Genome-wide identification of long non-coding RNAs in two contrasting rapeseed (Brassica napus L.) genotypes subjected to cold stress

Noncoding RNAs are typically more than 200 nucleotides in lengths with indiscernible protein coding potential defined as long non-coding RNA (lncRNAs). LncRNAs play a versatile role in plant growth, development, and responses to various ecological perturbations particularly cold. However, a comprehensive identification of lncRNAs responsive to cold stress in B. napus has not been identified. The aim of the present study was to identify potential lncRNAs in cold tolerant (CT-C18) and cold-sensitive (CS-C6) B. napus varieties under cold stress. A total of 11073 lncRNAs were identified in both varieties of Brassica. In CT-C18 variety, 2394 and 3508 lncRNAs were expressed at 1d and 7d after cold stress, respectively. Furthermore, 3347 and 3872 lncRNAs were expressed at 1d and 7d in CS-C6 variety, respectively. Fifteen lncRNAs were found to be target mimics of 23 miRNAs. Additionally, a total of 16 lncRNAs were predicted as precursors of B. napus miRNAs seven miRNA family. Moreover, weighted gene co-expression network analysis revealed that four modules correlate with the expression status of protein-coding genes with lncRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis shown that out of those 170 gene were tagged with 60 Enzyme Code, and 101 GO terms. Our study increased the understanding of the expression and characterization of B. napus lncRNAs in response to cold stress, which may use as a reference for functional-based studies of targeting putative lncRNAs particularly under cold stress.