Comparative transcriptome analysis of sweet sorghum provides insights into new lncRNAs acting as ceRNAs during salt responses

LncRNAs can act as competitive endogenous RNAs (ceRNAs) to competitively bind miRNAs, thereby indirectly regulating the transcription levels of other RNA transcripts to confer resistance to plants. But how specific ceRNAs respond to salt stress in sweet sorghum is still unclear. In this study, 126 and 133 differentially expressed lncRNAs were identified in salt-tolerant sweet sorghum (M-81E) and a salt-sensitive line (Roma) by high-throughput RNA-seq, respectively. And five new lncRNAs were identified in M-81E and Roma after salt stress treatment, lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929 and lncRNA14798 acted as ceRNAs to regulate the expression of target genes related to salt resistance by binding the five miRNAs sbi-MIR169b-p3, sbi-MIR5567-p3-2ss16CT17TC, sbi-MIR5567-p5-2, sbi-MIR5567-p5-2ss17CT18TC and PC-3p-270284-34, respectively. The target genes mainly included proton pump proteins, transport proteinsantioxidants, signal transduction proteins and transcription factors. However M-81E had more complex ceRNAs network than in Roma, which might be related with its different salt tolerance. In summary, this study identified a new ceRNA network within the transcriptome and revealed the effect of lncRNAs in the salt stress response.