Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

Abstract

BackgroundHeterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species.ResultsTo better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates.ConclusionOur study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4610-4) contains supplementary material, which is available to authorized users.

The Pattern and Function of DNA Methylation in Fungal Plant Pathogens

“…Microorganisms 2019, 7, x FOR PEER REVIEW 6 of 14 demethylated while C sites are methylated at different loci [74]. Variation in the methylome of H. parviporum is observed during its asexual development and different lifestyles, reinforcing the dynamic nature of DNA methylation [72]. In M. oryzae, methylation peaks in the regions flanking coding sequences in mycelia and disappears in conidia and appressoria [44], suggesting that DNA methylation patterns change according to developmental stage.…”

“…In the following sections, we further discuss the distribution of DNA methylation in different genomic regions. An increasing number of studies have reported the presence of cytosine methylation in the gene bodies of many eukaryotic organisms, including fungi [72]. The gene body is considered to begin after the first exon because methylation of the first exon, like promoter methylation, leads to gene silencing [73].…”

“…DNA methylation levels vary according to cell type in gametophytes and change dynamically during eukaryotic growth and development [36,44,71]. In Cordyceps militaris, the methylome undergoes global reprogramming during development, such that pre-existing 5mC sites are An increasing number of studies have reported the presence of cytosine methylation in the gene bodies of many eukaryotic organisms, including fungi [72]. The gene body is considered to begin after the first exon because methylation of the first exon, like promoter methylation, leads to gene silencing [73].…”

Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum

“…The recently published reference genome of H. parviporum 96026 [14] enables a wider range of studies conducted in this species. Therefore, in our study, by employing whole-genome bisulfite sequencing, we uncovered the genome-wide DNA methylation pattern associated with different lifestyles (saprotrophy and necrotrophy) and asexual lifecycle stages (free-living mycelia and conidiospores) of H. parviporum 96026.…”

Multiplex real‐time PCR assays for the detection and identification of Heterobasidion species attacking conifers in Europe

“…The LOD was also determined with 10-fold serial dilutions starting from 0.5 ng µL À1 genomic DNA extracts from strains 1987-1661/4 (H. parviporum), FOM0132 (H. irregulare), LSVM975 (H. abietinum) and 1960/ 56/4 (H. annosum s.s.). The genome size of H. annosum s.s. and H. irregulare was estimated to be approximately 31 and 33 Mb, respectively (Choi et al, 2017) and 33 Mb on average for H. parviporum (Zeng et al, 2018), whereas the genome size of H. abietinum remains to be determined. Because 1 pg of DNA corresponds to 965 Mb (Bennett & Smith, 1976), it is therefore possible to estimate the quantity of DNA in one nucleus of H. annosum s.s. (0.0321 pg), H. irregulare (0.0341 pg) and H. parviporum (0.0341 pg).…”