Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera.
Identifieur interne : 001856 ( Main/Exploration ); précédent : 001855; suivant : 001857Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in Nelumbo nucifera.
Auteurs : Qijiang Jin [République populaire de Chine] ; Xin Hu [République populaire de Chine] ; Xin Li [République populaire de Chine] ; Bei Wang [République populaire de Chine] ; Yanjie Wang [République populaire de Chine] ; Hongwei Jiang [République populaire de Chine] ; Neil Mattson [États-Unis] ; Yingchun Xu [République populaire de Chine]Source :
- Frontiers in plant science [ 1664-462X ] ; 2016.
Abstract
Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions. The dN /dS ratios were always less than 1 for different domains and regions outside domains, suggesting purifying selection on the lotus TPS gene family. The regions outside TPS domain evolved relatively faster than NnTPS domains. A phylogenetic tree was constructed using all predicted coding sequences of lotus TPS genes, together with those from Arabidopsis, poplar, soybean, and rice. The result indicated that those TPS genes could be clearly divided into two main subfamilies (I-II), where each subfamily could be further divided into 2 (I) and 5 (II) subgroups. Analyses of divergence and adaptive evolution show that purifying selection may have been the main force driving evolution of plant TPS genes. Some of the critical sites that contributed to divergence may have been under positive selection. Transcriptome data analysis revealed that most NnTPS genes were predominantly expressed in sink tissues. Expression pattern of NnTPS genes under copper and submergence stress indicated that NNU_014679 and NNU_022788 might play important roles in lotus energy metabolism and participate in stress response. Our results can facilitate further functional studies of TPS genes in lotus.
DOI: 10.3389/fpls.2016.01445
PubMed: 27746792
PubMed Central: PMC5040708
Affiliations:
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University Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University Nanjing</wicri:regionArea><wicri:noRegion>Nanjing Agricultural University Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Li, Xin" sort="Li, Xin" uniqKey="Li X" first="Xin" last="Li">Xin Li</name><affiliation wicri:level="1"><nlm:affiliation>Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou</wicri:regionArea><wicri:noRegion>Institute of Agricultural Science of Taihu Lake District Suzhou</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Bei" sort="Wang, Bei" uniqKey="Wang B" first="Bei" last="Wang">Bei Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University Nanjing</wicri:regionArea><wicri:noRegion>Nanjing Agricultural University Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Yanjie" sort="Wang, Yanjie" uniqKey="Wang Y" first="Yanjie" last="Wang">Yanjie Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University Nanjing</wicri:regionArea><wicri:noRegion>Nanjing Agricultural University Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Hongwei" sort="Jiang, Hongwei" uniqKey="Jiang H" first="Hongwei" last="Jiang">Hongwei Jiang</name><affiliation wicri:level="1"><nlm:affiliation>Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou</wicri:regionArea><wicri:noRegion>Institute of Agricultural Science of Taihu Lake District Suzhou</wicri:noRegion></affiliation></author><author><name sortKey="Mattson, Neil" sort="Mattson, Neil" uniqKey="Mattson N" first="Neil" last="Mattson">Neil Mattson</name><affiliation wicri:level="2"><nlm:affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticulture Section, School of Integrative Plant Science, Cornell University Ithaca, NY</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Xu, Yingchun" sort="Xu, Yingchun" uniqKey="Xu Y" first="Yingchun" last="Xu">Yingchun Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University Nanjing</wicri:regionArea><wicri:noRegion>Nanjing Agricultural University Nanjing</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available <i>Nelumbo nucifera</i> (lotus) genome sequence database was analyzed which led to identification of nine lotus <i>TPS</i> genes (<i>NnTPS</i>). It was found that at least two introns are included in the coding sequences of <i>NnTPS</i> genes. When the motif compositions were analyzed we found that <i>NnTPS</i> generally shared the similar motifs, implying that they have similar functions. The <i>d</i><sub><i>N</i></sub> /<i>d</i><sub><i>S</i></sub> ratios were always less than 1 for different domains and regions outside domains, suggesting purifying selection on the lotus <i>TPS</i> gene family. The regions outside TPS domain evolved relatively faster than NnTPS domains. A phylogenetic tree was constructed using all predicted coding sequences of lotus <i>TPS</i> genes, together with those from <i>Arabidopsis</i>, poplar, soybean, and rice. The result indicated that those <i>TPS</i> genes could be clearly divided into two main subfamilies (I-II), where each subfamily could be further divided into 2 (I) and 5 (II) subgroups. Analyses of divergence and adaptive evolution show that purifying selection may have been the main force driving evolution of plant <i>TPS</i> genes. Some of the critical sites that contributed to divergence may have been under positive selection. Transcriptome data analysis revealed that most <i>NnTPS</i> genes were predominantly expressed in sink tissues. Expression pattern of <i>NnTPS</i> genes under copper and submergence stress indicated that NNU_014679 and NNU_022788 might play important roles in lotus energy metabolism and participate in stress response. Our results can facilitate further functional studies of <i>TPS</i> genes in lotus.