A genome-wide comparative analysis of bZIP transcription factors in G. arboreum and G. raimondii (Diploid ancestors of present-day cotton)

Basic leucine zipper motif (bZIP) transcription factors (TFs) are involved in plant growth regulation, development, and environmental stress responses. These genes have been well characterized in model plants. In current study, a genome-wide analysis of bZIP genes was performed in Gossypium raimondii and Gossypium arboreum taking Arabidopsis thaliana as a reference genome. In total, 85 members of G. raimondii and 87 members of G. arboreum were identified and designated as GrbZIPs and GabZIPs respectively. Phylogenetic analysis clustered bZIP genes into 11 subgroups (A, B, C, D, F, G, H, I, S and X). Gene structure analysis to find the intro-exon structures revealed 1-14 exons in both species. The maximum number of introns were present in subgroup G and D while genes in subgroup S were intron-less except GrbZIP78, which is a unique characteristic as compared to other groups. Results of motif analysis predicted that all three species share a common bZIP motif. A detailed comparison of bZIPs gene distribution on chromosomes has shown a diverse arrangement of genes in both cotton species. Moreover, the functional similarity with orthologs was also predicted. The findings of this study revealed close similarity in gene structure of both cotton species and diversity in gene distribution on chromosomes. This study supports the divergence of both species from the common ancestor and later diversity in gene distribution on chromosomes due to evolutionary changes. Additionally, this work will facilitate the functional characterization of bZIP genes in cotton. Outcomes of this study represent foundation research on the bZIP TFs family in cotton and as a reference for other crops.