title: A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources.
abstract: MicroRNAs (miRNAs) are important regulators of many cellular processes and exist in a wide range of eukaryotes. High-throughput 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.
authors: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Jun-Zhi
authors: JZ
authors: Wen
authors: Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Jian-You
authors: JY
authors: Liao
authors: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Ling-Ling
authors: LL
authors: Zheng
authors: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Hui
authors: H
authors: Xu
authors: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Jian-Hua
authors: JH
authors: Yang
authors: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Dao-Gang
authors: DG
authors: Guan
authors: Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Si-Min
authors: SM
authors: Zhang
authors: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Hui
authors: H
authors: Zhou
authors: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China.
authors: Liang-Hu
authors: LH
authors: Qu
mesh_terms: D030541:Databases, Genetic; D019143:Evolution, Molecular; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics*; D028521:Musa / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs