Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae

Summary Micro RNA s (mi RNA s) are short RNA s involved in gene regulation through translational inhibition and transcript cleavage. After processing from imperfect fold‐back structures, mi RNA s are incorporated into RNA ‐induced silencing complexes ( RISC s) before targeting transcripts with varying degrees of complementarity. Some mi RNA s are evolutionarily deep‐rooted, and sequence complementarity with their targets is maintained through purifying selection. Both Arabidopsis and Capsella belong to the tribe Camelineae in the Brassicaceae, with Capsella rubella serving as an outgroup to the genus Arabidopsis . The genome sequence of C. rubella has recently been released, which allows characterization of its mi RNA complement in comparison with Arabidopsis thaliana and Arabidopsis lyrata . Through next‐generation sequencing, we identify high‐confidence mi RNA candidates specific to the C. rubella lineage. Only a few lineage‐specific mi RNA s have been studied for evolutionary constraints, and there have been no systematic studies of mi RNA target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in mi RNA s and their targets within A. thaliana , and between A. thaliana , A. lyrata and C. rubella . We document a surprising amount of small‐scale variation in mi RNA –target pairs, where many mi RNA s are predicted to have species‐specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many mi RNA –target pairs can be observed even on a relatively short evolutionary time‐scale, with non‐random occurrences of differences in mi RNA s and their complements in the mi RNA precursors, the mi RNA * sequences.