Non-coding RNAs having strong positive interaction with mRNAs reveal their regulatory nature during flowering in a wild relative of pigeonpea (Cajanus scarabaeoides).

In higher plants, flower development is a result of crosstalk between many factors like photoperiod, vernalization, hormone concentration, epigenetic modification etc. and is also regulated by non-coding RNAs (ncRNAs). In the present study, we are reporting the involvement of long non-coding RNAs (lncRNAs) and miRNAs during the process of flower development in Cajanus scarabaeoides, an important wild relative of pigeonpea. The transcriptome of floral and leaf tissues revealed a total of 1672 lncRNAs and 57 miRNAs being expressed during flower development. Prediction analysis of identified lncRNAs showed that 1593 lncRNAs were targeting 3420 mRNAs and among these, 98 were transcription factors (TFs) belonging to 48 groups. All the identified 57 miRNAs were novel, suggesting their genera specificity. Prediction of the secondary structure of lncRNAs and miRNAs followed by interaction analysis revealed that 199 lncRNAs could interact with 47 miRNAs where miRNAs were acting in the root of interaction. Gene Ontology of the ncRNAs and their targets showed the potential role of lncRNAs and miRNAs in the flower development of C. scarabaeoides. Among the identified interactions, 17 lncRNAs were endogenous target mimics (eTMs) for miRNAs that target flowering-related transcription factors. Expression analysis of identified transcripts revealed that higher expression of Csa-lncRNA_1231 in the bud sequesters Csa-miRNA-156b by indirectly mimicking the miRNA and leading to increased expression of flower-specific SQUAMOSA promoter-binding protein-like (SPL-12) TF indicating their potential role in flower development. The present study will help in understanding the molecular regulatory mechanism governing the induction of flowering in C. scarabaeoides.