Genome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions

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dc.authoridILHAN, EMRE/0000-0002-8404-7900
dc.authoridBuyuk, Ilker/0000-0002-0843-8299
dc.contributor.authorInal, Behcet
dc.contributor.authorBuyuk, Ilker
dc.contributor.authorIlhan, Emre
dc.contributor.authorAras, Sumer
dc.date.accessioned2024-12-24T19:25:04Z
dc.date.available2024-12-24T19:25:04Z
dc.date.issued2017
dc.departmentSiirt Üniversitesi
dc.description.abstractThe aim of this study was to identify and characterize the C2C2-YABBY family of genes by a genome-wide scale in common bean. Various in silico approaches were used for the study and the results were confirmed through common molecular biology techniques. Quantitative real-time PCR (qPCR) analysis was performed for identified putative PvulYABBY genes in leaf and root tissues of two common bean cultivars, namely Yakutiye and Zulbiye under salt stress condition. Eight candidate PvulYABBY proteins were discovered and the length of these proteins ranged from 173 to 256 amino acids. The isoelectric points (pIs) of YABBY proteins were between 5.18 and 9.34 and ranged from acidic to alkaline, and the molecular weight of PvulYABBYs were between 18978.4 and 28916.8 Da. Three segmentally duplicated gene couples among the identified eight PvulYABBY genes were detected. These segmentally duplicated gene couples were PvulYABBY-1/PvulYABBY-3, PvulYABBY-5/PvulYABBY-7 and PvulYABBY-6/PvulYABBY-8. The predicted number of exons among the PvulYABBY genes varied from 6 to 8 exons. Additionally, all genes found included introns within ORFs. PvulYABBY-2, -4, -5 and -7 genes were targeted by miRNAs of five plant species and a total of five miRNA families (miR5660, miR1157, miR5769, miR5286 and miR8120) were detected. According to RNA-seq analysis, all genes were up- or down-regulated except for PvulYABBY-1 and PvulYABBY-6 after salt stress treatment in leaf and root tissues of common bean. According to the qPCR analysis, six out of eight genes were expressed in the leaves but only four out of eight genes were expressed in the roots and these genes exhibited tissue-and cultivar-specific expression patterns.
dc.description.sponsorshipTUBITAK-BIDEB - International Postdoctoral Research Fellowship Programme [2219, 1059B191600028]
dc.description.sponsorshipIlker Buyuk received financial support from TUBITAK-BIDEB 2219- International Postdoctoral Research Fellowship Programme (Grant no: 1059B191600028) for his studies at Michigan State University in USA.
dc.identifier.doi10.1007/s13205-017-0933-0
dc.identifier.issn2190-572X
dc.identifier.issn2190-5738
dc.identifier.pmid28955602
dc.identifier.scopus2-s2.0-85029226773
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.1007/s13205-017-0933-0
dc.identifier.urihttps://hdl.handle.net/20.500.12604/6230
dc.identifier.volume7
dc.identifier.wosWOS:000409891100001
dc.identifier.wosqualityQ3
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherSpringer Heidelberg
dc.relation.ispartof3 Biotech
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241222
dc.subjectC2C2-YABBY
dc.subjectTranscription factors
dc.subjectRNA-seq
dc.subjectIn silico analysis
dc.subjectqPCR
dc.titleGenome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions
dc.typeArticle

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