Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play vital roles in plant defense responses against viral infections. However, there is no systematic understanding of lncRNAs and circRNAs and their competing endogenous RNA (ceRNA) networks in watermelon under cucumber green mottle mosaic virus (CGMMV) stress. Here, we present the characterization and expression profiles of lncRNAs and circRNAs in watermelon leaves 48-h post-inoculation (48 hpi) with CGMMV, with mock inoculation as a control. Deep sequencing analysis revealed 2373 lncRNAs and 606 circRNAs in the two libraries. Among them, 67 lncRNAs (40 upregulated and 27 downregulated) and 548 circRNAs (277 upregulated and 271 downregulated) were differentially expressed (DE) in the 48 hpi library compared with the control library. Furthermore, 263 cis-acting matched lncRNA-mRNA pairs were detected for 49 of the DE-lncRNAs. KEGG pathway analysis of the cis target genes of the DE-lncRNAs revealed significant associations with phenylalanine metabolism, the citrate cycle (TCA cycle), and endocytosis. Additionally, 30 DE-lncRNAs were identified as putative target mimics of 33 microRNAs (miRNAs), and 153 DE-circRNAs were identified as putative target mimics of 88 miRNAs. Furthermore, ceRNA networks of lncRNA/circRNA-miRNA-mRNA in response to CGMMV infection are described, with 12 DE-lncRNAs and 65 DE-circRNAs combining with 22 miRNAs and competing for the miRNA binding sites on 29 mRNAs. The qRT-PCR validation of selected lncRNAs and circRNAs showed a general correlation with the high-throughput sequencing results. This study provides a valuable resource of lncRNAs and circRNAs involved in the response to CGMMV infection in watermelon.

中文翻译：

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全基因组识别长的非编码RNA和环状RNA揭示了它们的ceRNA网络，以响应西瓜中的黄瓜绿斑驳花叶病毒感染。

长的非编码RNA（lncRNA）和环状RNA（circRNA）在植物防御病毒感染的反应中起着至关重要的作用。然而，对黄瓜绿斑驳花叶病毒（CGMMV）胁迫下西瓜中的lncRNA和circRNA及其竞争性内源RNA（ceRNA）网络没有系统的了解。在这里，我们介绍了CGMMV接种后48小时（48 hpi）西瓜叶片中lncRNA和circRNA的表征和表达谱，以模拟接种为对照。深度测序分析显示两个文库中有2373个lncRNA和606个circRNA。其中，与对照文库相比，在48 hpi文库中差异表达（DE）67个lncRNA（40个上调和27个下调）和548个circRNA（277个上调和271个下调）。此外，对于49个DE-lncRNA，检测到263个顺式作用匹配的lncRNA-mRNA对。对DE-lncRNA的顺式靶基因进行KEGG通路分析，发现与苯丙氨酸代谢，柠檬酸循环（TCA循环）和胞吞作用显着相关。此外，鉴定出30个DE-lncRNAs作为33个microRNA（miRNA）的推定靶标模拟物，而153个DE-circRNAs被鉴定为88个miRNA的推定靶标模拟物。此外，还描述了响应CGMMV感染的lncRNA / circRNA-miRNA-mRNA的ceRNA网络，其中12个DE-lncRNA和65个DE-circRNA与22个miRNA结合并竞争29个mRNA上的miRNA结合位点。选定的lncRNA和circRNA的qRT-PCR验证显示，与高通量测序结果具有普遍的相关性。