Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection.

Abstract

Recently, a large number of long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, how lncRNAs function during plant DNA virus infection is largely unknown. We performed strand-specific paired-end RNA sequencing of tomato samples infected with Tomato yellow leaf curl virus (TYLCV) with three biological replicates. Overall, we predicted 1565 lncRNAs including long intergenic ncRNAs (lincRNAs) and natural antisense transcripts (lncNATs) and definitively identified lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS). We also verified the functions of a set of lncRNAs that were differentially expressed between 0 and 7 days post inoculation (dpi). More importantly, we found that several lncRNAs acted as competing endogenous target mimics (eTMs) for tomato microRNAs involved in the TYLCV infection. These results provide new insight into lncRNAs involved in the response to TYLCV infection that are important components of the TYLCV network in tomatoes.

• Authors: Jinyan Wang, Wengui Yu, Yuwen Yang, Xiao Li, Tianzi Chen, Tingli Liu, Na Ma, Xu Yang, Renyi Liu, Baolong Zhang
• Journal: Scientific reports (Sci Rep) Vol. 5 Pg. 16946 (Dec 18 2015) ISSN: 2045-2322 [Electronic] England
• PMID: 26679690 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• MicroRNAs
• Oligonucleotides, Antisense
• RNA, Long Noncoding

Topics

• Base Sequence
• Begomovirus (physiology)
• Gene Expression Regulation, Plant
• Gene Silencing
• Genome, Plant
• Solanum lycopersicum (genetics, growth & development)
• MicroRNAs (antagonists & inhibitors, genetics, metabolism)
• Oligonucleotides, Antisense (metabolism)
• Plant Diseases (virology)
• RNA, Long Noncoding (metabolism)
• Real-Time Polymerase Chain Reaction
• Sequence Alignment
• Sequence Analysis, RNA