Diversity of cytosine methylation across the fungi tree of life
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ABSTRACT: Cytosine methylation is a conserved base modification, but explanations for its interspecific variation remain elusive. Only through taxonomic sampling of disparate groups can unifying explanations for interspecific variation be thoroughly tested. Here we leverage phylogenetic resolution of cytosine DNA methyltransferases (DNA MTases) and genome evolution to better understand widespread interspecific variation across 40 diverse fungal species. DNA MTase genotypes have diversified from the ancestral DNMT1+DNMT5 genotype through numerous loss events, and duplications, whereas, DIM-2 and RID-1 are more recently derived in fungi. Methylation is typically enriched at intergenic regions, which includes repeats and transposons. Unlike certain Insecta and Angiosperm species, Fungi lack canonical gene body methylation. Some fungi species possess large clusters of contiguous methylation encompassing many genes, repetitive DNA and transposons, and are not ancient in origin. Broadly, methylation is partially explained by DNA MTase genotype and repetitive DNA content. Basidiomycota on average have the highest level of methylation, and repeat content, compared to other phyla. However, exceptions exist across Fungi. Other traits, including DNA repair mechanisms, might contribute to interspecific methylation variation within Fungi. Our results show mechanism and genome evolution are unifying explanations for interspecific methylation variation across Fungi.
ORGANISM(S): Coemansia reversa Uncinocarpus reesii Hesseltinella vesiculosa Pleurotus ostreatus Coprinopsis cinerea Aureobasidium pullulans Phycomyces blakesleeanus Pyricularia oryzae KJ201 Podospora anserina Postia placenta Laccaria bicolor Aspergillus flavus Spinellus fusiger Clavispora lusitaniae Mixia osmundae Radiomyces spectabilis Plenodomus lingam Candida albicans Cryptococcus neoformans var. grubii Kirkomyces cordense Microbotryum lychnidis-dioicae Botrytis cinerea [Candida] auris Agaricus bisporus Wolfiporia cocos Phanerodontia chrysosporium Fusarium fujikuroi Sporobolomyces roseus Heterobasidion irregulare Saccharomyces cerevisiae Cordyceps militaris Metarhizium robertsii Parasitella parasitica Flammula alnicola Pseudogymnoascus destructans Neurospora crassa Coemansia spiralis Tilletiopsis washingtonensis Lobosporangium transversale Syncephalis fuscata
PROVIDER: GSE112636 | GEO | 2019/02/18
REPOSITORIES: GEO
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