Genome-wide identification and characterization of lncRNAs and miRNAs in cluster bean (Cyamopsis tetragonoloba)

Long non coding RNAs (lncRNAs) are a class of non-protein coding RNAs that play a crucial role in most of the biological activities like nodule metabolism, flowering time and male sterility. Quite often, the function of lncRNAs is species-specific in nature. Thus an attempt has been made in cluster bean (Cyamopsis tetragonoloba) for the first time to computationally identify lncRNAs based on a proposed index and study their targeted genes. Further, these targeted genes of lncRNAs were identified and characterized for their role in various biological processes like stress mechanisms, DNA damage repair, cell wall synthesis. Besides, lncRNAs and miRNAs bearing Simple Sequence Repeats (SSRs) were identified that contribute towards biogenesis of small non-coding RNAs. Moreover, five novel endogenous Target Mimic lncRNAs (eTMs) were identified that may disrupt the miRNA-mRNA regulations. For easy understanding and usability, a database CbLncRNAdb has been developed and made available at http://cabgrid.res.in/cblncrnadb.