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Open Access Highly Accessed Research article

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

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

  • * Corresponding author: Jeong-Hwan Mun munjh@rda.go.kr

  • † Equal contributors

Author Affiliations

1 Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea

2 Department of Life Sciences, The Catholic University of Korea, 43 Jibong-ro Wonmi-gu, Bucheon, 420-743, Korea

3 Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro Yuseong-gu, Daejeon, 305-806, Korea

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BMC Plant Biology 2012, 12:218  doi:10.1186/1471-2229-12-218

Published: 19 November 2012

Abstract

Background

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 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.

Results

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 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.

Conclusions

This 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 webcite [1].

Keywords:
Brassica rapa; Genome; miRNA; miRNA target; Small RNA sequencing; Database