AUTHOR=Xu Jiahong , Fang Meng , Li Zhihao , Zhang Maoning , Liu Xiaoyu , Peng Yuanyuan , Wan Yinglang , Chen Jinhui 

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

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00249

DOI=10.3389/fgene.2020.00249

ISSN=1664-8021

ABSTRACT=<p>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 <italic>Populus x canadensis</italic> 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<sub>2</sub>FC| ≥ 1 and <italic>q</italic>-value &lt; 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 <italic>cis</italic> 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 [<italic>Heat Shock Protein 82</italic> (<italic>HSP82</italic>), <italic>HSP83</italic>, <italic>Disease Resistance Protein 27</italic> (<italic>DRL27</italic>), <italic>DnaJ family protein</italic> (<italic>DNJH</italic>), and two other predicted protein-coding genes], which showed that lncRNAs could regulate HSP family genes in response to heat stress in <italic>Populus</italic>. Therefore, our third-generation sequencing has improved the description of the <italic>P. canadensis</italic> 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.</p>