open access publication

Article, 2021

Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

Horticulture Research, ISSN 2662-6810, 2052-7276, Volume 8, 1, Pages 1-21, 10.1038/s41438-021-00484-4

Contributors

Song, Xiao-Ming (Corresponding author) [1] [2] [3] Hu, Jingjing [1] Wu, Tong [1] Yang, Qihang [1] Feng, Xuehuan 0000-0002-0732-9322 [2] Lin, Hao 0000-0001-6265-2862 [3] Feng, Shu-Yan [1] Cui, Chun-Lin [1] Yu, Ying [1] Zhou, Rong 0000-0001-5755-1258 [4] Gong, Ke [1] Yu, Tong [1] Pei, Qiao-Ying [1] Li, Nan 0000-0002-0575-371X (Corresponding author) [1]

Affiliations

  1. [1] North China University of Science and Technology
    2. [NORA names: China; Asia, East];
  2. [2] University of Nebraska–Lincoln
    3. [NORA names: United States; America, North; OECD];
  3. [3] University of Electronic Science and Technology of China
    4. [NORA names: China; Asia, East];
  4. [4] Aarhus University
    5. [NORA names: AU Aarhus University; University; Denmark; Europe, EU; Nordic; OECD]

Abstract

Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the "protein processing in endoplasmic reticulum" and "plant hormone signal transduction" pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

Keywords

Chinese cabbage, DE, DE lncRNAs, HSP, PYL, PYL genes, RNA, abiotic stresses, abundance, abundance of resources, analysis, analysis of lncRNAs, angiosperms, cabbage, ceRNA, ceRNA network, characterization, characterization of long noncoding RNAs, cis, combined analysis, comparative analysis, comprehensive analysis, comprehensive analysis of lncRNAs, endoplasmic reticulum, expression, expression patterns, findings, function, functional studies, functions of lncRNAs, genes, genome-wide analysis, genome-wide analysis of lncRNAs, heat, heat response, heat stress, heat stress response, heat treatment, identified lncRNAs, knowledge, knowledge of lncRNAs, lncRNA sequences, lncRNA-mRNA, lncRNAs, long noncoding RNAs, mRNA, miRNA precursors, miRNAs, network, noncoding RNAs, pathway, patterns, precursor, qRT-PCR, resources, response, response to abiotic stress, response to heat stress, results, reticulum, sequence, species, stage, stages of heat treatment, stress, stress response, study, target, target genes, targets of DE lncRNAs, trans-regulated genes, treatment

Funders

  • National Natural Science Foundation of China
  • China Postdoctoral Science Foundation

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