Browsing by Subject "Forest pathology"

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  • Zeng, Zhen (Helsingin yliopisto, 2019)
    The fungus Heterobasidion parviporum is considered as the most destructive disease agent of conifers. The main host of H. parviporum is Norway spruce (Picea abies), and the primary infection is mediated by aerial sexual spores (basidiospores) landing on fresh stump surfaces or tree injuries. The secondary infection is mediated by vegetative spread of the fungus via root contacts formed between neighboring trees. H. parviporum features a dual and flexible lifestyle (saprotrophy and necrotrophy). Due to the unavailability of a reference genome, studies of the molecular pathology have heavily relied on parallel studies on its sibling species H. irregulare. The rapid development of next-generation sequencing techniques has revolutionized the scalability, reliability, and resolution of sequencing in life sciences. The first aim of this study was to provide a reference genome for H. parviporum by application of whole-genome sequencing. We selected a virulent isolate (isolate 96026) as the reference, which presented us a genome assembly of 37.76 Mb, hosting 10,502 protein-coding genes. To identify genomic variations potentially accountable for the virulence of the reference isolate, 14 less virulent isolates were also sequenced. Comparative genomic analysis uncovered not only the remarkable intraspecific level of polymorphism, but also two genomic regions exclusive to the reference isolate. The proteins encoded by genes situated in these two regions included a cytochrome P450, a major facilitator superfamily transporter, and secreted proteins, suggestive of their potential implication in the virulence of H. parviporum reference isolate. To propose candidate virulence factors for functional characterizations, secreted protein-coding genes under genome-wide selection pressure or possessing featured variants were explored, and examples were listed. We then targeted small-secreted proteins (SSPs) in H. parviporum reference isolate to provide promising SSP candidate(s) with functional evidence in terms of promoting disease development. A particular SSP (HpSSP35.8) was found capable of causing rapid cell death on the leaves of Nicotiana benthamiana and of triggering the expression of some defense-related genes in N. benthamiana. In addition, HpSSP35.8 was also highly expressed during the pre-symptomatic phase of H. parviporum infection of Norway spruce seedlings, in which some defense-related genes were also induced. Collectively, all evidence suggests this SSP as a potentially important virulence candidate, presumably in the early stage of pathogenic interaction with the host. Lastly, the transcriptome and DNA methylome profiles of the reference isolate growing as a necrotroph and as a saprotroph were obtained. A group of carbohydrate-active enzymes was found essential for its both necrotrophic and saprotrophic growth, and a small set of signaling- and transcription factors might be associated with the transition of saprotrophic to necrotrophic growth. DNA methylation was demonstrated to mostly target and repress the activity of transposable elements in the genome. A small group of genes with significantly varied methylation and expression levels were identified, implying the potential of DNA methylation as one of the transcriptional regulatory mechanisms in this fungus. Our study provided the reference genome and first methylome of H. parviporum. Follow-up research into the molecular mechanisms of Heterobasidion pathogenesis could be greatly facilitated by the availability of the genome, transcriptome, methylome and secretome data.