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Abstract

MicroRNAs (miRNAs) are short RNA sequences involved in gene regulation through translational inhibition and transcript cleavage that are found in both plants and animals. The miRNAs are processed from imperfect foldback structures and incorporated into RNA-induced silencing complexes before targeting transcripts with high sequence complementarity. Some miRNAs are evolutionarily deeply rooted and their homology with their targets is maintained through purifying selection. Only a few lineage-specific miRNAs have been studied for evolutionary constraints. The increasing number of related high-quality genomes will facilitate a better understanding of miRNA evolution. An emerging model species of the Camelineae and the Brassicaceae is Capsella rubella, which closely related to Arabidopsis thaliana and Arabidopsis lyrata. Here we describe the miRNA complement of C. rubella. In addition to verifying miRNAs conserved between C. rubella and A. thaliana, we identify new high-confidence miRNA candidates specific to the C. rubella lineage. We examine conservation of miRNAs and their targets between the three Camelineae species, C. rubella, A. lyrata and A. thaliana. miRNAs of the 20/21nt class are most deeply conserved and have significantly lower divergence than those of the 22nt size class that are less evolutionarily conserved. Most targets of miRNAs are predicted in only a single species and not conserved across the Camelineae indicating the transitive nature of most miRNA-target pairings on an evolutionary time scale. We present additional results on the polymorphism of miRNAs and their targets in 80 resequenced accessions of A. thaliana.