Canadian Forest Service Publications

Characterization of Heterobasidion occidentale transcriptomes reveals candidate genes and DNA polymorphisms for virulence variations. 2018. Liu, J-J, Shamoun, S.F., Leal, I., Kowbel, R., Sumampong, G., Zamany, A. Microbial Biotechnology, 11(3), 537–550.

Year: 2018

Available from: Pacific Forestry Centre

Catalog ID: 39136

Language: English

CFS Availability: PDF (download)

Available from the Journal's Web site.
DOI: 10.1111/1751-7915.13259

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Abstract

Characterization of genes involved in differentiation of pathogen species and isolates with variations of virulence traits provides valuable information to control tree diseases for meeting the challenges of sustainable forest health and phytosanitary trade issues. Lack of genetic knowledge and genomic resources hinders novel gene discovery, molecular mechanism studies and development of diagnostic tools in the management of forest pathogens. Here, we report on transcriptome profiling of Heterobasidion occidentale isolates with contrasting virulence levels. Comparative transcriptomic analysis identified orthologous groups exclusive to H. occidentale and its isolates, revealing biological processes involved in the differentiation of isolates. Further bioinformatics analyses identified an H. occidentale secretome, CYPome and other candidate effectors, from which genes with species- and isolate-specific expression were characterized. A large proportion of differentially expressed genes were revealed to have putative activities as cell wall modification enzymes and transcription factors, suggesting their potential roles in virulence and fungal pathogenesis. Next, large numbers of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were detected, including more than 14 000 interisolate non-synonymous SNPs. These polymorphic loci and species/isolate-specific genes may contribute to virulence variations and provide ideal DNA markers for development of diagnostic tools and investigation of genetic diversity.

Plain Language Summary

The objectives of this study were to identify genes involved in virulence traits in Heterobasidion occidendale isolates, and to provide genomic information and tools for management of forest disease and for meeting the challenges of phytosanitary trade issues caused by this fungal pathogen. Here we report on virulence assessment and transcriptome profiling of pathogenic isolates collected from different regions. We performed RNA-seq analysis and generated more than 100 million clean, 100-bp paired-end reads for two selected isolates with contrasting virulence levels. Bioinformatics analyses identified a H. occidentale secretome, CYProme, and other candidate effectors. We determined orthologous gene groups and genes exclusive to H. occidentale and its isolates by comparative transcriptomic analysis, and discussed potential roles of these genes in virulence and fungal pathogenesis. Next, we detected large numbers of simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs), including more than 14,000 inter-isolate non-synonymous SNPs, which provided ideal DNA markers and species/isolate-specific genes for development of diagnostic tools and investigation of genetic diversity contributing virulence variation. This study reports on the first comparative transcriptome analysis of H. occidentale isolates and advances genomic knowledge regarding H. occidentale virulence. This analysis will facilitate future investigation of the molecular mechanisms underlying virulent traits and development of efficient diagnostic tools, which will light up the path towards the detailed characterization of genome differentiation of H. occidentale from other Heterobasidion species.

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