Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response.
Identifieur interne : 000053 ( Main/Exploration ); précédent : 000052; suivant : 000054Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response.
Auteurs : Jiahong Xu [République populaire de Chine] ; Meng Fang [République populaire de Chine] ; Zhihao Li [République populaire de Chine] ; Maoning Zhang [République populaire de Chine] ; Xiaoyu Liu [République populaire de Chine] ; Yuanyuan Peng [République populaire de Chine] ; Yinglang Wan [République populaire de Chine] ; Jinhui Chen [République populaire de Chine]Source :
- Frontiers in genetics [ 1664-8021 ] ; 2020.
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 | log2FC| ≥ 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.
DOI: 10.3389/fgene.2020.00249
PubMed: 32457788
PubMed Central: PMC7221187
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xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Maoning" sort="Zhang, Maoning" uniqKey="Zhang M" first="Maoning" last="Zhang">Maoning Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key 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Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute 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Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Wan, Yinglang" sort="Wan, Yinglang" uniqKey="Wan Y" first="Yinglang" last="Wan">Yinglang Wan</name><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Jinhui" sort="Chen, Jinhui" uniqKey="Chen J" first="Jinhui" last="Chen">Jinhui Chen</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, 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J" first="Jiahong" last="Xu">Jiahong Xu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Fang, Meng" sort="Fang, Meng" uniqKey="Fang M" first="Meng" last="Fang">Meng Fang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Li, Zhihao" sort="Li, Zhihao" uniqKey="Li Z" first="Zhihao" last="Li">Zhihao Li</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Maoning" sort="Zhang, Maoning" uniqKey="Zhang M" first="Maoning" last="Zhang">Maoning Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Xiaoyu" sort="Liu, Xiaoyu" uniqKey="Liu X" first="Xiaoyu" last="Liu">Xiaoyu Liu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Peng, Yuanyuan" sort="Peng, Yuanyuan" uniqKey="Peng Y" first="Yuanyuan" last="Peng">Yuanyuan Peng</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Wan, Yinglang" sort="Wan, Yinglang" uniqKey="Wan Y" first="Yinglang" last="Wan">Yinglang Wan</name><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Jinhui" sort="Chen, Jinhui" uniqKey="Chen J" first="Jinhui" last="Chen">Jinhui Chen</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou</wicri:regionArea><wicri:noRegion>Haikou</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in genetics</title><idno type="ISSN">1664-8021</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 <i>Populus x canadensis</i> 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 <i>q</i>-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 <i>cis</i> 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 [<i>Heat Shock Protein 82</i> (<i>HSP82</i>), <i>HSP83</i>, <i>Disease Resistance Protein 27</i> (<i>DRL27</i>), <i>DnaJ family protein</i> (<i>DNJH</i>), and two other predicted protein-coding genes], which showed that lncRNAs could regulate HSP family genes in response to heat stress in <i>Populus</i>. Therefore, our third-generation sequencing has improved the description of the <i>P. canadensis</i> 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.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32457788</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-8021</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in genetics</Title><ISOAbbreviation>Front Genet</ISOAbbreviation></Journal><ArticleTitle>Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the <i>Populus x canadensis</i> Moench Heat Stress Response.</ArticleTitle><Pagination><MedlinePgn>249</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fgene.2020.00249</ELocationID><Abstract><AbstractText>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 <i>Populus x canadensis</i> 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 <i>q</i>-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 <i>cis</i> 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 [<i>Heat Shock Protein 82</i> (<i>HSP82</i>), <i>HSP83</i>, <i>Disease Resistance Protein 27</i> (<i>DRL27</i>), <i>DnaJ family protein</i> (<i>DNJH</i>), and two other predicted protein-coding genes], which showed that lncRNAs could regulate HSP family genes in response to heat stress in <i>Populus</i>. Therefore, our third-generation sequencing has improved the description of the <i>P. canadensis</i> 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.</AbstractText><CopyrightInformation>Copyright © 2020 Xu, Fang, Li, Zhang, Liu, Peng, Wan and Chen.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Jiahong</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fang</LastName><ForeName>Meng</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Zhihao</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Maoning</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Xiaoyu</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peng</LastName><ForeName>Yuanyuan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wan</LastName><ForeName>Yinglang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Jinhui</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Genet</MedlineTA><NlmUniqueID>101560621</NlmUniqueID><ISSNLinking>1664-8021</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus x canadensis Moench</Keyword><Keyword MajorTopicYN="N">heat shock protein</Keyword><Keyword MajorTopicYN="N">heat stress</Keyword><Keyword MajorTopicYN="N">lncRNAs</Keyword><Keyword MajorTopicYN="N">third-generation sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>11</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>02</Day></PubMedPubDate><PubMedPubDate 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Fang</name><name sortKey="Li, Zhihao" sort="Li, Zhihao" uniqKey="Li Z" first="Zhihao" last="Li">Zhihao Li</name><name sortKey="Li, Zhihao" sort="Li, Zhihao" uniqKey="Li Z" first="Zhihao" last="Li">Zhihao Li</name><name sortKey="Li, Zhihao" sort="Li, Zhihao" uniqKey="Li Z" first="Zhihao" last="Li">Zhihao Li</name><name sortKey="Liu, Xiaoyu" sort="Liu, Xiaoyu" uniqKey="Liu X" first="Xiaoyu" last="Liu">Xiaoyu Liu</name><name sortKey="Liu, Xiaoyu" sort="Liu, Xiaoyu" uniqKey="Liu X" first="Xiaoyu" last="Liu">Xiaoyu Liu</name><name sortKey="Liu, Xiaoyu" sort="Liu, Xiaoyu" uniqKey="Liu X" first="Xiaoyu" last="Liu">Xiaoyu Liu</name><name sortKey="Peng, Yuanyuan" sort="Peng, Yuanyuan" uniqKey="Peng Y" first="Yuanyuan" last="Peng">Yuanyuan Peng</name><name sortKey="Peng, Yuanyuan" sort="Peng, Yuanyuan" uniqKey="Peng Y" first="Yuanyuan" last="Peng">Yuanyuan Peng</name><name sortKey="Peng, Yuanyuan" sort="Peng, Yuanyuan" uniqKey="Peng Y" first="Yuanyuan" last="Peng">Yuanyuan Peng</name><name sortKey="Wan, Yinglang" sort="Wan, Yinglang" uniqKey="Wan Y" first="Yinglang" last="Wan">Yinglang Wan</name><name sortKey="Xu, Jiahong" sort="Xu, Jiahong" uniqKey="Xu J" first="Jiahong" last="Xu">Jiahong Xu</name><name sortKey="Xu, Jiahong" sort="Xu, Jiahong" uniqKey="Xu J" first="Jiahong" last="Xu">Jiahong Xu</name><name sortKey="Zhang, Maoning" sort="Zhang, Maoning" uniqKey="Zhang M" first="Maoning" last="Zhang">Maoning Zhang</name><name sortKey="Zhang, Maoning" sort="Zhang, Maoning" uniqKey="Zhang M" first="Maoning" last="Zhang">Maoning Zhang</name><name sortKey="Zhang, Maoning" sort="Zhang, Maoning" uniqKey="Zhang M" first="Maoning" last="Zhang">Maoning Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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