Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat

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.

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

“…It is desirable to understand the versatility and functioning of noncoding RNAs in regulating a wide range of biological processes, including developmental and physiological aspects of an organism. However, the detailed molecular mechanism The number of lncRNAs detected in this study was comparable with the previous studies on T. aestivum (44 698 lncRNAs) [22], maize (20 163 lncRNAs) [69], Populus trichocarpa (2542 lncRNAs) [17], Arabidopsis (6480 lncRNAs) [70], rice (2224 lncRNAs) [71], sea buckthorn (3428 lncRNAs) [23], Actinidia chinensis (7051 lncRNAs) [21], tomato (3558 lncRNAs) [72], Cajanus cajan (3919 lncRNAs) [24], and Vitis vinifera (3210 lncRNAs) [2] etc. However, out of the total lncRNAs detected in rose-scented geranium, only 1.8% could be annotated against the different public lncRNA databases, as high-confidence lncRNAs.…”

“…This study detected the expression of many lncRNA members, which could target transcripts of 18 genes involved in tartrate biogenesis. The expression analysis of lncRNAs and mRNAs suggested their similar and contrasting expression patterns, which is in accordance with the previous findings [13,22,23,73,74]. The wet-lab experimental validation of selected lncRNAs followed the respective in-silico expression pattern (i.e., FPKM analysis).…”

Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis

“…Currently, with the development of deep-sequencing technology, genome-wide lncRNA analyses have been performed on many species, such as Arabidopsis (Liu et al, 2012), rice (Zhang Y.C. et al, 2014), Zea mays (Boerner and McGinnis, 2012), wheat (Shumayla et al, 2017), and other species (Zhang and Chen, 2013). However, in many non-model plants, studies on lncRNAs are rather limited.…”

A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing

“…Genome-wide analysis of lncRNAs in bananas under cold stress revealed that many of lncRNA targets were transcription factor genes, such as MYB, WRKY, bZIP and GRAS transcription factors 77 . Similarly, the co-expression analysis of lncRNAs with transcription factors indicated that the transcription factors related to the WRKY, NAC, MYB and bZIP families were enriched in salt stress condition in wheat 78 . Several reports indicated that all these transcription factors are involved in response to salinity stress, for example numerous studies have established the important roles of WRKY proteins in various physiological processes such as seed germination 79 , lateral root formation 80 , flowering time 81 , fruit ripening 82 , leaf senescence 83 , and metabolic processes 84,85 .…”