Comparative evolutionary dynamics of the 5’cis-regulatory elements (CREs) of miR167 genes in diploid and allopolyploid cotton species

Cotton fiber morphogenesis is tightly regulated by several microRNAs (miRNAs) including miR167 which regulates auxin-signaling through the transcriptional regulation of its target genes during fiber development. To emphasize the evolution of spatiotemporal regulatory attributes of miR167 genes during fiber development, a comparative analysis of 5′cis-regulatory elements (CREs) and coding sequences of miR167 genes from progenitor diploid A2 (G. arboreum), D5 (G. raimondii) species and decedent allopolyploid AD1 (G. hirsutum) and AD2 (G. barbadense) species were performed in an evolutionary framework. Interestingly, different miR167 genes were conserved both in A- and D-subgenomes of AD1 and AD2 species (>90% sequence similarities) and acquired the least variations in gene sequences during allopolyploidy followed by species diversification. However, substantial accumulation of structural variations in 1.5kb long upstream regions exhibited that the regulatory regions had undergone extensive evolutionary changes during cotton evolution in both diploid and allopolyploid species. Several unique CREs could be identified and further classified into development-, light-, organ-, stress- and hormone-responsive motifs with their varied frequencies. Co-expression analyses of miR167 genes and their respective CREs-binding transcription factors (TFs) showed tissue- and developmental stage-specific correlation, especially with bHLH transcription factor (R2 = 0.93) during fiber initiation and elongation stages of AD1 species. The reconstructed gene networks of the most significant predicted TFs with CREs underscored the possible genetic control mechanisms of these factors during fiber development. These observations highlighted that various regulatory motifs were preserved during cotton evolution and may be exploited for future crop improvement programs.