micro RNA evolution and expression analysis in polyploidized cotton genome

Summary 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, micro RNA s (mi RNA s), a new class of gene regulators, have not been well studied in polyploidization. Here, we systematically investigated mi RNA 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 mi RNA s were likely to be lost, whereas certain were remained after genome polyploidization. Cotton‐specific mi RNA s might undergo remarkably expansion, resulting in overall mi RNA 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 mi RNA s and coding genes in upland cotton. Different genome‐derived mi RNA s and mi RNA *s displayed asymmetric expression pattern, implicating their diverse functions in upland cotton. No mi RNA targeting preference was observed between different genome‐derived mi RNA s. The origin of mi RNA s and coding genes has no impact on becoming mi RNA s and their targets, despite some mi RNA s and their targets are extremely conserved in the three cotton species. GO ‐ and KEGG ‐based analysis of conserved mi RNA s show that conserved mi RNA s and their targets participate in a series of important biological processes and metabolism pathways. Additionally, A‐derived mi RNA s might be more responsible for ovule and fibre development.