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

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Abstract

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.

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Acknowledgements

This research was supported by the funds from Bio-industry Technology Development Program (No. 312033-5) and Golden Seed Project (Center for Vegetable Seed Development, No. 213003-05-1-SBW30), Ministry of Agriculture, Food and Rural Affairs (MAFRA) of Korea, and iPET (Korea Institute of Planning and Evaluation for Technology in Agriculture, Food and Rural Affairs).

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  1. Department of Horticulture, Chungnam National University, Daejeon, 34134, South Korea

    Saminathan Subburaj, Yongsam Jeon, Luhua Tu, Yong-Tae **, Shipra Kumari & Geung-Joo Lee

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  1. Saminathan Subburaj
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10725_2018_410_MOESM1_ESM.tif

Supplementary Figure S1. Functional annotation of protein-coding genes identified as neighboring to the CsalncRNAs. All the genes are classified into three different categories as annotated by the GO terms. (A) Primary functions; (B) Biological processes; (C) Cellular components of the neighboring genes. (TIF 995 KB)

10725_2018_410_MOESM2_ESM.tif

Supplementary Figure S2. Hierarchical clustering analysis of all expressed CsalncRNAs and their nearest PC genes from the drought-induced Camelina leaf transcriptome library. Co-expression patterns of CsalncRNAs and their 5’ and 3’ neighboring PC genes were assessed by Log2 fold-change expression values from the EST transcriptome resource. In heatmap, red (A1–3) and green (B1–3) boxes represent CsalncRNA up-regulation: PC gene down-regulation and CsalncRNA down-regulation: PC gene up-regulation during drought conditions (10 kPa, 100 kPa, and Re-hyd), respectively. Reverse or positive correlation in expression between CsalncRNAs and neighboring PC genes are indicated by a blue bracket in heatmap. On the right-side panel, Venn analysis shows the number of CsalncRNAs that were up-regulated (A1–3) and down-regulated (B1–3) during each drought and in all drought conditions. Below, a color bar scale indicating either up- (red) or down- (green) regulation of expression. (TIF 2191 KB)

10725_2018_410_MOESM3_ESM.docx

Supplementary Table S1. List of primers designed and used in RT-qPCR analysis to determine the expression levels of lncRNAs in this study. (DOCX 12 KB)

Supplementary Table S2. List of lncRNAs identified in the Camelina leaf transcriptome library. (XLSX 1004 KB)

10725_2018_410_MOESM5_ESM.xlsx

Supplementary Table S3. List of identified protein-coding genes detected immediately upstream and downstream of the CsalncRNAs. (XLSX 135 KB)

Supplementary Table S4. Repeat elements in lncRNAs of C. Sativa. (DOCX 29 KB)

Supplementary Table S5. List of identified intergenic-CsalncRNAs as putative targets of miRNAs. (XLSX 27 KB)

10725_2018_410_MOESM8_ESM.xlsx

Supplementary Table S6. List of functional encoding genes targeted by Camelina drought-responsive miRNAs regulating intergenic CsalncRNAs. (XLSX 48 KB)

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Subburaj, S., Jeon, Y., Tu, L. et al. Genome-wide identification, functional prediction and expression profiling of long non-coding RNAs in Camelina sativa. Plant Growth Regul 86, 49–63 (2018). https://doi.org/10.1007/s10725-018-0410-8

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