Computational Identification Noncoding RNAs in Salvia Miltiorrhiza Bunge, Including 46 Conserved and Non-Conserved miRNAs

Regulatory non-coding RNAs (ncRNAs) including miRNAs, play important roles in diverse biological processes including chromatin modification, mRNA synthesis or stability, and protein synthesis or repression. Now more and more experimental validated ncRNA have been founded, in fact there are more regulatory ncRNA than we expected, with increasing transcribed data, it is the time for us to data mining ncRNA in plant and animal. Focusing on the functional genomics research of Danshen (a medicinal plant, Salvia miltiorrhiza Bunge) in our lab, in this article we use the EST data of Danshen to predict Danshen ncRNAs, but out method can apply to other plants and animals.To attempt to identify regulatory ncRNAs encoded by Danshen, we applied a computational method to predict ncRNAs and miRNAs. Altogether, we predicted of 3234 ncRNAs, including 301 assembled and 2933 singleton ncRNAs. Also we predicted of 46 miRNAs based on predicted ncRNA, 2 of them are conserved in other model plants. At last, we predicted 29 miRNA targets for these predicted miRNAs.