Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoe
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RESEARCH ARTICLE
Open Access
Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings Jiahong Xu1,2, Yao Zheng1,2, Shouqin Pu1,2, Xiujie Zhang1,2, Zhihao Li1,2 and Jinhui Chen1,2*
Abstract Background: As air temperatures increase globally, more and more plants are exposed to heat-stress conditions. Although many studies have explored regulation networks in plants with the aim of improving their heat-stress tolerance, only few have revealed them in trees. Here, individuals of Populus qiongdaoensis seedlings, which grows naturally in tropical areas, exposed to heat at 40 °C and the non-coding regulation networks were explored using the PacBio RSII and the Illumina sequencing platform. Results: In total, we obtained 88,161 full-length transcripts representing 39,343 genes using 5,498,988 long reads and 350,026,252 clean reads, and also 216 microRNAs (miRNAs) via 95,794,107 reads. We then identified 928 putative long non-coding RNAs (lncRNAs), consisting of 828 sense lncRNAs (89.22%), 34 long intergenic non-coding RNAs (3.66%), 16 antisense (1.72%), and 50 sense intronic lncRNAs (5.39%). Under the dual criteria of |log2foldchange| ≥ 1 and P-value < 0.05, 1690 genes, 25 lncRNAs, and 15 miRNAs were found differentially expressed under the heat stress treatment. Furthermore, 563 and 595 mRNAs were detected as target genes of 14 differently expressed miRNAs and 26 differentially expressed lncRNAs. Functional annotation analysis of these target genes demonstrated they were related to cell membrane stability, plant hormone signal transduction, antioxidation, and aldarate metabolism. Lastly, we uncovered a key interaction network of lncRNAs, miRNAs and mRNAs that consisted of miR1444d, miR482a.1, miR530a, lncHSP18.2, HSP18.1, and HSP18.2. Expression level analysis showed that miRNAs in the network were up-regulated, while mRNAs and lncRNA were down-regulated, and also found that lncHSP18.2 may cis-regulate HSP18.2. (Continued on next page)
* Correspondence: [email protected] 1 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 570228, P. R. China 2 Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, College of Forestry, Hainan University, Haikou 570228, P. R. China © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indic
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