Physical map of lncRNAs and lincRNAs linked with stress responsive miRs and genes network of pigeonpea (Cajanus cajan L.)

Pigeonpea (Cajanus cajan L.) is one of economically significant comestible legume crop possessing huge agricultural as well as therapeutic value. Though many reports have been published in identification of lncRNAs from recognized plant models viz., arabidopsis, maize and rice, less has been studied about lncRNAs of legume crops of Fabaceae family. Pigeonpea comprehensive transcriptome assembly data available at Legume Information System was used in this investigation. Chromosome physical maps were drawn by using locations of lncRNAs and lincRNAs in C. cajan (L.) chromosomes. The GO enrichment was extracted for all the neighbouring protein coding genes and more abundant terms were computed for each category of molecular function, biological process and cellular components by Blast2go. The targets and target mimics were predicted using psRNATarget pooled with native scripts in accordance with rules. Sixty-three novel lincRNAs were identified from pigeonpea transcriptome assembly. Stringent in-silico analyses were done to identify novel lincRNAs. Gene ontology and enrichment analysis of identified transcripts were carried out to functionally characterize lincRNAs. The result showed that 43 lincRNAs could perfectly be mapped on pigeonpea genome. We report 50 lncRNA targeting cca-miRs and 36 cca-miRs processed from lncRNAs as pre-miRs. LncRNAs act as eTM for functional mRNAs. Target networks and similar lincRNAs and targets clusters of related species are also elucidated. The results presented here will facilitate future studies to unravel the function of lincRNAs in pigeonpea proposing that the genome-wide computational analysis is a reliable method for identifying new lincRNAs and accelerating the development of biotic and abiotic stress tolerant pigeonpea varieties.