Abstract
BackgroundLong non-coding RNAs (lncRNAs) are a class of non-coding RNAs with more than 200 nucleotides in length, which play vital roles in a wide range of biological processes. Powdery mildew disease (PM) has become a major threat to the production of melon. To investigate the potential roles of lncRNAs in resisting to PM in melon, it is necessary to identify lncRNAs and uncover their molecular functions. In this study, we compared the lncRNAs between a resistant and a susceptible melon in response to PM infection.ResultsIt is reported that 11,612 lncRNAs were discovered, which were distributed across all 12 melon chromosomes, and > 85% were from intergenic regions. The melon lncRNAs have shorter transcript lengths and fewer exon numbers than protein-coding genes. In addition, a total of 407 and 611 lncRNAs were found to be differentially expressed after PM infection in PM-susceptible and PM-resistant melons, respectively. Furthermore, 1232 putative targets of differently expressed lncRNAs (DELs) were discovered and gene ontology enrichment (GO) analysis showed that these target genes were mainly enriched in stress-related terms. Consequently, co-expression patterns between LNC_018800 and CmWRKY21, LNC_018062 and MELO3C015771 (glutathione reductase coding gene), LNC_014937 and CmMLO5 were confirmed by qRT-PCR. Moreover, we also identified 24 lncRNAs that act as microRNA (miRNA) precursors, 43 lncRNAs as potential targets of 22 miRNA families and 13 lncRNAs as endogenous target mimics (eTMs) for 11 miRNAs.ConclusionThis study shows the first characterization of lncRNAs involved in PM resistance in melon and provides a starting point for further investigation into the functions and regulatory mechanisms of lncRNAs in the resistance to PM.
Highlights
Long non-coding RNAs are a class of non-coding RNAs with more than 200 nucleotides in length, which play vital roles in a wide range of biological processes
Our results indicated that a large number of Long non-coding RNAs (lncRNAs) were responsive to Powdery mildew disease (PM) infection, including those that act as endogenous miRNA target or mimics, which provided a foundation for further functional analysis of lncRNAs in the resistance to PM
Previous transcriptome profiling analysis of genes in melon after PM inoculation revealed that the expression of genes involved in the response to biotic stimulus resistance, response to external stimuli, signal transduction, kinase activity, transcription factor activity and plant-pathogen interactions was increased at 24 hpi and high expression levels were maintained to 48 hpi, and was subsequently decreased after 48 hpi [22]
Summary
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with more than 200 nucleotides in length, which play vital roles in a wide range of biological processes. The ncRNA families are composed of small and long non-coding RNA (lncRNAs) based on the length of mature transcripts. Small ncRNAs (approximately 18–30 nucleotides) include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which have been well characterized for their involvement in the regulation of gene expression at transcriptional and post-transcriptional level in almost all eukaryotes [3]. LncRNAs are a class of non-coding RNAs with more than 200 nucleotides in length, which have been demonstrated to participate in the regulation of gene expression during plant growth and development, and various. Gao et al BMC Genomics (2020) 21:125 stress responses of plants [4,5,6] According to their position on the genome, lncRNAs can be classified into long intergenic non-coding RNA (lincRNA), long intronic non-coding RNAs and natural antisense transcripts (lncNATs) [7]
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