In silico Detection of Novel MicroRNAs Genes in Soybean Genome  

作　　者：LIU Yong-xin CHANG Wei HAN Ying-peng ZOU Quan GUO Mao-zu LI Wen-bin 

机构地区：[1]Key Laboratory of Soybean Biology, Chinese Ministry of Education/Soybean Research Institute, Northeast AgricUltural University, Harbin 150030, P.R.China [2]School of Information Science and Technology, Xiamen University, Xiamen 361005, P.R. China [3]Department of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R.China

出　　处：《Agricultural Sciences in China》2011年第9期1336-1345,共10页中国农业科学（英文版）

基　　金：supported by the National High-Tech R&D Program of China (863 Program, 2006AA100104-4);the 948 Project, Ministry of Agriculture, China (2006-G5);the National Natural Science Foundation of China (30971810, 60932008);the National Basic Research Program of China (973 Program, 2009CB118400);the National Genetically Modified Organisms Breeding Major Projects of China (2009ZX08009-088B);the Postdoctoral Fund in Heilongjiang Province, China (LBH-Z07228);the Technology Project of Ministry of Education, Heilongjiang Province, China (11541025);the Technology Project of Harbin, China (2009RFQXN085)

摘　　要：The importance of microRNAs （miRNAs） at the post-transcriptional regulation level has recently been recognized in both animals and plants. In this study, the simple and most effective method of comparative genomic approach was used. First known plants miRNAs BLAST against the soybean genome, and then the located candidates were searched for novel miRNAs by RNA folding method in the vicinity （±400 nt） of the candidates. The results showed that a total of 521 novel soybean miRNA genes, including 236 mature miRNAs, were identified. All these mature miRNAs were grouped into 58 families, of which 21 of them were novel family in soybean. The upstream 2 000 nt of potential pre-miRNAs was used for promoter prediction, in order to investigate prediction of miRNAs and detect transcript unit and clustering. In this study, rniRNA genes less tend to be present as clusters in soybean. Only 9 clusters, containing 2l miRNA genes （accounted for 4.0% of the total）, were observed as part of polycistronic transcripts. Detailed analysis of sequence characteristics of novel miRNAs in soybean and all previous known plants miRNAs, were carried out. These results of this study provide a reference point for further study on miRNAs identification in plants, and improve the understanding of genome in soybean.The importance of microRNAs （miRNAs） at the post-transcriptional regulation level has recently been recognized in both animals and plants. In this study, the simple and most effective method of comparative genomic approach was used. First known plants miRNAs BLAST against the soybean genome, and then the located candidates were searched for novel miRNAs by RNA folding method in the vicinity （±400 nt） of the candidates. The results showed that a total of 521 novel soybean miRNA genes, including 236 mature miRNAs, were identified. All these mature miRNAs were grouped into 58 families, of which 21 of them were novel family in soybean. The upstream 2 000 nt of potential pre-miRNAs was used for promoter prediction, in order to investigate prediction of miRNAs and detect transcript unit and clustering. In this study, rniRNA genes less tend to be present as clusters in soybean. Only 9 clusters, containing 2l miRNA genes （accounted for 4.0% of the total）, were observed as part of polycistronic transcripts. Detailed analysis of sequence characteristics of novel miRNAs in soybean and all previous known plants miRNAs, were carried out. These results of this study provide a reference point for further study on miRNAs identification in plants, and improve the understanding of genome in soybean.

关 键 词：soybean genome MICRORNA in sillico comparative genomic approach promoters prediction CLUSTER 

分 类 号：Q943[生物学—植物学] TQ920.1[轻工技术与工程—发酵工程]