microRNA evolution and expression analysis in polyploidized cotton genome.

Cotton (Gossypium hirsutum L.), the most important fibre plant in the world, is a tetraploid species, originating from the reunion of two ancestral cotton species ~1-2 million years ago. It has been reported that a great number of genes were quickly erased or preferentially remained after whole-genome duplication, ultimately leading to morphogenesis evolution. However, microRNAs (miRNAs), a new class of gene regulators, have not been well studied in polyploidization. Here, we systematically investigated miRNA evolution amongst cultivated upland cotton G. hirsutum (AADD) and its two ancestors, G. arboreum (AA) and G. raimondii (DD). Our results show that certain highly conserved miRNAs were likely to be lost, whereas certain were remained after genome polyploidization. Cotton-specific miRNAs might undergo remarkably expansion, resulting in overall miRNA increase in upland cotton. Based on the sequenced genomes of G. arboreum and G. raimondii, we are capable for the first time to categorize the origin of miRNAs and coding genes in upland cotton. Different genome-derived miRNAs and miRNA*s displayed asymmetric expression pattern, implicating their diverse functions in upland cotton. No miRNA targeting preference was observed between different genome-derived miRNAs. The origin of miRNAs and coding genes has no impact on becoming miRNAs and their targets, despite some miRNAs and their targets are extremely conserved in the three cotton species. GO- and KEGG-based analysis of conserved miRNAs show that conserved miRNAs and their targets participate in a series of important biological processes and metabolism pathways. Additionally, A-derived miRNAs might be more responsible for ovule and fibre development.