Comparative phylogenomic analysis of 5'cis-regulatory elements (CREs) of miR160 gene family in diploid and allopolyploid cotton (Gossypium)

Cotton fiber development is a complex process regulated by numerous microRNAs (miRNAs), including miR160 that regulates auxin signaling in a grwoing cell. However, the evolution of cis-regulatory elements (CREs) in the 5'upstream regulatory regions of miR160 genes during cotton allopolyploidy is least known. Therefore, 1.5 kb upstream DNA sequences (-1 to-1500 bp) of miR160 genes from progenitor diploid A2 (G. arboreum), D5 (G. raimondii) and descendant allopolyploid AD1 (G. hirsutum) and AD2 (G. barbadense) cotton species were analyzed to visualize the evolutionary patterns preserved within the promoter regions of these homologous sequences. Several light-responsive, developmental-responsive, organ-specific, stress-responsive (biotic and abiotic), and hormone-responsive CREs were identified with diverse frequencies and wide distribution patterns. The structural alterations in the promoter regions were more prominent than the evolutionary changes acquired by miR160 genes, suggesting that miR160 gene sequences have been conserved throughout evolution, and the observed expression variations across cotton species are primarily due to the structural differences of their regulatory regions. The abiotic stress-responsive and hormone-responsive CREs exhibited prominent clustering at both proximal and distal ends, displaying varying frequencies. Thus, the origin of these CREs can be attributed to the genomic hybridization of diploid species that had led to the allopolyploid formation, or to the natural speciation/diversification of an allopolyploid event. Also, there is a high correlation between CREs-binding transcription factors and miR160 gene expression, suggesting a regulatory mechanism for spatiotemporal expression profiles of miR160 genes during cotton fiber development.