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27746792</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Genome-Wide Identification and Evolution Analysis of Trehalose-6-Phosphate Synthase Gene Family in <i>Nelumbo nucifera</i>.</ArticleTitle><Pagination><MedlinePgn>1445</MedlinePgn></Pagination><Abstract><AbstractText>Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available <i>Nelumbo nucifera</i> (lotus) genome sequence database was analyzed which led to identification of nine lotus <i>TPS</i> genes (<i>NnTPS</i>). It was found that at least two introns are included in the coding sequences of <i>NnTPS</i> genes. When the motif compositions were analyzed we found that <i>NnTPS</i> generally shared the similar motifs, implying that they have similar functions. The <i>d</i><sub><i>N</i></sub> /<i>d</i><sub><i>S</i></sub> ratios were always less than 1 for different domains and regions outside domains, suggesting purifying selection on the lotus <i>TPS</i> gene family. The regions outside TPS domain evolved relatively faster than NnTPS domains. A phylogenetic tree was constructed using all predicted coding sequences of lotus <i>TPS</i> genes, together with those from <i>Arabidopsis</i>, poplar, soybean, and rice. The result indicated that those <i>TPS</i> genes could be clearly divided into two main subfamilies (I-II), where each subfamily could be further divided into 2 (I) and 5 (II) subgroups. Analyses of divergence and adaptive evolution show that purifying selection may have been the main force driving evolution of plant <i>TPS</i> genes. Some of the critical sites that contributed to divergence may have been under positive selection. Transcriptome data analysis revealed that most <i>NnTPS</i> genes were predominantly expressed in sink tissues. Expression pattern of <i>NnTPS</i> genes under copper and submergence stress indicated that NNU_014679 and NNU_022788 might play important roles in lotus energy metabolism and participate in stress response. Our results can facilitate further functional studies of <i>TPS</i> genes in lotus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jin</LastName><ForeName>Qijiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Xin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Xin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Bei</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yanjie</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Hongwei</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Leisure Agricultural Section, Institute of Agricultural Science of Taihu Lake District Suzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mattson</LastName><ForeName>Neil</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Horticulture Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yingchun</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Horticulture, Nanjing Agricultural University Nanjing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>09</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Nelumbo nucifera</Keyword><Keyword MajorTopicYN="N">expression pattern</Keyword><Keyword MajorTopicYN="N">molecular evolution</Keyword><Keyword MajorTopicYN="N">protein properties</Keyword><Keyword MajorTopicYN="N">trehalose-6-phosphate synthase</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>06</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>09</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>10</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>10</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>10</Month><Day>18</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27746792</ArticleId><ArticleId IdType="doi">10.3389/fpls.2016.01445</ArticleId><ArticleId IdType="pmc">PMC5040708</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Genetics. 1999 Apr;151(4):1531-45</Citation><ArticleIdList><ArticleId 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Wang</name><name sortKey="Wang, Yanjie" sort="Wang, Yanjie" uniqKey="Wang Y" first="Yanjie" last="Wang">Yanjie Wang</name><name sortKey="Xu, Yingchun" sort="Xu, Yingchun" uniqKey="Xu Y" first="Yingchun" last="Xu">Yingchun Xu</name></country><country name="États-Unis"><region name="État de New York"><name sortKey="Mattson, Neil" sort="Mattson, Neil" uniqKey="Mattson N" first="Neil" last="Mattson">Neil Mattson</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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