Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange.
Identifieur interne : 000275 ( PubMed/Corpus ); précédent : 000274; suivant : 000276Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange.
Auteurs : Xiao-Jin Hou ; Si-Bei Li ; Sheng-Rui Liu ; Chun-Gen Hu ; Jin-Zhi ZhangSource :
- PloS one [ 1932-6203 ] ; 2014.
English descriptors
- KwdEn :
- Citrus sinensis (genetics), Citrus sinensis (metabolism), Gene Expression Regulation, Plant (physiology), Genome-Wide Association Study, Multigene Family (physiology), Plant Proteins (biosynthesis), Plant Proteins (classification), Plant Proteins (genetics), Transcription Factors (biosynthesis), Transcription Factors (classification), Transcription Factors (genetics).
- MESH :
- chemical , biosynthesis : Plant Proteins, Transcription Factors.
- chemical , classification : Plant Proteins, Transcription Factors.
- genetics : Citrus sinensis, Plant Proteins, Transcription Factors.
- metabolism : Citrus sinensis.
- physiology : Gene Expression Regulation, Plant, Multigene Family.
- Genome-Wide Association Study.
Abstract
MYB family genes are widely distributed in plants and comprise one of the largest transcription factors involved in various developmental processes and defense responses of plants. To date, few MYB genes and little expression profiling have been reported for citrus. Here, we describe and classify 177 members of the sweet orange MYB gene (CsMYB) family in terms of their genomic gene structures and similarity to their putative Arabidopsis orthologs. According to these analyses, these CsMYBs were categorized into four groups (4R-MYB, 3R-MYB, 2R-MYB and 1R-MYB). Gene structure analysis revealed that 1R-MYB genes possess relatively more introns as compared with 2R-MYB genes. Investigation of their chromosomal localizations revealed that these CsMYBs are distributed across nine chromosomes. Sweet orange includes a relatively small number of MYB genes compared with the 198 members in Arabidopsis, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative studies of CsMYBs and Arabidopsis showed that CsMYBs had fewer gene duplication events. Expression analysis revealed that the MYB gene family has a wide expression profile in sweet orange development and plays important roles in development and stress responses. In addition, 337 new putative microsatellites with flanking sequences sufficient for primer design were also identified from the 177 CsMYBs. These results provide a useful reference for the selection of candidate MYB genes for cloning and further functional analysis forcitrus.
DOI: 10.1371/journal.pone.0112375
PubMed: 25375352
Links to Exploration step
pubmed:25375352Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange.</title><author><name sortKey="Hou, Xiao Jin" sort="Hou, Xiao Jin" uniqKey="Hou X" first="Xiao-Jin" last="Hou">Xiao-Jin Hou</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Si Bei" sort="Li, Si Bei" uniqKey="Li S" first="Si-Bei" last="Li">Si-Bei Li</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25375352</idno><idno type="pmid">25375352</idno><idno type="doi">10.1371/journal.pone.0112375</idno><idno type="wicri:Area/PubMed/Corpus">000275</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange.</title><author><name sortKey="Hou, Xiao Jin" sort="Hou, Xiao Jin" uniqKey="Hou X" first="Xiao-Jin" last="Hou">Xiao-Jin Hou</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Si Bei" sort="Li, Si Bei" uniqKey="Li S" first="Si-Bei" last="Li">Si-Bei Li</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Liu, Sheng Rui" sort="Liu, Sheng Rui" uniqKey="Liu S" first="Sheng-Rui" last="Liu">Sheng-Rui Liu</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Hu, Chun Gen" sort="Hu, Chun Gen" uniqKey="Hu C" first="Chun-Gen" last="Hu">Chun-Gen Hu</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jin Zhi" sort="Zhang, Jin Zhi" uniqKey="Zhang J" first="Jin-Zhi" last="Zhang">Jin-Zhi Zhang</name><affiliation><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Citrus sinensis (genetics)</term><term>Citrus sinensis (metabolism)</term><term>Gene Expression Regulation, Plant (physiology)</term><term>Genome-Wide Association Study</term><term>Multigene Family (physiology)</term><term>Plant Proteins (biosynthesis)</term><term>Plant Proteins (classification)</term><term>Plant Proteins (genetics)</term><term>Transcription Factors (biosynthesis)</term><term>Transcription Factors (classification)</term><term>Transcription Factors (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Plant Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Plant Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term><term>Plant Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Multigene Family</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome-Wide Association Study</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">MYB family genes are widely distributed in plants and comprise one of the largest