{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Dauphin B"],"funding":["Office of Science of the U.S. Department of Energy","DOE Office of Science User Facility","U.S. Department of Energy Joint Genome Institute"],"pagination":["evag017"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12910237"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["18(2)"],"pubmed_abstract":["Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome cons"],"journal":["Genome biology and evolution"],"pubmed_title":["Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism."],"pmcid":["PMC12910237"],"funding_grant_id":["DE-AC02-05CH11231"],"pubmed_authors":["Grigoriev IV","Martin F","Baril T","Kohler A","Dauphin B","De Freitas Pereira M","Peter M","Morin E","Pfister S","Croll D","Oggenfuss U"],"additional_accession":[]},"is_claimable":false,"name":"Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism.","description":"Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome cons","dates":{"release":"2026-01-01T00:00:00Z","publication":"2026 Jan","modification":"2026-07-09T13:26:17.26Z","creation":"2026-07-09T13:10:26.659Z"},"accession":"S-EPMC12910237","cross_references":{"pubmed":["41566997"],"doi":["10.1093/gbe/evag017"]}}