Abstract
Comprehensive transcriptome analysis was conducted to elucidate the molecular basis of the interaction between chestnut blight fungus, Cryphonectria parasitica, and single-stranded RNA (ssRNA) mycovirus Cryphonectria hypovirus 1 (CHV1), using RNA-sequencing (RNA-seq). A total of 1,023 differentially expressed genes (DEGs) were affected by CHV1 infection, of which 753 DEGs were upregulated and 270 DEGs were downregulated. Significant correlations in qRT-PCR analysis of 20 randomly selected DEGs and agreement with previously characterized marker genes validated our RNA-seq analysis as representing global transcriptional profiling of virus-free and -infected isogenic strains of C. parasitica. Gene Ontology (GO) analysis of DEGs indicated that “cellular aromatic compound metabolic process” and “transport” were the two most enriched components in the “biological process.” In addition, “cytoplasm” was the most enriched term in the “cellular component” and “nucleotide binding” and “cation binding” were the two most enriched terms in the “molecular function” category. These results suggested that altered expression of genes encoding numerous intracellular proteins due to hypoviral infection resulted in changes in specific metabolic processes as well as transport processes. Kyoto Encyclopedia of Genes and Genomes function analysis demonstrated that pathways for “biosynthesis of other secondary metabolites,” “amino acid metabolism,” “carbohydrate metabolism,” and “translation” were enriched among the DEGs in C. parasitica. These results demonstrate that hypoviral infection resulted in massive but specific changes in primary and secondary metabolism, of which antiviral fungal metabolites were highly induced. The results of this study provide further insights into the mechanism of fungal gene regulation by CHV1 at the transcriptome level.
Highlights
The Cryphonectria parasitica–Cryphonectria hypovirus 1 (CHV1) interaction is a successful natural biocontrol system mediated by a mycovirus
Gene Involved in Viral Replication We found an interesting gene correlated with viral gene expression, with a significantly upregulated differentially expressed genes (DEGs) identified as a putative zinc knuckle domain-containing protein, which is similar to the ATP-dependent RNA helicase glh-4 of Caenorhabditis elegans
Transcriptome data provide comprehensive elucidation of fungal responses to hypoviral infection based on RNA sequencing (RNA-seq) technology
Summary
The Cryphonectria parasitica–Cryphonectria hypovirus 1 (CHV1) interaction is a successful natural biocontrol system mediated by a mycovirus. The interaction between C. parasitica and CHV1 has been studied intensively at the molecular and cellular levels, aiming to identify genes involved in symptom development and the novel defense mechanism of fungi in response to hypoviral infection. Differential mRNA display (Chen et al, 1996; Kang et al, 2000) and cDNA microarray analysis representing approximately 2,200 unique genes (Allen et al, 2003) were conducted in C. parasitica to determine genes involved in key regulatory pathways affected by hypoviral infection. Differential mRNA display requires considerable additional effort to determine the identities of differentially expressed genes (DEGs) and microarrays can provide information only on given sequences (Allen et al, 2003). Recent study using RNAseq found 2,717 DEGs (Li et al, 2018), no further transcriptomic analysis of virus-infected and virus-free strains has been reported
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