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| Status |
Public on Feb 18, 2019 |
| Title |
Diversity of cytosine methylation across the fungi tree of life |
| Platform organisms |
Plenodomus lingam; Fusarium fujikuroi; Pleurotus ostreatus; Agaricus bisporus; Coprinopsis cinerea; Candida albicans; Aureobasidium pullulans; Mixia osmundae; Parasitella parasitica; Clavispora lusitaniae; Botrytis cinerea; Sporobolomyces roseus; Tilletiopsis washingtonensis; Coemansia reversa; Lobosporangium transversale; Radiomyces spectabilis; Wolfiporia cocos; Spinellus fusiger; Hesseltinella vesiculosa; Flammula alnicola; Microbotryum lychnidis-dioicae; Coemansia spiralis; [Candida] auris; Kirkomyces cordensis; Pseudogymnoascus destructans; Heterobasidion irregulare; Syncephalis fuscata; Podospora anserina; Phanerodontia chrysosporium |
| Sample organisms |
Phycomyces blakesleeanus; Saccharomyces cerevisiae; Plenodomus lingam; Aspergillus flavus; Fusarium fujikuroi; Neurospora crassa; Pleurotus ostreatus; Agaricus bisporus; Coprinopsis cinerea; Candida albicans; Aureobasidium pullulans; Laccaria bicolor; Uncinocarpus reesii; Mixia osmundae; Parasitella parasitica; Clavispora lusitaniae; Botrytis cinerea; Sporobolomyces roseus; Tilletiopsis washingtonensis; Coemansia reversa; Lobosporangium transversale; Radiomyces spectabilis; Cordyceps militaris; Wolfiporia cocos; Spinellus fusiger; Hesseltinella vesiculosa; Postia placenta; Flammula alnicola; Cryptococcus neoformans var. grubii; Microbotryum lychnidis-dioicae; Coemansia spiralis; [Candida] auris; Kirkomyces cordensis; Metarhizium robertsii; Pseudogymnoascus destructans; Heterobasidion irregulare; Pyricularia oryzae KJ201; Syncephalis fuscata; Podospora anserina; Phanerodontia chrysosporium |
| Experiment type |
Methylation profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
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.
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| 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.
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| Contributor(s) |
Schmitz RJ, Bewick AJ |
| Citation(s) |
30778188 |
| Submission date |
Apr 03, 2018 |
| Last update date |
May 20, 2019 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
|
| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platforms (29)
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| GPL22403 |
Illumina NextSeq 500 (Candida albicans) |
| GPL24692 |
Illumina NextSeq 500 (Clavispora lusitaniae) |
| GPL24808 |
Illumina NextSeq 500 (Agaricus bisporus) |
| GPL24809 |
Illumina NextSeq 500 (Aureobasidium pullulans) |
| GPL24810 |
Illumina NextSeq 500 (Botrytis cinerea) |
| GPL24811 |
Illumina NextSeq 500 ([Candida] auris) |
| GPL24813 |
Illumina NextSeq 500 (Coemansia reversa) |
| GPL24814 |
Illumina NextSeq 500 (Coemansia spiralis) |
| GPL24816 |
Illumina NextSeq 500 (Fusarium fujikuroi) |
| GPL24817 |
Illumina NextSeq 500 (Hesseltinella vesiculosa) |
| GPL24819 |
Illumina NextSeq 500 (Kirkomyces cordense) |
| GPL24820 |
Illumina NextSeq 500 (Leptosphaeria maculans) |
| GPL24821 |
Illumina NextSeq 500 (Lobosporangium transversale) |
| GPL24823 |
Illumina NextSeq 500 (Mixia osmundae) |
