MeSH), Oryza (génétique), Phylogenèse (MeSH), Populus (génétique), Protéines de transport membranaire (génétique), Séquençage par oligonucléotides en batterie (MeSH), Vitis (génétique), Évolution moléculaire (MeSH).
- MESH :
- génétique : ADN des plantes, Arabidopsis, Oryza, Populus, Protéines de transport membranaire, Vitis.
- Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Duplication de gène, Famille multigénique, Gènes de plante, Génome végétal, Phylogenèse, Séquençage par oligonucléotides en batterie, Évolution moléculaire.
English descriptors
- KwdEn :
- Arabidopsis (genetics), DNA, Plant (genetics), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Gene Expression Profiling (MeSH), Genes, Plant (MeSH), Genome, Plant (MeSH), Membrane Transport Proteins (genetics), Multigene Family (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Oryza (genetics), Phylogeny (MeSH), Populus (genetics), Sequence Analysis, DNA (MeSH), Vitis (genetics).
- MESH :
- chemical , genetics : DNA, Plant, Membrane Transport Proteins.
- genetics : Arabidopsis, Oryza, Populus, Vitis.
- Evolution, Molecular, Gene Duplication, Gene Expression Profiling, Genes, Plant, Genome, Plant, Multigene Family, Oligonucleotide Array Sequence Analysis, Phylogeny, Sequence Analysis, DNA.
Abstract
BACKGROUND
Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis.
RESULTS
In the present study, a comprehensive analysis of the OPT gene family in Populus (P. trichocarpa) and Vitis (V. vinifera) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection.
CONCLUSIONS
Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.
DOI: 10.1186/1471-2164-12-465
PubMed: 21943393
PubMed Central: PMC3188535
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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sort="Yang, Yongping" uniqKey="Yang Y" first="Yongping" last="Yang">Yongping Yang</name></author><author><name sortKey="Hu, Xiangyang" sort="Hu, Xiangyang" uniqKey="Hu X" first="Xiangyang" last="Hu">Xiangyang Hu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21943393</idno><idno type="pmid">21943393</idno><idno type="doi">10.1186/1471-2164-12-465</idno><idno type="pmc">PMC3188535</idno><idno type="wicri:Area/Main/Corpus">002C83</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002C83</idno><idno type="wicri:Area/Main/Curation">002C83</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002C83</idno><idno type="wicri:Area/Main/Exploration">002C83</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Analyses of the oligopeptide transporter gene family in poplar and grape.</title><author><name sortKey="Cao, Jun" sort="Cao, Jun" uniqKey="Cao J" first="Jun" last="Cao">Jun Cao</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Institute of Tibet Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650204, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Institute of Tibet Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650204</wicri:regionArea><wicri:noRegion>650204</wicri:noRegion></affiliation></author><author><name sortKey="Huang, Jinling" sort="Huang, Jinling" uniqKey="Huang J" first="Jinling" last="Huang">Jinling Huang</name></author><author><name sortKey="Yang, Yongping" sort="Yang, Yongping" uniqKey="Yang Y" first="Yongping" last="Yang">Yongping Yang</name></author><author><name sortKey="Hu, Xiangyang" sort="Hu, Xiangyang" uniqKey="Hu X" first="Xiangyang" last="Hu">Xiangyang Hu</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>DNA, Plant (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Membrane Transport Proteins (genetics)</term><term>Multigene Family (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Oryza (genetics)</term><term>Phylogeny (MeSH)</term><term>Populus (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Vitis (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Arabidopsis (génétique)</term><term>Duplication de gène (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Oryza (génétique)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Protéines de transport membranaire (génétique)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term><term>Vitis (génétique)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term><term>Membrane Transport Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Oryza</term><term>Populus</term><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Arabidopsis</term><term>Oryza</term><term>Populus</term><term>Protéines de transport membranaire</term><term>Vitis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Gene Expression Profiling</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Multigene Family</term><term>Oligonucleotide Array Sequence Analysis</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ADN</term><term>Duplication de gène</term><term>Famille multigénique</term><term>Gènes de plante</term><term>Génome végétal</term><term>Phylogenèse</term><term>Séquençage par oligonucléotides en batterie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>In the present study, a comprehensive analysis of the OPT gene family in Populus (P. trichocarpa) and Vitis (V. vinifera) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21943393</PMID><DateCompleted><Year>2012</Year><Month>01</Month><Day>11</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>12</Volume><PubDate><Year>2011</Year><Month>Sep</Month><Day>26</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Analyses of the oligopeptide transporter gene family in poplar and grape.</ArticleTitle><Pagination><MedlinePgn>465</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-12-465</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In the present study, a comprehensive analysis of the OPT gene family in Populus (P. trichocarpa) and Vitis (V. vinifera) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Institute of Tibet Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650204, China.</Affiliation></AffiliationInfo></Author><Author 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