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Open Access Highly Accessed Research article

Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis

Miao Y Xu2, Yun Dong123, Qiu X Zhang2, Lan Zhang2, Yan Z Luo2, Jie Sun1, Yun L Fan2 and Lei Wang2*

Author affiliations

1 College of Agriculture/Key Laboratory of Oasis Ecology Agriculture of BINTUAN, Shihezi University, Shihezi, 832003, China

2 Biotechnology Research Institute, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

3 Crops institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China

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Citation and License

BMC Genomics 2012, 13:421  doi:10.1186/1471-2164-13-421

Published: 24 August 2012

Abstract

Background

MicroRNAs (miRNAs) are endogenous regulators of a broad range of physiological processes and act by either degrading mRNA or blocking its translation. Oilseed rape (Brassica napus) is one of the most important crops in China, Europe and other Asian countries with publicly available expressed sequence tags (ESTs) and genomic survey sequence (GSS) databases, but little is known about its miRNAs and their targets. To date, only 46 miRNAs have been identified in B. napus.

Results

Forty-one conserved and 62 brassica-specific candidate B. napus miRNAs, including 20 miRNA* sequences, were identified using Solexa sequencing technology. Furthermore, 33 non-redundant mRNA targets of conserved brassica miRNAs and 19 new non-redundant mRNA targets of novel brassica-specific miRNAs were identified by genome-scale sequencing of mRNA degradome.

Conclusions

This study describes large scale cloning and characterization of B. napus miRNAs and their potential targets, providing the foundation for further characterization of miRNA function in the regulation of diverse physiological processes in B. napus.