Identification and profiling of novel microRNAs in the Brassica rapagenome based on small RNA deep sequencing

BMC Plant Biology

Research Article

Mijin Oh¹  Sin-Gi Park¹  Bumjin Kim¹  Ja Young Shin¹  Jeong-Hwan Mun¹  Hee-Ju Yu²  Namshin Kim³ 

[1] Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, 441-707, Suwon, Korea;Department of Life Sciences, The Catholic University of Korea, 43 Jibong-ro Wonmi-gu, 420-743, Bucheon, Korea;Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro Yuseong-gu, 305-806, Daejeon, Korea;

关键词: Brassica rapa;    Genome;    miRNA;    miRNA target;    Small RNA sequencing;    Database;   

DOI  :  10.1186/1471-2229-12-218

 received in 2012-06-01, accepted in 2012-11-14,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (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 Brassica rapa genome enables us to identify miRNAs and their putative target genes. In this study, we sought to provide a more comprehensive prediction of B. rapa miRNAs based on high throughput small RNA deep sequencing.ResultsWe 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 B. rapa 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 B. rapa and Arabidopsis thaliana genomes demonstrated that redundant copies of conserved miRNAs in the B. rapa genome may have been deleted after whole genome triplication. Novel miRNA members seemed to have spontaneously arisen from the B. rapa and A. thaliana genomes, suggesting the species-specific expansion of miRNAs. We have made this data publicly available in a miRNA database of B. rapa 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.ConclusionsThis is the first report to identify novel miRNAs from Brassica 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 B. rapa and other closely related Brassica species. The database is available at the following link: http://bramrs.rna.kr [1].

【 授权许可】

Unknown   
© Kim et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.