| GPL24824 |
Illumina NextSeq 500 (Parasitella parasitica) |
| GPL24825 |
Illumina NextSeq 500 (Phanerochaete chrysosporium) |
| GPL24826 |
Illumina NextSeq 500 (Flammula alnicola) |
| GPL24827 |
Illumina NextSeq 500 (Pleurotus ostreatus) |
| GPL24828 |
Illumina NextSeq 500 (Podospora anserina) |
| GPL24829 |
Illumina NextSeq 500 (Pseudogymnoascus destructans) |
| GPL24830 |
Illumina NextSeq 500 (Radiomyces spectabilis) |
| GPL24831 |
Illumina NextSeq 500 (Spinellus fusiger) |
| GPL24832 |
Illumina NextSeq 500 (Sporobolomyces roseus) |
| GPL24833 |
Illumina NextSeq 500 (Syncephalis fuscata) |
| GPL24834 |
Illumina NextSeq 500 (Tilletiopsis washingtonensis) |
| GPL24835 |
Illumina NextSeq 500 (Wolfiporia cocos) |
| GPL24836 |
Illumina NextSeq 500 (Microbotryum lychnidis-dioicae) |
| GPL25136 |
Illumina HiSeq 4000 (Heterobasidion irregulare) |
| GPL25137 |
Illumina HiSeq 4000 (Coprinopsis cinerea) |
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| Samples (31)
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| GSM3074692 |
Candida albicans, WGBS |
| GSM3074693 |
Candida auris, WGBS |
| GSM3074694 |
Clavispora lusitianiae, WGBS |
| GSM3074695 |
Coemansia reversa, WGBS |
| GSM3074696 |
Coemansia spiralis, WGBS |
| GSM3074697 |
Coprinopsis cinerea, WGBS |
| GSM3074698 |
Fusarium fujikuroi, WGBS |
| GSM3074699 |
Hesseltinella vesiculosa WGBS run1 |
| GSM3074700 |
Hesseltinella vesiculosa WGBS run2 |
| GSM3074701 |
Heterobasidion irregulare, WGBS |
| GSM3074702 |
Kirkomyces cordense, WGBS |
| GSM3074703 |
Leptosphaeria maculans, WGBS |
| GSM3074704 |
Lobosporangium transversale, WGBS |
| GSM3074705 |
Microbotryum lychnidis, WGBS |
| GSM3074706 |
Mixia osmundae, WGBS |
| GSM3074707 |
Parasitella parasitica, WGBS, run 1 |
| GSM3074708 |
Parasitella parasitica, WGBS, run 2 |
| GSM3074709 |
Phanerochaete chrysosporium, WGBS |
| GSM3074710 |
Pholiota alnicola, WGBS |
| GSM3074711 |
Pleurotus ostreatus, WGBS |
| GSM3074712 |
Podospora anserina, WGBS |
| GSM3074713 |
Pseudogymnoascus destructans, WGBS |
| GSM3074714 |
Radiomyces spectabilis, WGBS |
| GSM3074715 |
Spinellus fusiger, WGBS |
| GSM3074716 |
Sporobolomyces roseus, WGBS |
| GSM3074717 |
Syncephalis fuscata, WGBS |
| GSM3074718 |
Tilletiopsis washingtonensis, WGBS |
| GSM3074719 |
Wolfiporia cocos, WGBS |
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| Relations |
| Reanalysis of |
GSM797578 |
| Reanalysis of |
GSM1634321 |
| Reanalysis of |
GSM1134615 |
| Reanalysis of |
GSM497256 |
| Reanalysis of |
GSM1072037 |
| Reanalysis of |
GSM2064588 |
| Reanalysis of |
GSM2143335 |
| Reanalysis of |
GSM497262 |
| Reanalysis of |
GSM497266 |
| Reanalysis of |
GSM1634054 |
| Reanalysis of |
GSM497274 |
| BioProject |
PRJNA448591 |
| SRA |
SRP137011 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112636_RAW.tar |
1.5 Gb |
(http)(custom) |
TAR (of TSV) |
| GSE112636_Re-analyzed_data_information.xls.gz |
11.6 Kb |
(ftp)(http) |
XLS |
| GSE112636_Re-analyzed_processed_data.tar.gz |
652.2 Mb |
(ftp)(http) |
TAR |
| GSE112636_metafile.txt.gz |
226 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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