Genome-Wide Identification of Powdery Mildew Responsive Long Non-Coding RNAs in Cucurbita pepo

Abstract

Cucurbita pepo L. is an essential economic vegetable crop worldwide, and its production is severely affected by powdery mildew (PM). However, our understanding of the molecular mechanism of PM resistance in C. pepo is very limited. Long non-coding RNAs (lncRNAs) play an important role in regulating plant responses to biotic stress. Here, we systematically identified 2,363 reliably expressed lncRNAs from the leaves of PM-susceptible (PS) and PM-resistant (PR) C. pepo. The C. pepo lncRNAs are shorter in length and expressed at a lower level than the protein-coding transcripts. Among the 2,363 lncRNAs, a total of 113 and 146 PM-responsive lncRNAs were identified in PS and PR, respectively. Six PM-responsive lncRNAs were predicted as potential precursors of microRNAs (miRNAs). In addition, 58 PM-responsive lncRNAs were predicted as targets of miRNAs and one PM-responsive lncRNA was predicted as an endogenous target mimic (eTM). Furthermore, a total of 5,200 potential cis target genes and 5,625 potential trans target genes were predicted for PM-responsive lncRNAs. Functional enrichment analysis showed that these potential target genes are involved in different biological processes, such as the plant-pathogen interaction pathway, MAPK signaling pathway, and plant hormone signal transduction pathway. Taken together, this study provides a comprehensive view of C. pepo lncRNAs and explores the putative functions of PM-responsive lncRNAs, thus laying the foundation for further study of the regulatory mechanisms of lncRNAs responding to PM.

Emphasizing the Role of Long Non-Coding RNAs (lncRNA), Circular RNA (circRNA), and Micropeptides (miPs) in Plant Biotic Stress Tolerance

“…RNA-DNA hybrid (R-loop)-associated long non-coding RNAs (lncRNAs), e.g., AUXIN-REGULATED PROMOTER LOOP (APOLO), is found to be involved in DNA methylation and epigenetic control in Arabidopsis [30]. A genome-wide analysis of lncRNA in Camellia sinensis in response to nitrogen stress revealed a total of 16,452 lncRNAs, out of which 9451 were differentially expressed [31]. The detailed functional variability of lncRNA in plants includes growth and development, flowering and vernalization, light response, seed formation, yield, and stress response [32] (Table 1).…”

Identification, characterization and transcriptional analysis of the long non-coding RNA landscape in the familyCucurbitaceae

“…Recent studies have revealed the potential importance of lncRNAs as modulators of the development (22, 23) or the response to biotic (24–26) or abiotic (27, 28) stress conditions in diverse Cucurbitaceae family members. However, detailed information about lncRNAs in cucurbits is limited, and only a list of unclassified and barely characterized lncRNAs in cucumber, melon and watermelon are currently available in GreeNC (29), PLncDB V2.0 (30) or CANTATAdb 2.0 (31), the most relevant databases containing plant lncRNAs.…”

Long Non-Coding RNA lncWOX11a Suppresses Adventitious Root Formation of Poplar by Regulating the Expression of PeWOX11a

“…Most plant lncRNAs have specific secondary structures and spatiotemporal expression patterns, and their regulatory mechanisms are complex and diverse [ 28 ]. With the continuous updating of new sequencing technologies and biological prediction algorithms, the action trace of lncRNA has been found in many links between plant growth [ 29 , 30 , 31 , 32 , 33 ] and stress response [ 25 , 34 ]. The authenticity identification and annotation of these lncRNAs have been enormously challenging, and there is still a long way to go for further experimental verification and validation.…”