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.
Highlights
Salinity is one of the most important environmental factors limiting plant growth and development and results in crop loss in semiarid and arid areas (Boyer, 1982)
We identified 4,199 (39.4% of the total; 5.3% belonging to long noncoding natural antisense transcripts (lncNATs); 49.2% belonging to lincRNAs; 36.7% belonging to long intronic noncoding RNAs, 8.8% belonging to overlapping Long noncoding RNAs (lncRNAs)), and 6,048 (60.8% of total; 4.8% belonging to lncNATs; 45.7% belonging to lincRNAs; 38.8% belonging to long intronic noncoding RNAs; 10.8% belonging to overlapping lncRNAs) lncRNAs that responded to salt stress in P. euphratica and P. alba var. pyramidalis, respectively (Figures 4A, B, Supplementary Data S5–6). 38 and 53 conserved elements were identified in these Differentially Expressed (DE) lncRNAs in two poplars (Supplementary Data S4)
We identified and characterized lncRNAs from four tissue types in the two species of poplar and explored their roles in the salt response
Summary
Salinity is one of the most important environmental factors limiting plant growth and development and results in crop loss in semiarid and arid areas (Boyer, 1982). The molecular mechanisms underlying the response to salt stress in plants have been well characterized, and most studies have mainly focused on the functional study of protein-coding genes, such as HKT1, Na+/H+ exchanger (NHX), and SALT OVERLY SENSITIVE (SOS, known as NHX7) (Shi et al, 2002; Venema et al, 2003; Byrt et al, 2007). LncRNAs in Response to Salt Stress have been identified to function as precursors of microRNAs (miRNAs) and other small RNAs or as miRNA target mimics, and involved in plant response to salt stress. 7,361 and 7,874 long ncRNAs (lncRNAs) were identified from salt stress-treated the leaf and root of Medicago truncatula (Wang et al, 2015). The regulatory mechanism of lncRNAs underlying the response to salt stress remains largely unknown
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