Identification and profiling of novel microRNAs in the <it>Brassica rapa</it> genome based on small RNA deep sequencing

• Main Authors: Kim Bumjin, Yu Hee-Ju, Park Sin-Gi, Shin Ja Young, Oh Mijin, Kim Namshin, Mun Jeong-Hwan
• Format: Article
• Language: English
• Published: BMC 2012-11-01
• Series: BMC Plant Biology
• Subjects: <it>Brassica rapa</it>; Genome; miRNA; miRNA target; Small RNA sequencing; Database
• Online Access: http://www.biomedcentral.com/1471-2229/12/218

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are one of the functional non-coding small RNAs involved in the epigenetic control of the plant genome. Although plants contain both evolutionary conserved miRNAs and species-specific miRNAs within their genomes, computational methods often only identify evolutionary conserved miRNAs. The recent sequencing of the <it>Brassica rapa</it> genome enables us to identify miRNAs and their putative target genes. In this study, we sought to provide a more comprehensive prediction of <it>B. rapa</it> miRNAs based on high throughput small RNA deep sequencing.</p> <p>Results</p> <p>We sequenced small RNAs from five types of tissue: seedlings, roots, petioles, leaves, and flowers. By analyzing 2.75 million unique reads that mapped to the <it>B. rapa</it> genome, we identified 216 novel and 196 conserved miRNAs that were predicted to target approximately 20% of the genome’s protein coding genes. Quantitative analysis of miRNAs from the five types of tissue revealed that novel miRNAs were expressed in diverse tissues but their expression levels were lower than those of the conserved miRNAs. Comparative analysis of the miRNAs between the <it>B. rapa</it> and <it>Arabidopsis thaliana</it> genomes demonstrated that redundant copies of conserved miRNAs in the <it>B. rapa</it> genome may have been deleted after whole genome triplication. Novel miRNA members seemed to have spontaneously arisen from the <it>B. rapa</it> and <it>A. thaliana</it> genomes, suggesting the species-specific expansion of miRNAs. We have made this data publicly available in a miRNA database of <it>B. rapa</it> called BraMRs. The database allows the user to retrieve miRNA sequences, their expression profiles, and a description of their target genes from the five tissue types investigated here.</p> <p>Conclusions</p> <p>This is the first report to identify novel miRNAs from <it>Brassica</it> crops using genome-wide high throughput techniques. The combination of computational methods and small RNA deep sequencing provides robust predictions of miRNAs in the genome. The finding of numerous novel miRNAs, many with few target genes and low expression levels, suggests the rapid evolution of miRNA genes. The development of a miRNA database, BraMRs, enables us to integrate miRNA identification, target prediction, and functional annotation of target genes. BraMRs will represent a valuable public resource with which to study the epigenetic control of <it>B. rapa</it> and other closely related <it>Brassica</it> species. The database is available at the following link: <url>http://bramrs.rna.kr</url> [1].</p>