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Article|01 Mar 2021|OPEN
Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
Xiaoming Song1,2,3,, Jingjing Hu3, Tong Wu3, Qihang Yang3, Xuehuan Feng1, Hao Lin1, Shuyan Feng3, Chunlin Cui3, Ying Yu3, Rong Zhou4, Ke Gong3, Tong Yu3, Qiaoying Pei3 & Nan Li3,
1Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE, USA
2School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
3College of Life Sciences/Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei, China
4Department of Food Science, Aarhus University, Aarhus, Denmark

Horticulture Research 8,
Article number: 48 (2021)
doi: 10.1038/hortres.2021.48
Views: 275

Received: 09 Aug 2020
Revised: 30 Oct 2020
Accepted: 13 Dec 2020
Published online: 01 Mar 2021

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.