Identification and functional prediction of lncRNAs in response to PEG and ABA treatment in cassava

Abstract

LncRNAs play crucial roles in plant drought stress, in which abscisic acid (ABA) was recognized as an essential signal molecule in stress regulatory networks. However, the mechanisms of lncRNAs participated in drought stress with or without the involvement of ABA signaling remain elusive in cassava, an important tropical and sub-tropical crop. In this study, a total of 1379 reliable lncRNAs were identified in cassava leaves using strand-specific RNA-seq method, of which 194 were differentially expressed between ABA or polyethylene glycol (PEG) treatment and the control condition. Trans-regulatory co-expression network revealed that ABA-uniquely-responsive DE lncRNAs were primarily participated in receptor kinases signaling, hormone metabolism, and cell wall modification; PEG-uniquely-responsive DE lncRNAs were mainly involved in jasmonate metabolism, biotic and abiotic stress, calcium signaling, and transport; and ABA/PEG-both-responsive DE lncRNAs were mainly referred to light reaction of photosynthesis, nitrogen metabolism, tetrapyrrole synthesis, secondary metabolism, RNA regulation of transcription, and calcium signaling. In addition, 41 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes through ABA signaling regulation, RNA regulation of transcriptions, and biotic and abiotic stress. Besides, 34 lncRNAs were identified as putative targets of cassava known miRNAs, and especially, TCONS_00129136, TCONS_00122745, TCONS_00088201, and TCONS_00067612 were targeted by functionally well-known miRNAs (such as miR156 and miR159) that involved in ABA- and drought-response, suggesting their roles in cassava drought response via ABA-dependent pathways with the participation of miRNA regulation. These findings provide a comprehensive view of cassava lncRNAs in response to PEG and ABA treatment, which will enable in-depth functional analysis in the near future.