transcription factors involved in various developmental processes and defense responses of plants. To date, few MYB genes and little expression profiling have been reported for citrus. Here, we describe and classify 177 members of the sweet orange MYB gene (CsMYB) family in terms of their genomic gene structures and similarity to their putative Arabidopsis orthologs. According to these analyses, these CsMYBs were categorized into four groups (4R-MYB, 3R-MYB, 2R-MYB and 1R-MYB). Gene structure analysis revealed that 1R-MYB genes possess relatively more introns as compared with 2R-MYB genes. Investigation of their chromosomal localizations revealed that these CsMYBs are distributed across nine chromosomes. Sweet orange includes a relatively small number of MYB genes compared with the 198 members in Arabidopsis, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative studies of CsMYBs and Arabidopsis showed that CsMYBs had fewer gene duplication events. Expression analysis revealed that the MYB gene family has a wide expression profile in sweet orange development and plays important roles in development and stress responses. In addition, 337 new putative microsatellites with flanking sequences sufficient for primer design were also identified from the 177 CsMYBs. These results provide a useful reference for the selection of candidate MYB genes for cloning and further functional analysis forcitrus.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25375352</PMID><DateCreated><Year>2014</Year><Month>11</Month><Day>7</Day></DateCreated><DateCompleted><Year>2015</Year><Month>12</Month><Day>15</Day></DateCompleted><DateRevised><Year>2014</Year><Month>11</Month><Day>7</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>11</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Genome-wide classification and evolutionary and expression analyses of citrus MYB transcription factor families in sweet orange.</ArticleTitle><Pagination><MedlinePgn>e112375</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0112375</ELocationID><Abstract><AbstractText>MYB family genes are widely distributed in plants and comprise one of the largest transcription factors involved in various developmental processes and defense responses of plants. To date, few MYB genes and little expression profiling have been reported for citrus. Here, we describe and classify 177 members of the sweet orange MYB gene (CsMYB) family in terms of their genomic gene structures and similarity to their putative Arabidopsis orthologs. According to these analyses, these CsMYBs were categorized into four groups (4R-MYB, 3R-MYB, 2R-MYB and 1R-MYB). Gene structure analysis revealed that 1R-MYB genes possess relatively more introns as compared with 2R-MYB genes. Investigation of their chromosomal localizations revealed that these CsMYBs are distributed across nine chromosomes. Sweet orange includes a relatively small number of MYB genes compared with the 198 members in Arabidopsis, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative studies of CsMYBs and Arabidopsis showed that CsMYBs had fewer gene duplication events. Expression analysis revealed that the MYB gene family has a wide expression profile in sweet orange development and plays important roles in development and stress responses. In addition, 337 new putative microsatellites with flanking sequences sufficient for primer design were also identified from the 177 CsMYBs. These results provide a useful reference for the selection of candidate MYB genes for cloning and further functional analysis forcitrus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hou</LastName><ForeName>Xiao-Jin</ForeName><Initials>XJ</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Si-Bei</ForeName><Initials>SB</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Sheng-Rui</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Chun-Gen</ForeName><Initials>CG</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jin-Zhi</ForeName><Initials>JZ</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType 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MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="Y">Plant Proteins</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="Y">Transcription Factors</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4223058</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>7</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>10</Month><Day>2</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>11</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>11</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>12</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25375352</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0112375</ArticleId><ArticleId IdType="pii">PONE-D-14-31501</ArticleId><ArticleId IdType="pmc">PMC4223058</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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