Integrated Analysis of Long Non-Coding RNAs and mRNAs Reveals Key Trans-Target Genes Associated with Heat Stress Response in Rhododendron delavayi

Long non-coding RNAs (lncRNAs) have been defined as non-coding transcripts exceeding 200 nucleotides, which play essential roles during transcriptional and post-transcriptional regulation in multiple biological processes. Understanding <i>R. delavayi</i> lncRNAs is of great significance as it is profoundly influenced by heat stress. In this research, a total of 1145 differentially expressed lncRNAs (DE-lncRNAs) and 9447 differentially expressed genes (DEGs) (log₂|FC| > 1, <i>p</i> < 0.05) were characterized between heat-stress-treated groups and control groups. Further analysis showed that 229 DE-lncRNAs (144 upregulated and 85 downregulated) were commonly distributed in two comparisons (CK_vs._H3 and CK_vs._H6). We further investigated the cis- and trans-acting genes of the upregulated DE-lncRNAs, and found that 142 upregulated DE-lncRNAs corresponded to 1565 cis-acting DEGs, and 143 upregulated DE-lncRNAs corresponded to 3417 trans-acting DEGs. KEGG enrichment analysis of these target genes revealed that cis- and trans-acting DEGs of upregulated DE-lncRNA were primarily enriched in five and twelve KEGG pathways, respectively. Co-expression network analysis of upregulated DE-lncRNAs and DEGs enriched in the common KEGG pathways revealed 57 co-expression relationships between 28 DE-lncRNAs and 43 cis-acting DEGs and 554 co-expression relationships between 26 DE-lncRNAs and 90 trans-acting DEGs. Six DE-lncRNAs and six of their target DEGs were used as candidate genes to verify the RNA-seq data using qRT-PCR. Further analysis revealed three target genes (<i>TrxG</i>, <i>PEPC</i>, and <i>CCR</i>) out of six candidate DEGs that were selected as candidate genes for subsequent research. This study examined the relationship between DE-lncRNAs and DEGs and further screened out candidate DE-lncRNAs that can potentially provide an important theoretical basis and experimental data for the genetic improvement of heat tolerance in <i>R. delavayi</i>.