Genomes and population genomics of Cenococcum geophilum highlight the genetic diversity, evolution, and stress responses of ectomycorrhizal fungi

Genomes and population genomics of Cenococcum geophilum highlight the genetic diversity, evolution, and stress responses of ectomycorrhizal fungi | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Genomes and population genomics of Cenococcum geophilum highlight the genetic diversity, evolution, and stress responses of ectomycorrhizal fungi Chunlan Lian, Chaofeng Li, Chao Yuan, Yuyu Shi, Qifang Geng, Jiali Li, and 25 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4894562/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Cenococcum geophilum is among the most globally abundant ectomycorrhizal (ECM) fungi and often dominates the root systems of woody plants, particularly in extreme environments. Therefore, C. geophilum is an ideal model for studying genetic diversity and adaptation of ectomycorrhizal symbiosis. In this study, we constructed a C. geophilum pan-genome using six high-quality whole-genome sequences representing the global diversity and found that dispensable genes are important for its environmental adaptation. We identified millions of single-nucleotide polymorphisms, hundreds of thousands of small insertions/deletions, 0.04–0.2% structural variation, and 21 horizontally transferred genes from non-host plants. Based on resequencing data from 304 global isolates, we investigated the geographic structure of C. geophilum populations. Genome-wide association and transcriptome studies identified 161 genomic regions significantly associated with nine biological and environmental adaption characteristics, including 2738 candidate genes such as EVM0002574 for cadmium, salt, and high temperature stresses. These reference genomes and diversity datasets provide resources and a comparative genomic platform for the study of ectomycorrhizal symbioses. Biological sciences/Microbiology/Fungi/Fungal genomics Earth and environmental sciences/Ecology/Biogeography Full Text Additional Declarations There is NO Competing Interest. Table 1 is available in the Supplementary Files section Supplementary Files Table1.xlsx Table1 SupplementaryData.pdf SupplementaryMaterialsandMethods.pdf SupplementaryTables.pdf Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4894562","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":345669947,"identity":"1f340da9-3c71-40ac-aa5a-6a63ca208c8d","order_by":0,"name":"Chunlan 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Therefore, C. geophilum is an ideal model for studying genetic diversity and adaptation of ectomycorrhizal symbiosis. In this study, we constructed a C. geophilum pan-genome using six high-quality whole-genome sequences representing the global diversity and found that dispensable genes are important for its environmental adaptation. We identified millions of single-nucleotide polymorphisms, hundreds of thousands of small insertions/deletions, 0.04–0.2% structural variation, and 21 horizontally transferred genes from non-host plants. Based on resequencing data from 304 global isolates, we investigated the geographic structure of C. geophilum populations. Genome-wide association and transcriptome studies identified 161 genomic regions significantly associated with nine biological and environmental adaption characteristics, including 2738 candidate genes such as EVM0002574 for cadmium, salt, and high temperature stresses. 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