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In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several  MIRNA  genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved  MIRNA  genes in  Arabidopsis thaliana . 48 non-conserved  MIRNA  families, nearly all of which were represented by single genes, were identified. Sequence similarity analyses of miRNA precursor foldback arms revealed evidence for recent evolutionary origin of 16  MIRNA  loci through inverted duplication events from protein-coding gene sequences. Interestingly, these recently evolved  MIRNA  genes have taken distinct paths. Whereas some non-conserved miRNAs interact with and regulate target transcripts from gene families that donated parental sequences, others have drifted to the point of non-interaction with parental gene family transcripts. Some young  MIRNA  loci clearly originated from one gene family but form miRNAs that target transcripts in another family. We suggest that  MIRNA  genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks.

High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes