Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean

Kavas, Musa; Kurt Kızıldoğan, Aslıhan; Gökdemir, Gökhan; Baloğlu, Mehmet Cengiz

Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean

dc.contributor.author	Kavas, Musa
dc.contributor.author	Kurt Kızıldoğan, Aslıhan
dc.contributor.author	Gökdemir, Gökhan
dc.contributor.author	Baloğlu, Mehmet Cengiz
dc.date.accessioned	2016-06-06T13:52:53Z
dc.date.available	2016-06-06T13:52:53Z
dc.date.issued	2015-11-27
dc.description.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 AP2-ERF 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 (Phaseolus vulgaris). 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 AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species’ miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, 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.	en
dc.identifier.doi	10.17179/excli2015-600
dc.identifier.issn	1611-2156
dc.identifier.uri	http://hdl.handle.net/2003/35059
dc.identifier.uri	http://dx.doi.org/10.17877/DE290R-17107
dc.language.iso	en
dc.relation.ispartofseries	EXCLI Journal;Vol. 14, 2015	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/
dc.subject	AP2-ERF family	en
dc.subject	miRNA	en
dc.subject	interactome	en
dc.subject	salt resistance	en
dc.subject	transcriptome analyses	en
dc.subject.ddc	610
dc.title	Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean	en
dc.type	Text
dc.type.publicationtype	article
dcterms.accessRights	open access
eldorado.dnb.zdberstkatid	2132560-1