Research article

Identification of novel and candidate miRNAs in rice by high throughput sequencing

Ramanjulu Sunkar^{* 1} , Xuefeng Zhou^{* 2} , Yun Zheng² , Weixiong Zhang² and Jian-Kang Zhu³

¹Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA

²Department of Computer Science and Engineering, Washington University in St. Louis, 1 Brookings Drive, St Louis MO 63130, USA

³Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

author email corresponding author email* Contributed equally

BMC Plant Biology 2008, 8:25doi:10.1186/1471-2229-8-25

Published:	29 February 2008

Abstract

Background

Small RNA-guided gene silencing at the transcriptional and post-transcriptional levels has emerged as an important mode of gene regulation in plants and animals. Thus far, conventional sequencing of small RNA libraries from rice led to the identification of most of the conserved miRNAs. Deep sequencing of small RNA libraries is an effective approach to uncover rare and lineage- and/or species-specific microRNAs (miRNAs) in any organism.

Results

In order to identify new miRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing. A total of 58,781, 43,003 and 80,990 unique genome-matching small RNAs were obtained from the control, drought and salt stress libraries, respectively. Sequence analysis confirmed the expression of most of the conserved miRNAs in rice. Importantly, 23 new miRNAs mostly each derived from a unique locus in rice genome were identified. Six of the new miRNAs are conserved in other monocots. Additionally, we identified 40 candidate miRNAs. Allowing not more than 3 mis-matches between a miRNA and its target mRNA, we predicted 20 targets for 9 of the new miRNAs.

Conclusion

Deep sequencing proved to be an effective strategy that allowed the discovery of 23 low-abundance new miRNAs and 40 candidate miRNAs in rice.