Global DNA Methylation in the Chestnut Blight Fungus Cryphonectria parasitica and Genome-Wide Changes in DNA Methylation Accompanied with Sectorization

Abstract

Mutation in CpBck1, an ortholog of the cell wall integrity mitogen-activated protein kinase kinase kinase (MAPKKK) of Saccharomyces cerevisiae, in the chestnut blight fungus Cryphonectria parasitica resulted in a sporadic sectorization as culture proceeded. The progeny from the sectored area maintained the characteristics of the sector, showing a massive morphogenetic change, including robust mycelial growth without differentiation. Epigenetic changes were investigated as the genetic mechanism underlying this sectorization. Quantification of DNA methylation and whole-genome bisulfite sequencing revealed genome-wide DNA methylation of the wild-type at each nucleotide level and changes in DNA methylation of the sectored progeny. Compared to the wild-type, the sectored progeny exhibited marked genome-wide DNA hypomethylation but increased methylation sites. Expression analysis of two DNA methyltransferases, including two representative types of DNA methyltransferase (DNMTase), demonstrated that both were significantly down-regulated in the sectored progeny. However, functional analysis using mutant phenotypes of corresponding DNMTases demonstrated that a mutant of CpDmt1, an ortholog of RID of Neurospora crassa, resulted in the sectored phenotype but the CpDmt2 mutant did not, suggesting that the genetic basis of fungal sectorization is more complex. The present study revealed that a mutation in a signaling pathway component resulted in sectorization accompanied with changes in genome-wide DNA methylation, which suggests that this signal transduction pathway is important for epigenetic control of sectorization via regulation of genes involved in DNA methylation.

The Pattern and Function of DNA Methylation in Fungal Plant Pathogens

“…In gene bodies of M. oryzae, 5mC is frequently found near the start and end of coding regions and distant from the center [44]. Within the genic regions in Cryphonectria parasitica, exons present the highest proportion (28-45%) of strain-specific 5mC sites [75].…”

“…In contrast, DNA methylation in fungi usually is regarded as a genomic defense mechanism, because fungal DNA methylation primarily spreads over TEs, repeated sequences, and heterochromatic regions, leading to silencing these genomic regions and affecting the development process [37,44,57]. Apart from its functions in fungal genomic defense [44,71,75], DNA methylation is confirmed to make essential contributions to development in M. oryzae [44], regulation of secondary metabolism in Ganoderma sinense [76], and morphogenetic change in C. parasitica [75] by regulating the transcription of relevant genes. DNA methylation changes dynamically during the asexual stages of M. oryzae [44].…”

“…Methylome analysis showed that the DNA methylation loci in conidia and appressoria of M. oryzae are relatively fewer than in mycelia [44]. Mutation of CpBck1 in C. parasitica leads to the significant changes of the DNA methylation proportion and a sporadic occurrence of sectors [75]. DNA methylation impacts fungal development by regulating the transcription of genes related to metabolic activities and energetic metabolism in the M. robertsii [67].…”

Arbuscular mycorrhizal fungi: intraspecific diversity and pangenomes

“…As discussed earlier, optimal reference genomes from most AMF families and genera will be crucial to investigate intraspecific variation in transcriptional patterns across the Glomeromycotina phylogeny. These data will also be key to identifying intraspecific variability in the epigenome using ChIPseq (chromatin immunoprecipitation sequencing), or wholegenome bisulfite sequencing approaches (Chung et al, 2014;Jeon et al, 2015;So et al, 2018). Such techniques respectively allow the detection of binding sites for transcription factors and methylation patterns that have direct effects on the fungal phenotype (Chujo & Scott, 2014;Jeon et al, 2015;Kronholm et al, 2016).…”

A RID-like cytosine methyltransferase homologue controls sexual development in the fungusPodospora anserina

“…On the contrary, neither barren perithecia nor fertility defect are observed in N. crassa crosses homozygous for the rid null allele [12], although this fungus shows heavy DNA methylation of repeats subjected to RIP. The function of rid orthologs has also been addressed in fungal species that reproduce asexually ( Aspergillus flavus [87], Cryphonectria parasitica [88], Metarhizium robertsii [89]). Interestingly, in these species, in addition to a decrease of DNA methylation contents, the absence of DMT-like fungal specific Masc1/RID proteins results in a large palette of phenotypes including reduction of clonal dispersion (conidiation and sclerotial production), defects of mycelium morphology, decrease in secondary metabolite production and/or virulence toward plant hosts.…”