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

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.

Response and tolerance mechanism of food crops under high temperature stress: a review

“…Long noncoding RNAs (lncRNAs) are molecules of > 200 nucleotide and lack discernible coding potential (Palazzo and Koonin, 2020;Rai et al, 2019). In plants, lncRNAs regulate different biological processes, including growth and development, sexual reproduction, and also drought and heat stress responses (Csorba et al, 2014;Liu et al, 2017a;Song et al, 2021). Long noncoding RNAs affect all the elements of the genes such as promoters, untranslated regions, introns, exons, and terminators, regulating gene expression at various levels such as transcription, chromatin remodeling, splicing and translation (Wierzbicki et al, 2021).…”

Advances in Non-Coding RNA Sequencing

“…Notably, crop species such as Chinese cabbage and rice have come under scrutiny recently. By employing NGS based approaches (e.g., small RNA sequencing) the roles of ncRNAs in conferring resistance against infections [ 198 , 199 , 200 ], and in adapting to environmental factors (e.g., heat resistance) [ 201 ] have been highlighted.…”

Comprehensive Analysis of Long Non-coding RNA Modulates Axillary Bud Development in Tobacco (Nicotiana tabacum L.)

“…LncRNAs also regulate stress response in plants. For example, lncRNA354 plays an important role in regulating salt tolerance in upland cotton ( Zhang et al, 2021 ), and genome-wide analysis has revealed the role of lncRNAs in regulating heat tolerance in Chinese cabbage ( Song et al, 2021 ).…”