High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes

• Published in: PloS one 2007-02, Vol.2 (2), p.e219-e219
• Main Authors: Fahlgren, Noah, Howell, Miya D, Kasschau, Kristin D, Chapman, Elisabeth J, Sullivan, Christopher M, Cumbie, Jason S, Givan, Scott A, Law, Theresa F, Grant, Sarah R, Dangl, Jeffery L, Carrington, James C
• Format: Article
• Language: English
• Subjects: Acids; Angiosperms; Arabidopsis; Arabidopsis - genetics; Arabidopsis thaliana; Base Sequence; Biological evolution; Birth; Cellular biology; Computational Biology/Genomics; Computer applications; Conservation; Conserved Sequence; Depth profiling; DNA methylation; Evolution (Biology); Evolutionary Biology/Plant Genomes and Evolution; Family; Foldback; Gene expression; Gene families; Gene sequencing; Genes; Genes, Plant; Genetics and Genomics/Functional Genomics; Genomes; High-Throughput Screening Assays; Identification methods; Loci; MicroRNA; MicroRNAs; MicroRNAs - analysis; MicroRNAs - genetics; miRNA; Molecular biology; Molecular Sequence Data; Morphogenesis; Next-generation sequencing; Plant Biology/Plant Genomes and Evolution; Plant Biology/Plant-Biotic Interactions; Plant genetics; Plant pathology; Plant sciences; Post-transcription; Proteins; Regulators; RNA, Plant - analysis; RNA, Plant - genetics; Sequence Alignment; Sequence Analysis, RNA; Sequence Homology, Nucleic Acid; Trends
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0000219

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.