Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response

Abstract

Long non-coding RNAs (lncRNAs) regulate plant responses to abiotic stresses. However, the short reads produced by second-generation sequencing technology make it difficult to accurately explore full-length transcripts, limiting the study of lncRNAs. In this study, we used third-generation long-read sequencing technology with the PacBio Sequel and Illumina platform to explore the role of lncRNAs in the heat stress response of Populus x canadensis Moench trees. We using 382,034,416 short reads to correct 4,297,179 long reads by resulted in 66,657 full-length transcripts, representing 33,840 genes. Then, 753 putative lncRNAs were identified, including 658 sense lncRNAs (87.38%), 41 long intervening/intergenic non-coding RNAs (lincRNAs) (5.44%), 12 antisense lncRNAs (1.59%), and 42 sense intronic lncRNAs (5.58%). Using the criteria | log 2 FC| ≥ 1 and q-value < 0.05, 3,493 genes and 78 lncRNAs were differentially expressed under the heat treatment. Furthermore, 923 genes were detected as targets of 43 differently expressed lncRNAs by cis regulation. Functional annotation demonstrated that these target genes were related to unfolded protein binding, response to stress, protein folding, and response to stimulus. Lastly, we identified a lncRNA-gene interaction network consisting of four lncRNAs and six genes [Heat Shock Protein 82 (HSP82), HSP83, Disease Resistance Protein 27 (DRL27), DnaJ family protein (DNJH), and two other predicted protein-coding genes], which showed that lncRNAs could regulate HSP family genes in response to heat stress in Populus. Therefore, our third-generation sequencing has improved the description of the P. canadensis transcriptome. The potential lncRNAs and HSP family genes identified here present a genetic resource to improve our understanding of the heat-adaptation mechanisms of trees.

A long noncoding RNA HILinc1 enhances pear thermotolerance by stabilizing PbHILT1 transcripts through complementary base pairing

“…The second way is to identify a specific association with the sequences of protein-coding genes, such as the existence of complementary base fragments 44 . The third is to examine correlations in expression patterns between lincRNAs and protein-coding genes 45,46 . To reveal the potential target gene of HILinc1, we analyzed its neighboring genes and found two ORFs, one located upstream and one downstream of HILinc1 (Fig.…”

Identification and Functional Analysis of Long Non-Coding RNA (lncRNA) in Response to Seed Aging in Rice

“…In the study of Yang et al [ 46 ], a total of 91 DELs were obtained in upland rice under drought stress, including 141 upregulated and 50 downregulated lncRNAs, which was different from our results. Xu et al obtained 78 significantly differentially expressed lncRNAs, including 67 upregulated lncRNAs and 11 downregulated lncRNAs in the Populus x canadensis moench heat stress response experiment [ 65 ]. In addition, 26 differentially expressed lncRNAs were obtained in Populus qiongdaoensis seedlings under heat stress conditions, among which 25 were upregulated and one was downregulated, in contrast to our results [ 66 ].…”

Transcriptomic Analysis Reveals LncRNAs Associated with Flowering of Angelica sinensis during Vernalization

“…Heat-responsive lncRNAs have been found to be differentially expressed in Brassica juncea, and cold-responsive lncRNAs have been identified in grape and Arabidopsis [71][72][73]. lncR-NAs could regulate HSP family genes (HSP82 and HSP83) in response to heat stress in Populus x canadensis Moench, and HSP18.1 in response to Cd stress Betula platyphylla [74,75]. For the eight representative coexpressed mRNAs of the 14 lncRNAs linked with the temperature response, ACBP6 confers resistance to cold and freezing [76]; ENO2 acts as a positive regulator in response to cold stress [77]; ADH1 is required for survival and acclimation in response to abiotic stresses (e.g., cold, salt, and drought) [78,79]; CSP2 contributes to the enhancement of cold and freezing tolerance [80]; and HSP17.8, HSP70-3, HSP70-10, and HSP90-3 play vital roles in adapting to biotic and abiotic stresses [81,82].…”