title: Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration.
abstract: Members of basic helix-loop-helix (bHLH) gene family found in all eukaryotes play crucial roles in response to stress. Though, most eukaryotes carry the proteins of this family, biological functions of the most bHLH family members are not deeply evaluated in plants. In this study, we conducted a comprehensive genome-wide analysis of bHLH transcription factors in salt tolerant common bean. We identified 155 bHLH protein-encoding genes (PvbHLH) by using in silico comparative genomics tools. Based on the phylogenetic tree, PvbHLH genes were classified into 8 main groups with 21 subfamilies. Exon-intron analysis indicated that proteins belonging to same main groups exhibited a closely related gene structure. While, the PvbHLH gene family has been mainly expanded through segmental duplications, a total of 11 tandem duplication were detected. Genome-wide expression analysis of bHLH genes showed that 63 PvbHLH genes were differentially expressed in at least one tissue. Three of them displayed higher expression values in both leaf and root tissues. The in silico micro-RNA target transcript analyses revealed that totally 100 PvHLH genes targeted by 86 plant miRNAs. The most abundant transcripts, which were targeted by all 18 plant miRNA, were belonging to PvHLH-22 and PvHLH-44 genes. The expression of 16 PvbHLH genes in the root and leaf tissues of salt-stressed common bean was evaluated using qRT-PCR. Among them, two of PvbHLHs, PvbHLH-54, PvbHLH-148, were found to be up-regulated in both tissues in correlation with RNA-seq measurements. The results of this study could help improve understanding of biological functions of common bean bHLH family under salt stress. Additionally, it may provide basic resources for analyzing bHLH protein function for improving economic, agronomic and ecological benefit in common bean and other species.
authors.affiliation: Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey. musa.kavas@omu.edu.tr.
authors.forename: Musa
authors.initials: M
authors.lastname: Kavas
authors.affiliation: Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey.
authors.forename: Mehmet Cengiz
authors.initials: MC
authors.lastname: Baloğlu
authors.affiliation: Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey.
authors.forename: Elif Seda
authors.initials: ES
authors.lastname: Atabay
authors.affiliation: Department of Biology, Faculty of Science, Çankırı Karatekin University, Cankiri, Turkey.
authors.forename: Ummugulsum Tanman
authors.initials: UT
authors.lastname: Ziplar
authors.affiliation: Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey.
authors.forename: Hayriye Yıldız
authors.initials: HY
authors.lastname: Daşgan
authors.affiliation: Department of Biology, Faculty of Science, Çankırı Karatekin University, Cankiri, Turkey.
authors.forename: Turgay
authors.initials: T
authors.lastname: Ünver
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D005091:Exons / Q000235:genetics; D020440:Gene Duplication / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D007438:Introns / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D012965:Sodium Chloride / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D035683:MicroRNAs; D012965:Sodium Chloride
keywords: Phaseolus vulgaris; Salt stress response; Transcription factor; bHLH gene family