Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings
Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon due to high temperatures, resulting in a significant reduction in yield. The molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata under heat stress and room temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, catalytic and binding activity. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed in two test conditions.  According to the analysis, genes and miRNAs associated with regulation of transcription, DNA-templated, transcription factor activity and sequence-specific DNA binding pathway, may play a major role in the resistance to heat stress in P. ternata. Integration of expression data of transcriptome and miRNAome determined high confidence 41 miRNA-mRNA pairs forming 25 modules. MYB-like protein and calcium-responsive transcription coactivator may play an integral role in the resistance to heat stress in P. ternata. In addition, the candidate genes and miRNAs were subjected to quantitative real-time PCR to evaluate their expression patterns. These results offer a foundation for future studies exploring the mechanism and critical genes of resistance to heat stress in P. ternata. Overall design: In order to examine the gene expression patterns of P. ternata under heat stress, six libraries were constructed from two leaf samples, with three biological replicates each (C: control, G: heat stress). To comprehensively evaluate how heat stress influenced transcript profiles, six small RNA libraries were also constructed.