Expansion of MIR482/2118 by a Class II transposable element in cotton.

Some plant miRNA families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study in two tetraploid cottons Gossypium hirsutum and G. barbadense, and their extant diploid progenitors G. arboreum and G. raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. raimondii, G. hirsutum and G. barbadense, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives has resulted from an initial capture of a MIR482/2118d by a Class II DNA transposable element (TE) in G. raimondii prior to the tetraploidisation event followed by transposition to new genomic locations in G. raimondii, G. hirsutum and G. barbadense. The "GosTE" involved in capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily generating a 3-bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. hirsutum and G. barbadense, suggesting a dynamic co-evolution of miR482/2118 and its NBS-LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.