Expansion Ofmir482/2118by A Class-Ii Transposable Element In Cotton

Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons,Gossypium hirsutumandGossypium barbadense, and their extant diploid progenitors,Gossypium arboreumandGossypium 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 ofMIR482/2118dinG. barbadense,G. hirsutumandG. raimondii, but not inG. arboreum. Several newly expandedMIR482/2118dloci have mutated to produce different miR482/2118 variants with altered target-gene specificity. Based on detailed analysis of sequences flanking theseMIR482/2118loci, we found that this expansion ofMIR482/2118dand its derivatives resulted from an initial capture of anMIR482/2118dby a class-II DNA transposable element (TE) inG. raimondiiprior to the tetraploidization event, followed by transposition to new genomic locations inG. barbadense,G. hirsutumandG. raimondii. The 'GosTE' involved in the capture and proliferation ofMIR482/2118dand its derivatives belongs to thePIF/Harbingersuperfamily, generating a 3-bp target site duplication upon insertion at new locations. All orthologousMIR482/2118loci 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 bothG. barbadenseandG. hirsutum, suggesting a dynamic co-evolution of miR482/2118 and itsNBS-LRRtargets. Our results provide fresh insights into the mechanisms contributing toMIRNAproliferation and enrich our knowledge on TEs.