Third-Generation Sequencing Indicated that LncRNA Could Regulate eIF2D to Enhance Protein Translation Under Heat Stress in Populus simonii

As global temperatures rise, plants are being increasingly exposed to high-temperature stress. Although long non-coding RNAs (lncRNAs) are regulatory elements of gene expression under heat stress in trees, the limitation of sequencing technology and methods in identifying lncRNAs has hindered the exploration of their roles. To explore the role of lncRNAs in response to heat stress, we treated Populus simonii seedlings at 40 °C for 1 h and performed third-generation sequencing (Iso-Seq) and high-throughput RNA sequencing (RNA-seq). A total of 239,142,803 short reads were used to correct 101,791 long reads (average length 2400 bp) resulting in 101,791 full-length transcripts and representing 45,217 genes. Then, 829 lncRNAs were identified, including 757 sense lncRNAs (91.31%), 25 long intergenic non-coding RNAs (3.02%), seven antisense lncRNAs (0.84%), and 40 sense intronic lncRNAs (4.83%). Using the criteria |log 2 Fold Change| ≥ 1 and q-value < 0.05, 2787 genes and 21 lncRNAs were observed to be differentially expressed under heat stress. Functional annotation showed that these genes were associated with “response to stress”, “response to stimulus”, and “unfolded protein binding”. Furthermore, 149 genes were predicted as targets of 17 significantly differentially expressed lncRNAs. A total of 11 genes in significantly enriched gene ontology (GO) terms were annotated, including four genes encoding disease resistance proteins targeted by lncPs2 and seven eukaryotic translation initiation factor 2D ( eIF2D ) genes targeted by lncPs3. Expression and functional analysis revealed that lncPs3 and five eIF2Ds were synergistically upregulated, indicating that lncPs3 may enhance protein translation by regulating eIF2D in response to heat stress.