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.
Highlights
Kiwifruit is becoming an increasingly popular fruit worldwide owing to its high vitamin C content and balanced nutritional components of minerals, dietary fiber and health-promoting metabolites[1,2,3]
We found that the expression of genes in different Actinidia taxa were remodeled in a species-specific pattern, corresponding to leaf symptoms associated with Psa infection
Samples of AH and AJ which exhibited severe symptoms were classified in the same clade, while samples of A. eriantha (Ae) and Aa without obvious symptoms were clustered into another clade (Supplementary Figure S8) indicating that leaf symptoms were in accord with the expression level of genes in the plant–pathogen interaction pathway., Based on gene expression of transcripts within the plant–pathogen interaction pathway, we identified 25, 13 and 4 transcripts which were uniquely expressed in Actinidia chinensis (Ac), Ae and Aa, respectively (Supplementary Figure S9, Supplementary Data S4)
Summary
Kiwifruit is becoming an increasingly popular fruit worldwide owing to its high vitamin C content and balanced nutritional components of minerals, dietary fiber and health-promoting metabolites[1,2,3]. Strains of biovar 3 cannot produce both phaseolotoxin and coronatine, but possess four putative clade-specific hop genes: hopH1, hopZ5, hopAM1-2, and hopAA1-2, which encode effector proteins as part of the type III secretion system in P. syringae species[7]. In kiwifruit, these Psa strains can enter the host through natural orifices or wounds, and can be disseminated through pollen[15]. As microbe-associated molecular patterns (MAMPs), these molecules are recognized by the plant membrane proteins recognition receptors (PRRs)[17], which result in the invasion of pathogenic microbes is suppressed This immune system is known as pattern-triggered immunity (PTI)[18]. The TGA-bZIP family can regulate the plant defense system through the SA signaling pathway[23]
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