Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes

生物 丁香假单胞菌 转录组 基因 遗传学 RNA序列 长非编码RNA 猕猴桃 计算生物学 核糖核酸 基因表达 植物
作者
Zupeng Wang,Yifei Liu,Li Li,Dawei Li,Qiong Zhang,Yangtao Guo,Shuaibin Wang,Caihong Zhong,Hongwen Huang
出处
期刊:Scientific Reports [Nature Portfolio]
卷期号:7 (1) 被引量:54
标识
DOI:10.1038/s41598-017-05377-y
摘要

Abstract An outbreak of kiwifruit bacterial canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) beginning in 2008 caused disaster to the kiwifruit industry. However the mechanisms of interaction between kiwifruit and Psa are unknown. Long noncoding RNAs (lncRNAs) are known to regulate many biological processes, but comprehensive repertoires of kiwifruit lncRNAs and their effects on the interaction between kiwifruit and Psa are unknown. Here, based on in-depth transcriptomic analysis of four kiwifruit materials at three stages of infection with Psa, we identified 14,845 transcripts from 12,280 loci as putative lncRNAs. Hierarchical clustering analysis of differentially-expressed transcripts reveals that both protein-coding and lncRNA transcripts are expressed species-specifically. Comparing differentially-expressed transcripts from different species, variations in pattern-triggered immunity (PTI) were the main causes of species-specific responses to infection by Psa. Using weighted gene co-expression network analysis, we identified species-specific expressed key lncRNAs which were closely related to plant immune response and signal transduction. Our results illustrate that different kiwifruit species employ multiple different plant immunity layers to fight against Psa infection, which causes distinct responses. We also discovered that lncRNAs might affect kiwifruit responses to Psa infection, indicating that both protein-coding regions and noncoding regions can affect kiwifruit response to Psa infection.
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