Genome-wide identification, functional prediction and expression profiling of long non-coding RNAs in Camelina sativa

Long non-coding RNAs (lncRNAs) are a class of RNA regulatory molecules having roles in wide range of biological processes. They have been demonstrated to regulate gene expression at the posttranscriptional and transcriptional levels and to function in stress responses in plants and animals, but nothing is known about lncRNAs in Camelina (Camelina sativa L.), an emerging oil crop. Here, we report the first prediction of lncRNAs in the Camelina genome using comprehensive genomic approaches. We examined a Camelina drought stress cDNA library, and 5390 candidate Camelina sativa lncRNAs (CsalncRNAs) were identified, including 670 sense, 692 antisense, 1347 intergenic, and 2681 intronic harboring CsalncRNAs. The identified CsalncRNAs had an average nucleotide (nt) length of 497 bp and were mapped on each chromosome of C. sativa. Functional characterization through gene ontology (GO) and GO motif (GOMo) analysis of neighboring protein coding (PC) genes and motifs in the intergenic CsalncRNAs, respectively, indicated that these CsalncRNAs were involved in transcription-related activity, proteins, DNA and RNA binding, and abiotic/biotic stress response. Approximately 4.6% of CsalncRNA sequences were masked as repeat elements enriched with many repetitive sequences of transposable elements (TE), indicating the involvement of transposon silencing. Additionally, 55 intergenic CsalncRNAs were predicted as targets of miRNA, whereas nine target mimics were identified. Expression profiling of seven randomly selected CsalncRNAs using real-time quantitative polymerase chain reaction (RT-qPCR) showed tissue-specific expression, and these were highly up-regulated in Camelina leaves under extreme drought. Results of expression profiling indicated that these CsalncRNAs are involved in the progression of Camelina growth and development as well as its response to drought stress. Our results provide a basis for the functional study of lncRNAs in C. sativa that will serve as a valuable resource for future studies of the regulatory mechanisms underlying its growth and development as well as its stress response.