Abstract
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs). Similar to the mRNAs, lncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of lncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of lncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA) biosynthesis, and gene ontology mapping inferred their regulatory roles in numerous biological processes. A few lncRNAs were predicted as precursor (19 lncRNAs), while some as target mimics (1,047 lncRNAs) of known miRNAs involved in various regulatory functions. The results suggested numerous functions of lncRNAs in T. aestivum, and unfolded the opportunities for functional characterization of individual lncRNA in future studies.
Highlights
About 90% of the genome of an organism is transcribed into RNAs, but majority of them are noncoding (Ariel et al, 2015)
The number of Long non-coding RNAs (lncRNAs) identified in T. aestivum lncRNA in Bread Wheat was much higher than the other plants, which is probably due to- (i) the large (∼17 Gb) composite allohexaploid (AABBDD) nature of T. aestivum genome (Marcussen et al, 2014), or/and (ii) the number of RNA sequence (RNA seq) data utilized in present study was more than the earlier studies in other plants
A total of 44,698 lncRNAs were identified in T. aestivum genome after the analysis of 52 RNA seq data, which were distributed throughout the various sub-genomes and chromosomes
Summary
About 90% of the genome of an organism is transcribed into RNAs, but majority of them are noncoding (Ariel et al, 2015). The lncRNAs are key regulatory elements, involved in numerous developmental processes and stress responses (Kim and Sung, 2012). These are usually ≥200 bp in length, which lack coding potential. Natural anti-sense RNAs (NATs) are a class of lncRNA that represent partial or complete base complementation to the coding transcripts They may act as cis- or transregulatory elements and regulate gene transcription during tissue development and stress conditions (Kim and Sung, 2012)
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