Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)

Abstract

Recent researches on long noncoding RNAs (lncRNAs) have expanded our horizon of gene regulation and the cellular complexity. However, the number, characteristics and expression patterns of lncRNAs remain poorly characterized and how these lncRNAs biogenesis are regulated in response to drought stress in cotton are still largely unclear. In the study, using a reproducibility-based RNA-sequencing and bioinformatics strategy to analyze the lncRNAs of 9 samples under three different environment stresses (control, drought stress and re-watering, three replications), we totally identified 10,820 lncRNAs of high-confidence through five strict steps filtration, of which 9,989 were lincRNAs, 153 were inronic lncRNAs, 678 were anti-sense lncRNAs. Coding function analysis showed 6,470 lncRNAs may have the ability to code proteins. Small RNAs precursor analysis revealed that 196 lncRNAs may be the precursors to small RNAs, most of which (35.7%, 70) were miRNAs. Expression patterns analysis showed that most of lncRNAs were expressed at a low level and most inronic lncRNAs (75.95%) had a consistent expression pattern with their adjacent protein-coding genes. Further analysis of transcriptome data uncovered that lncRNAs XLOC_063105 and XLOC_115463 probably function in regulating two adjacent coding genes CotAD_37096 and CotAD_12502, respectively. Investigations of the content of plant hormones and proteomics analysis under drought stress also complemented the prediction. We analyzed the characteristics and the expression patterns of lncRNAs under drought stress and re-watering treatment, and found lncRNAs may be likely to involve in regulating plant hormones pathway in response to drought stress.

Gene expression differs in codominant prairie grasses under drought

“…Andropogon emphasized misfolded protein and amino acid salvage under drought, which could reflect alleviation of the symptoms of drought stress with greater sensitivity to temperature‐induced misfolding. Aberrant mRNA surveillance and spliceosome regulation pathways are also implicated in drought tolerance (Lee et al., ; Lu et al., ). On the other hand, Sorghastrum upregulated transcripts related to osmotic and salinity stress, which could reflect its greater sensitivity to soil water content (Nippert et al., ).…”

The role of the long non‐coding RNA TDRG1 in epithelial ovarian carcinoma tumorigenesis and progression through miR‐93/RhoC pathway

“…LncRNAs have recently emerged as central regulators of gene expression in various biological settings, such as tumor growth and development, apoptosis, proliferation, differentiation, and autophagy. Therefore, they are closely related to carcinogenesis and other diseases, which broadens the horizon of gene regulation and cellular complexity . Given that the function of LncRNA TDRG1 in ovarian carcinoma is unknown, we investigated the role and underlying mechanism of LncRNA TDRG1 in the tumorigenesis and progression of epithelial ovarian carcinoma (EOC).…”

“…Therefore, they are closely related to carcinogenesis and other diseases, which broadens the horizon of gene regulation and cellular complexity. [10][11][12][13] Given that the function of LncRNA TDRG1 in ovarian carcinoma is unknown, we investigated the role and underlying mechanism of LncRNA TDRG1 in the tumorigenesis and progression of epithelial ovarian carcinoma (EOC).…”

Long Non-Coding RNAs Responsive to Witches’ Broom Disease in Paulownia tomentosa

“…Large numbers of lncRNAs have been identified in Arabidopsis thaliana [25][26][27], rice [28,29], wheat [30,31], maize [32], cotton [33,34], Brassica napus [35], and Populus [36,37], and have been found to play important roles in growth, development, differentiation, and stress responses. LncRNAs involved in the responses of plants to biotic stresses have also been identified.…”