Functional Genomics: Small RNAs and Long Noncoding RNAs in Salvia miltiorrhiza

Noncoding RNAs (ncRNAs) play crucial regulatary roles in plant development and are current research hotspots of RNA biology. ncRNAs can be divided into small RNAs (<40nt), such as microRNAs (miRNAs) and small-interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs) (>40nt), such as mRNA-like noncoding RNAs (mlncRNAs). Salvia miltiorrhiza Bunge is a well-known Salvia species in the Labiatae family. It has been widely used in the treatment of cardiovascular, hyperlipidemia, cerebrovascular and acute ischemic stroke diseases, and is an emerging model medicinal plant. There is no information available for ncRNAs in S. miltiorrhiza. Using the Solexa deep sequencing technology, five small RNA libraries from S. miltiorrhiza roots at different developmental stages were sequenced. From over 50 million small RNA reads, hundreds of miRNAs and ta-siRNAs were computationally idntified. Through the prediction of their targets, it showed that these small RNAs were associated with root development and involved in plant response to stress. Moreover, over 8 million S. miltiorrhiza ESTs from GenBank database and PlantGDB were assembled into 44422 unigenes, from which 5446 mlncRNA candidates were identified.  It includes a signigicant number of siRNA-generating mlncRNAs and two conserved miRNA-producing ones. miRNA targets were predicted and eight of them were experimentally validated. Among the 5446 mlncRNA candidates, 2030 unigenes were grouped into 470 families with at least two members in a family. Based on conservation analysis, the majority of mlncRNAs were species-specific. Additionally, about 1207 mlncRNAs contain regions significantly homologous or complementary to 3902 S. miltiorrhiza protein-coding genes, of which 38 encode transcription factors, 10 are related to secondary metabolism and 23 are associated with diseases. Using the quantitative real-time PCR method, tissue-specific expression patterns of mlncRNA candidates with at least 900nt were obtained. The results provide a basis for elucidating the function of noncoding RNAs in S. miltiorrhiza.