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

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Xiaoming Song, North China University of Science and Technology, University of Nebraska–Lincoln, University of Electronic Science and Technology of China
  • ,
  • Jingjing Hu, North China University of Science and Technology
  • ,
  • Tong Wu, North China University of Science and Technology
  • ,
  • Qihang Yang, North China University of Science and Technology
  • ,
  • Xuehuan Feng, University of Nebraska–Lincoln
  • ,
  • Hao Lin, University of Electronic Science and Technology of China
  • ,
  • Shuyan Feng, North China University of Science and Technology
  • ,
  • Chunlin Cui, North China University of Science and Technology
  • ,
  • Ying Yu, North China University of Science and Technology
  • ,
  • Rong Zhou
  • Ke Gong, North China University of Science and Technology
  • ,
  • Tong Yu, North China University of Science and Technology
  • ,
  • Qiaoying Pei, North China University of Science and Technology
  • ,
  • Nan Li, North China University of Science and Technology

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.

Original languageEnglish
Article number48
JournalHorticulture Research
Volume8
Issue1
Number of pages21
ISSN2052-7276
DOIs
Publication statusPublished - Mar 2021

See relations at Aarhus University Citationformats

ID: 213441396