Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean
Identifieur interne : 000615 ( Main/Exploration ); précédent : 000614; suivant : 000616Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean
Auteurs : Musa Kavas [Turquie] ; Aslihan Kizildogan [Turquie] ; Gökhan Gökdemir [Turquie] ; Mehmet Cengiz Baloglu [Turquie]Source :
- EXCLI Journal [ 1611-2156 ] ; 2015.
Abstract
Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the
Url:
DOI: 10.17179/excli2015-600
PubMed: 27152109
PubMed Central: 4849109
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean</title><author><name sortKey="Kavas, Musa" sort="Kavas, Musa" uniqKey="Kavas M" first="Musa" last="Kavas">Musa Kavas</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Baloglu, Mehmet Cengiz" sort="Baloglu, Mehmet Cengiz" uniqKey="Baloglu M" first="Mehmet Cengiz" last="Baloglu">Mehmet Cengiz Baloglu</name><affiliation wicri:level="1"><nlm:aff id="A2">Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu</wicri:regionArea><wicri:noRegion>Kastamonu</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27152109</idno><idno type="pmc">4849109</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849109</idno><idno type="RBID">PMC:4849109</idno><idno type="doi">10.17179/excli2015-600</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000284</idno><idno type="wicri:Area/Pmc/Curation">000283</idno><idno type="wicri:Area/Pmc/Checkpoint">000481</idno><idno type="wicri:Area/Ncbi/Merge">002018</idno><idno type="wicri:Area/Ncbi/Curation">002018</idno><idno type="wicri:Area/Ncbi/Checkpoint">002018</idno><idno type="wicri:Area/Main/Merge">000615</idno><idno type="wicri:Area/Main/Curation">000615</idno><idno type="wicri:Area/Main/Exploration">000615</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean</title><author><name sortKey="Kavas, Musa" sort="Kavas, Musa" uniqKey="Kavas M" first="Musa" last="Kavas">Musa Kavas</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><affiliation wicri:level="1"><nlm:aff id="A1">Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Ondokuz Mayis University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun</wicri:regionArea><wicri:noRegion>Samsun</wicri:noRegion></affiliation></author><author><name sortKey="Baloglu, Mehmet Cengiz" sort="Baloglu, Mehmet Cengiz" uniqKey="Baloglu M" first="Mehmet Cengiz" last="Baloglu">Mehmet Cengiz Baloglu</name><affiliation wicri:level="1"><nlm:aff id="A2">Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu</wicri:regionArea><wicri:noRegion>Kastamonu</wicri:noRegion></affiliation></author></analytic><series><title level="j">EXCLI Journal</title><idno type="eISSN">1611-2156</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the <italic>AP2-ERF</italic> genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (<italic>Phaseolus vulgaris</italic>). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of <italic>AP2-ERF</italic> genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of <italic>AP2-ERF</italic> genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all <italic>PvAP2-ERF</italic> genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were <italic>PvAP2/ERF-20-25-62-78-113-173</italic>. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor <italic>PvAP2-ERF78</italic>, an ortholog of Arabidopsis <italic>At2G28550</italic>, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Baloglu, Mc" uniqKey="Baloglu M">MC Baloglu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baloglu, Mc" uniqKey="Baloglu M">MC Baloglu</name></author><author><name sortKey="Eldem, V" uniqKey="Eldem V">V Eldem</name></author><author><name sortKey="Hajyzadeh, M" uniqKey="Hajyzadeh M">M Hajyzadeh</name></author><author><name sortKey="Unver, T" uniqKey="Unver T">T Unver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Berman, Hm" uniqKey="Berman H">HM Berman</name></author><author><name sortKey="Westbrook, J" uniqKey="Westbrook J">J 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Cengiz" sort="Baloglu, Mehmet Cengiz" uniqKey="Baloglu M" first="Mehmet Cengiz" last="Baloglu">Mehmet Cengiz Baloglu</name><name sortKey="Gokdemir, Gokhan" sort="Gokdemir, Gokhan" uniqKey="Gokdemir G" first="Gökhan" last="Gökdemir">Gökhan Gökdemir</name><name sortKey="Kizildogan, Aslihan" sort="Kizildogan, Aslihan" uniqKey="Kizildogan A" first="Aslihan" last="Kizildogan">Aslihan Kizildogan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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