Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars

Abstract

Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (Populus euphratica and Populus alba var. pyramidalis), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in P. euphratica but not in P. alba var. pyramidalis and 3,425 lncRNAs were identified to be species-specific in P. euphratica in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included Aux/IAA, NAC, MYB, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

“…10). In poplar, more than 10,000 lncRNAs were identified, and approximately 40% of them responded to salt stress with tissue-specific expression patterns [34]. In cotton, lncRNA973 was localized in the nucleus and increased by salt treatment.…”

“…In rice, Ding et al found that the lncRNA long-day-specific malefertility-associated RNA is essential for the normal pollen development of plants grown under long-day conditions [30]. And also, more and more researches suggest that lncRNAs play important roles in the regulation of gene expression in response to various stresses [33][34][35][36][37][38]. An Arabidopsis lncRNA, DROUGHT IN-DUCED lncRNA (DRIR), was a new positive regulator of the plant response to drought and salt stress [37].…”

Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

“…Thus far, there are no annotated and characterized oxidative stress-responsive cassava lncRNAs. However, there have been a few reports on lncRNAs involved in oxidative stress processes in plants such as Medicago, tobacco, and poplar [61][62][63].…”

The Arabidopsis Hypoxia Inducible AtR8 Long Non-Coding RNA also Contributes to Plant Defense and Root Elongation Coordinating with WRKY Genes under Low Levels of Salicylic Acid

“…After exposure of Arabidopsis thaliana to drought, cold, high salt, or abscisic acid, the expression of 1832 lncRNAs was up-regulated markedly when compared with the control group [8]. More recently, genome-wide studies showed that lncRNAs respond to heat and salt stress in Chinese cabbage (Brassica rapa) and poplar (Populus trichocarpa), respectively [9,10].…”