Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).
Identifieur interne : 000169 ( PubMed/Checkpoint ); précédent : 000168; suivant : 000170Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).
Auteurs : Yuantao Xu [République populaire de Chine] ; Guizhi Wu [République populaire de Chine] ; Baohai Hao [République populaire de Chine] ; Lingling Chen [République populaire de Chine] ; Xiuxin Deng [République populaire de Chine] ; Qiang Xu [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- classification : Citrus sinensis.
- genetics : Citrus sinensis.
- physiology : Citrus sinensis.
- Base Composition, Cell Lineage, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Plant, Genetic Structures, Genome, Plant.
Abstract
With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions.
DOI: 10.1186/s12864-015-2211-z
PubMed: 26597278
Affiliations:
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430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Lingling" sort="Chen, Lingling" uniqKey="Chen L" first="Lingling" last="Chen">Lingling Chen</name><affiliation wicri:level="1"><nlm:affiliation>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070, China. llchen@mail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural 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type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26597278</idno><idno type="pmid">26597278</idno><idno type="doi">10.1186/s12864-015-2211-z</idno><idno type="wicri:Area/PubMed/Corpus">000109</idno><idno type="wicri:Area/PubMed/Curation">000109</idno><idno type="wicri:Area/PubMed/Checkpoint">000109</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).</title><author><name sortKey="Xu, Yuantao" sort="Xu, Yuantao" uniqKey="Xu Y" first="Yuantao" last="Xu">Yuantao Xu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. xuyuantao@webmail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Guizhi" sort="Wu, Guizhi" uniqKey="Wu G" first="Guizhi" last="Wu">Guizhi Wu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. wuguizhi@webmail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Hao, Baohai" sort="Hao, Baohai" uniqKey="Hao B" first="Baohai" last="Hao">Baohai Hao</name><affiliation wicri:level="1"><nlm:affiliation>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070, China. bio.whu@gmail.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Lingling" sort="Chen, Lingling" uniqKey="Chen L" first="Lingling" last="Chen">Lingling Chen</name><affiliation wicri:level="1"><nlm:affiliation>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070, China. llchen@mail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. xxdeng@mail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. xuqiang@mail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term><term>Cell Lineage</term><term>Citrus sinensis (classification)</term><term>Citrus sinensis (genetics)</term><term>Citrus sinensis (physiology)</term><term>Gene Expression</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Genetic Structures</term><term>Genome, Plant</term><term>Plant Proteins (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Composition</term><term>Cell Lineage</term><term>Gene Expression</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Genetic Structures</term><term>Genome, Plant</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26597278</PMID><DateCreated><Year>2015</Year><Month>11</Month><Day>24</Day></DateCreated><DateCompleted><Year>2016</Year><Month>09</Month><Day>23</Day></DateCompleted><DateRevised><Year>2015</Year><Month>11</Month><Day>26</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><PubDate><Year>2015</Year><Month>Nov</Month><Day>23</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).</ArticleTitle><Pagination><MedlinePgn>995</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-015-2211-z</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Two set of citrus LSGs, 296 citrus-specific genes (CSGs) and 1039 orphan genes specific to sweet orange, were identified by comparative analysis between the sweet orange genome sequences and 41 genomes and 273 transcriptomes. With the two sets of genes, gene structure and gene expression pattern were investigated. On average, both the CSGs and orphan genes have fewer exons, shorter gene length and higher GC content when compared with those evolutionarily conserved genes (ECs). Expression profiling indicated that most of the LSGs expressed in various tissues of sweet orange and some of them exhibited distinct temporal and spatial expression patterns. Particularly, the orphan genes were preferentially expressed in callus, which is an important pluripotent tissue of citrus. Besides, part of the CSGs and orphan genes expressed responsive to abiotic stress, indicating their potential functions during interaction with environment.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">This study identified and characterized two sets of LSGs in citrus, dissected their sequence features and expression patterns, and provided valuable clues for future functional analysis of the LSGs in sweet orange.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yuantao</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. xuyuantao@webmail.hzau.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Guizhi</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. wuguizhi@webmail.hzau.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hao</LastName><ForeName>Baohai</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070, China. bio.whu@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Lingling</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan, 430070, China. llchen@mail.hzau.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Deng</LastName><ForeName>Xiuxin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. xxdeng@mail.hzau.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Qiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China. xuqiang@mail.hzau.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>Nov</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Curr Opin Genet Dev. 2004 Dec;14(6):616-9</RefSource><PMID Version="1">15531155</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Plant Physiol. 2004 Jul;135(3):1179-97</RefSource><PMID Version="1">15266052</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Hum Mol Genet. 2006 Apr 15;15 Spec No 1:R17-29</RefSource><PMID Version="1">16651366</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9935-9</RefSource><PMID Version="1">16777968</PMID></CommentsCorrections><CommentsCorrections 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Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040342" MajorTopicYN="N">Genetic Structures</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4657247</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>5</Month><Day>7</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>11</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26597278</ArticleId><ArticleId IdType="doi">10.1186/s12864-015-2211-z</ArticleId><ArticleId IdType="pii">10.1186/s12864-015-2211-z</ArticleId><ArticleId IdType="pmc">PMC4657247</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Xu, Yuantao" sort="Xu, Yuantao" uniqKey="Xu Y" first="Yuantao" last="Xu">Yuantao Xu</name></noRegion><name sortKey="Chen, Lingling" sort="Chen, Lingling" uniqKey="Chen L" first="Lingling" last="Chen">Lingling Chen</name><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><name sortKey="Hao, Baohai" sort="Hao, Baohai" uniqKey="Hao B" first="Baohai" last="Hao">Baohai Hao</name><name sortKey="Wu, Guizhi" sort="Wu, Guizhi" uniqKey="Wu G" first="Guizhi" last="Wu">Guizhi Wu</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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