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Re-analysis of long non-coding RNAs and prediction of circRNAs reveal their novel roles in susceptible tomato following TYLCV infection

文献类型： 外文期刊

作者： Wang, Jinyan 1 ; Yang, Yuwen 1 ; Jin, Lamei 1 ; Ling, Xitie 1 ; Liu, Tingli 1 ; Chen, Tianzi 1 ; Ji, Yinghua 2 ; Yu, Weng 1 ;

作者机构： 1.Jiangsu Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Prov Key Lab Agrobiol, Nanjing 210014, Jiangsu, Peoples R China

2.Jiangsu Acad Agr Sci, Inst Plant Protect, Nanjing 210014

关键词： Susceptible tomato; Long non-coding RNA circRNA; TYLCV

期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）

ISSN： 1471-2229

年卷期： 2018 年 18 卷

页码：

收录情况： SCI

摘要： Background: Long Noncoding-RNAs (LncRNAs) are known to be involved in some biological processes, but their roles in plant-virus interactions remain largely unexplored. While circular RNAs (circRNAs) have been studied in animals, there has yet to be extensive research on them in a plant system, especially in tomato-tomato yellow leaf curl virus (TYLCV) interaction. Results: In this study, RNA transcripts from the susceptible tomato line JS-CT-9210 either infected with TYLCV or untreated, were sequenced in a pair-end strand-specific manner using ribo-zero rRNA removal library method. A total of 2056 IncRNAs including 1767 long intergenic non-coding RNA (lincRNAs) and 289 long non-coding natural antisense transcripts (IncNATs) were obtained. The expression patterns in IncRNAs were similar in susceptible tomato plants between control check (CK) and TYLCV infected samples. Our analysis suggested that IncRNAs likely played a role in a variety of functions, including plant hormone signaling, protein processing in the endoplasmic reticulum, RNA transport, ribosome function, photosynthesis, glulathione metabolism, and plant-pathogen interactions. Using virus-induced gene silencing (VIGS) analysis, we found that reduced expression of the IncRNA S-slylnc0957 resulted in enhanced resistance to TYLCV in susceptible tomato plants. Moreover, we identified 184 circRNAs candidates using the CircRNA Identifier (CIRI) software, of which 32 circRNAs were specifically expressed in untreated samples and 83 circRNAs in TYLCV samples. Approximately 62% of these circRNAs were derived from exons. We validated the circRNAs by both PCR and Sanger sequencing using divergent primers, and found that most of circRNAs were derived from the exons of protein coding genes. The silencing of these circRNAs parent genes resulted in decreased TYLCV virus accumulation. Conclusion: In this study, we identified novel IncRNAs and drcRNAs using bioinformatic approaches and showed that these RNAs function as negative regulators of TYLCV infection. Moreover, the expression patterns of IncRNAs in susceptible tomato plants were different from that of resistant tomato plants, while exonic circRNAs expression positively associated with their respective protein coding genes. This work provides a foundation for elaborating the novel roles of IncRNAs and circRNAs in susceptible tomatoes following TYLCV infection.

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