Genome-Wide Survey and Characterization of AP2/Erf and HSP90 Gene Family in Five Legume Species

APETALA2/Ethylene Response Factor (AP2/ERF) and Heat Shock Protein 90 (HSP90) are important classes of transcription factor and chaperone proteins known to play a significant role under stress. Productivity and yield of legume crops are severely affected by environmental and pathogen stresses. Genome sequences of chickpea, pigeonpea, common bean along with model legumes like medicago and lotus has aided in genome-wide identification of stress responsive AP2/ERF and HSP90 genes. HMM (Hidden Markov Model), blastp searches followed by domain scanning identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 179 in common bean, 131 in medicago and 140 in lotus. Sequences with one and two AP2 domains were classified as ERFs and AP2s respectively while sequences with AP2 and B3 domain were identified as RAVs. ERFs were further sub-classified into DREBs. Number of ERFs and DREBs ranged from 67 to 98 and 41 to 55 respectively in these crops. Two soloists were identified each in chickpea, pigeonpea and lotus; common bean with one and none in medicago. However, a very less number of HSP90 genes were identified in chickpea (5), pigeonpea (7), common bean (6), medicago (5) and lotus (5). Gene, protein structures, phylogenetic analyses, functional annotation and interaction networks provided basic insights in understanding the function of AP2/ERF and HSP90 genes. Expression studies using RNA-seq and qRT-PCR in response to heat and pathogen stress were also conducted in chickpea and pigeonpea respectively in search of probable candidate genes.