A contig-based strategy for the genome-wide discovery of MicroRNAs without complete genome resources

Jun Zhi Wen, Jian You Liao, Ling Ling Zheng, Hui Xu, Jian Hua Yang, Daogang Guan, Si Min Zhang, Hui Zhou, Liang Hu Qu

Research output: Contribution to journalJournal articlepeer-review

10 Citations (Scopus)


MicroRNAs (miRNAs) are important regulators of many cellular processes and exist in a wide range of eukaryotes. Highthroughput sequencing is a mainstream method of miRNA identification through which it is possible to obtain the complete small RNA profile of an organism. Currently, most approaches to miRNA identification rely on a reference genome for the prediction of hairpin structures. However, many species of economic and phylogenetic importance are non-model organisms without complete genome sequences, and this limits miRNA discovery. Here, to overcome this limitation, we have developed a contig-based miRNA identification strategy. We applied this method to a triploid species of edible banana (GCTCV-119, Musa spp. AAA group) and identified 180 pre-miRNAs and 314 mature miRNAs, which is three times more than those were predicted by the available dataset-based methods (represented by EST +GSS). Based on the recently published miRNA data set of Musa acuminate, the recall rate and precision of our strategy are estimated to be 70.6% and 92.2%, respectively, significantly better than those of EST+GSS-based strategy (10.2% and 50.0%, respectively). Our novel, efficient and cost-effective strategy facilitates the study of the functional and evolutionary role of miRNAs, as well as miRNA-based molecular breeding, in non-model species of economic or evolutionary interest.

Original languageEnglish
Article numbere88179
Number of pages8
JournalPLoS ONE
Issue number2
Publication statusPublished - 7 Feb 2014

Scopus Subject Areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General


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