Strand-specific RNA-seq based identification and functional prediction of lncRNAs in response to melatonin and simulated drought stresses in cassava

Abstract

Melatonin (MT) plays important roles in mediating plant responses to abiotic stresses such as drought. lncRNAs also play crucial roles in regulating responses to drought stress, however, their roles in MT-mediated drought stress responses in plants remain largely unknown. In this study, a total of 1405 high-confidence lncRNAs were identified in leaves of cassava, an important food crop in tropical and sub-tropical regions, using strand-specific RNA-seq technology. Of which, 185 were differentially expressed between polyethylene glycol (PEG) or MT treatment and the control condition. Trans-regulatory co-expression network revealed that MT-uniquely-responsive lncRNAs were mainly involved in tetrapyrrole synthesis, cytochrome P450, and cell wall modification; PEG-uniquely-responsive lncRNAs mainly participated in RNA regulation of transcription, calcium signaling, mitochondrial electron transport/ATP synthesis, hormone metabolism, and transport; and MT and PEG both-responsive lncRNAs were mainly involved in light reaction, light signaling, FA synthesis and FA elongation, secondary metabolism, and tetrapyrrole synthesis. In addition, 28 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through calcium signaling, RNA regulation of transcription, ABA and ethylene metabolism, and redox homeostasis. Besides, 78 lncRNAs (especially TCONS_00003360, TCONS_00015102, and TCONS_00149293) responsive to MT and/or PEG treatment were identified as putative targets of cassava known miRNAs. These findings provide a comprehensive view of the lncRNAs and their roles in response to MT and drought stress in cassava, which will enable in-depth functional analyses in the near future.