GSE112636
Diversity of cytosine methylation across the fungi tree of life
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. Overall design: MethylC-seq libraries for newly sequenced fungi species were prepared according to the protocol described in (Urich et al. 2015; doi: 10.1038/nprot.2014.114). Libraries were single-end 50, 75, or 150 bp sequenced on an Illumina NextSeq500 machine. Un-methylated lambda phage DNA or mitochondrial genome was used to as a control for sodium bisulfite conversion. WGBS data was aligned to each species respective genome assembly using the methylpy pipeline (Schultz et al. 2015; doi:10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). In brief, reads were trimmed of sequencing adapters using Cutadapt (Martin and Marcel 2011; doi: http://dx.doi.org/10.14806/ej.17.1.200), and then mapped to both a converted forward strand (cytosines to thymines) and converted reverse strand (guanines to adenines) using bowtie v1.1.1 (Langmead et al. 2009; doi: 10.1186/gb-2009-10-3-r25). This series contains re-analyzed data. Links to re-analyzed GSMs can be found below. Re-analyzed sample information and processed data fiels are available at the foot of this record. Previously published WGBS data for Aspergillus flavus (Liu, Lin, Wu et al. 2012; doi: 10.1371/journal.pone.0030349) (SRR345557), Cordyceps militaris (Wang et al. 2015; doi: 10.1016/j.funbio.2015.08.017) (SRR1916344, SRR1916345, SRR1916346, and SRR1916347), Cryptococcus neoformans (Huff and Zilberman 2014; doi: 10.1016/j.cell.2014.01.029) (SRR847298), Laccaria bicolor (Zemach et al. 2010; doi: 10.1126/science.1186366) (SRR042632, and SRR042633), Magnaporthe oryzae (Jeon et al. 2015; doi: 10.1038/srep08567) (SRR653493), Metarhizium robertsii (Li et al. 2017; doi: 10.1016/j.funbio.2017.01.002) (SRR3175452), Neurospora crassa (Honda et al. 2012; doi: 10.1073/pnas.1614279113) (SRR3476867), Phycomyces blakesleeanus (Zemach et al. 2010; ; doi: 10.1126/science.1186366) (SRR042643), Postia placenta (Zemach et al. 2010; doi: 10.1126/science.1186366) (SRR042648, and SRR042649), Saccharomyces cerevisiae (Moreselli et al. 2015; doi: 10.7554/eLife.06205) (SRR1916130), and Uncinocarpus reesii (Zemach et al. 2010; doi: 10.1126/science.1186366) (SRR042657) were downloaded from the Short Read Archive (SRA), and processed and aligned identically as described above.