Genome-wide identification of long non-coding RNAs and circular RNAs reveal their ceRNA networks in response to cucumber
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ORIGINAL ARTICLE
Genome‑wide identification of long non‑coding RNAs and circular RNAs reveal their ceRNA networks in response to cucumber green mottle mosaic virus infection in watermelon Yuyan Sun1 · Huiqing Zhang1 · Min Fan1 · Yanjun He1 · Pingan Guo1 Received: 27 December 2019 / Accepted: 11 February 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract 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.
Introduction Transcriptomic analysis has shown that >90% of plants’ genomes are transcribed and that many of the transcripts are noncoding RNAs (ncRNAs) [1, 2]. ncRNAs are functional RNAs that lack protein-coding potential. Many types of ncRNAs, including microRNA (miRNA) [3], small interfering RNA (siRNA) [4], trans-acting siRNA (tasiRNA) [5], long noncoding RNA (lncRNA) [6], and circular RNA (circRNA) Handling Editor: Massimo Turina. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04589-4) contains supplementary material, which is available to authorized users. * Min Fan [email protected] 1
Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
[7], have been identified and characterized in plants using high-throughput sequencing technologies. In recent years, lncRNAs and circRNAs have become hotspots in research on plant development processes and
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