1/12/2024 0 Comments Phyre2 clc genomics workbenchHigh-salt content in soil is an adverse environmental factor that threatens growth and productivity of plants thereby reducing agricultural sustainability in affected lands (Munns, 2002 Qin et al., 2011). Its release further extended genome-wide identification and expression analyses of genes and their regulatory networks to improve knowledge about common bean (Formey et al., 2015). Meanwhile, the complete genome sequence of common bean has been recently published (Schmutz et al., 2014). Analysis of gene expression upon exposure to biotic and abiotic stresses (Liu et al., 2012 Hiz et al., 2014) or post-transcriptional regulation of gene expression (Contreras-Cubas et al., 2012) are among the common approaches performed. Due to its economic value especially for developing countries, studies have focused on improvement of agronomic and nutritional traits of this legume. As a crucial nutritional source, the global production of common bean is estimated to be 23 million metric tons and India is in first rank with 3.3 million tons annual bean production (FAO, 2014). It is marketed in different forms such as canned beans, green beans or dried beans and it is consumed mostly in grain form worldwide (Broughton et al., 2003). Common bean, Phaseolus vulgaris L., is the most important leguminous crop in human diet as a natural nutritional source with its high protein, complex carbohydrate and micronutrients content. Pulse crops are very well known species with their nitrogen fixation capacity via nodulation in symbiosis with rhizobia. Keywords: AP2-ERF family, miRNA, interactome, salt resistance, transcriptome analyses Introduction 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. 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. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST 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. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. 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. 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. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean ( Phaseolus vulgaris). 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. Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants.
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