In silico Analysis of Dreb2a Gene among Diploid Oryza Species Reveal Gene Retrogression in Cultivated Species

Abstract

The dehydration-responsive element-binding (DREB) genes are types of plant-specific transcription factors that bind to DRE/CRT elements in response to abiotic stresses. It belongs to the AP2 superfamily and contains highly conserved APETELA2 (AP2) domain. In this  study, comparative analysis of DREB2A gene from diploid Oryza species was performed using BLASTN approach. The OglDREB2A  sequence (KU159742.1) was used as query against 11 diploid Oryza species in the Gramene database for identification of DREB2A  orthologs. Molecular characterization, subcellular localization, conserved motifs and promoter analysis were also performed using  bioinformatics tools. Molecular characterization of DREB2A protein in the diploid Oryza showed an AP2 conserved domain and nuclear  localized protein which is similar to putative transcription factor involved in stress responses. Motif analysis using MEME suites identified  7 significant motifs across all the diploid Oryza species with motif 2, 3, 4 and 5 as the common motifs with ~50 amino acids length.  Analysis of 1kb upstream of TSS of DREB2A of the 11 diploid Oryza species revealed many CAREs associated with stress (DRE, LTRE, ERE,  G-box, TCC-motif and Sp1) and hormonal regulations (ABREs, MeJA, GARE, and GC-motif) with ABRE as the common element in all the  diploid species. Additionally, wild species has more number of cis elements than the cultivated species suggesting a possible role in  genome evolution. Overall, the 11 DREB2A orthologs are conserved in terms of sequence homology and protein structure but cultivated  species has less number of transcripts than their progenitors suggesting gene retrogression in cultivated Oryza species.