OPENAIRE OpenAire Bielefeld Academic Search Engine (BASE) eScholarship - University of California Archivio istituzionale della ricerca - Fondazione Edmund Mach Recolector de Ciencia Abierta, RECOLECTA IRIS - Institutional Research Information System of the University of Trento DIGITAL.CSIC Crossref European Union Open Data Portal https://iris.unitn.it/bitstream/11572/450837/1/FUDI_Coleine%20et%20al%20v2..pdf https://iris.unitn.it/bitstream/11572/450837/3/s13225-024-00533-y.pdf https://escholarship.org/content/qt86f967px/qt86f967px.pdf https://doi.org/10.1007/s13225-024-00533-y Fungal Diversity Open Access 2024-02-26 2025-05-27 2024-02-29 Open AccessPeer reviewed Open AccessPeer reviewed C.C. is supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No. 702057 (DRYLIFE). M.D-B. is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014–2020 Objetivo temático '01 – Refuerzo de la investigación, el desarrollo tecnológico y la innovación') associated with the research project P20_00879 (ANDABIOMA). N.S. receives funding from the ERC (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015). J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. T.K. and J.E.S. were partially supported by NIH NIAID R01-GM108492. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. Open AccessPeer reviewed C.C. is supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No. 702057 (DRYLIFE). M.D-B. is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014–2020 Objetivo temático '01 – Refuerzo de la investigación, el desarrollo tecnológico y la innovación') associated with the research project P20_00879 (ANDABIOMA). N.S. receives funding from the ERC (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015). J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. T.K. and J.E.S. were partially supported by NIH NIAID R01-GM108492. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide. Yet, despite the growing interest in these fungi, there is a considerable gap of knowledge on their functionality. Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited. Here, we supply a genome catalog of 118 black fungi, encompassing different ecologies, phylogenies and lifestyles, as a first example of a comparative genomic study at high level of diversity. Results indicate that, as a rule, Dothideomycetes show more variable genome size and that larger genomes are associated with harshest conditions; low temperature tolerance and DNA repair capacity are overrepresented in their genomes. In Eurotiomycetes high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence. The genomic features are consistent with the prevalent ecologies in the two classes. Indeed, Dothideomycetes are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats; in contrast, Eurotiomycetes spread mainly in hot human-impacted sites with industrial pollution. Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in Dothideomycetes, suggesting that, despite their preference for the cold, they are potentially equipped to survive even when temperatures rise due to the global warming. Open AccessPeer reviewed C.C. is supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No. 702057 (DRYLIFE). M.D-B. is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014–2020 Objetivo temático '01 – Refuerzo de la investigación, el desarrollo tecnológico y la innovación') associated with the research project P20_00879 (ANDABIOMA). N.S. receives funding from the ERC (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015). J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. T.K. and J.E.S. were partially supported by NIH NIAID R01-GM108492. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide. Yet, despite the growing interest in these fungi, there is a considerable gap of knowledge on their functionality. Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited. Here, we supply a genome catalog of 118 black fungi, encompassing different ecologies, phylogenies and lifestyles, as a first example of a comparative genomic study at high level of diversity. Results indicate that, as a rule, Dothideomycetes show more variable genome size and that larger genomes are associated with harshest conditions; low temperature tolerance and DNA repair capacity are overrepresented in their genomes. In Eurotiomycetes high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence. The genomic features are consistent with the prevalent ecologies in the two classes. Indeed, Dothideomycetes are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats; in contrast, Eurotiomycetes spread mainly in hot human-impacted sites with industrial pollution. Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in Dothideomycetes, suggesting that, despite their preference for the cold, they are potentially equipped to survive even when temperatures rise due to the global warming. 18 páginas.- 5 figuras.- 2 tablas.- referencias.- Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s13225-024-00533-y 570 Black Fungi Plant Biology Mycology & Parasitology Evolutionary biology Microbiology Genetics Black fungi · Stress resistance · Comparative genomics · Extreme environments 14. Life underwater Plant biology 2. Zero hunger Evolutionary Biology Black fungi Comparative genomics Human Genome 500 Extreme environments Biological Sciences 15. Life on land 3. Good health Health Disparities 13. Climate action 8. Economic growth Stress resistance Settore BIO/19 - MICROBIOLOGIA GENERALE Biotechnology Coleine, Claudia, Kurbessoian, Tania, Calia, Giulia, Delgado-Baquerizo, Manuel, Cestaro, Alessandro, Pindo, Massimo, Armanini, Federica, Asnicar, Francesco, Isola, Daniela, Segata, Nicola, Donati, Claudio, Stajich, Jason E., de Hoog, Sybren, Selbmann, Laura, 2024-02-26 journalpaper Open AccessPeer reviewed Open AccessPeer reviewed C.C. is supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No. 702057 (DRYLIFE). M.D-B. is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014–2020 Objetivo temático '01 – Refuerzo de la investigación, el desarrollo tecnológico y la innovación') associated with the research project P20_00879 (ANDABIOMA). N.S. receives funding from the ERC (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015). J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. T.K. and J.E.S. were partially supported by NIH NIAID R01-GM108492. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. Open AccessPeer reviewed C.C. is supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No. 702057 (DRYLIFE). M.D-B. is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014–2020 Objetivo temático '01 – Refuerzo de la investigación, el desarrollo tecnológico y la innovación') associated with the research project P20_00879 (ANDABIOMA). N.S. receives funding from the ERC (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015). J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. T.K. and J.E.S. were partially supported by NIH NIAID R01-GM108492. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide. Yet, despite the growing interest in these fungi, there is a considerable gap of knowledge on their functionality. Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited. Here, we supply a genome catalog of 118 black fungi, encompassing different ecologies, phylogenies and lifestyles, as a first example of a comparative genomic study at high level of diversity. Results indicate that, as a rule, Dothideomycetes show more variable genome size and that larger genomes are associated with harshest conditions; low temperature tolerance and DNA repair capacity are overrepresented in their genomes. In Eurotiomycetes high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence. The genomic features are consistent with the prevalent ecologies in the two classes. Indeed, Dothideomycetes are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats; in contrast, Eurotiomycetes spread mainly in hot human-impacted sites with industrial pollution. Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in Dothideomycetes, suggesting that, despite their preference for the cold, they are potentially equipped to survive even when temperatures rise due to the global warming. Open AccessPeer reviewed C.C. is supported by the European Commission under the Marie Sklodowska-Curie Grant Agreement No. 702057 (DRYLIFE). M.D-B. is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014–2020 Objetivo temático '01 – Refuerzo de la investigación, el desarrollo tecnológico y la innovación') associated with the research project P20_00879 (ANDABIOMA). N.S. receives funding from the ERC (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015). J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. T.K. and J.E.S. were partially supported by NIH NIAID R01-GM108492. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. The classes Dothideomycetes and Eurotiomycetes include constitutively melanized fungi adapted to extreme conditions and they are widely distributed in diverse hostile habitats worldwide. Yet, despite the growing interest in these fungi, there is a considerable gap of knowledge on their functionality. Their genomic analysis is still in its infancy and the possibility to understand their adaptive strategies and exploit their potentialities in bioremediation is very limited. Here, we supply a genome catalog of 118 black fungi, encompassing different ecologies, phylogenies and lifestyles, as a first example of a comparative genomic study at high level of diversity. Results indicate that, as a rule, Dothideomycetes show more variable genome size and that larger genomes are associated with harshest conditions; low temperature tolerance and DNA repair capacity are overrepresented in their genomes. In Eurotiomycetes high temperature tolerance and capacity to metabolize hydrocarbons are more frequently present and these abilities are positively correlated with the human presence. The genomic features are consistent with the prevalent ecologies in the two classes. Indeed, Dothideomycetes are more common in cold and dry environments with high capacity for DNA repair being consistent with the normally highly UV-impacted conditions in their habitats; in contrast, Eurotiomycetes spread mainly in hot human-impacted sites with industrial pollution. Mean annual temperature and isothermality are positively correlated with tolerance to high temperatures in Dothideomycetes, suggesting that, despite their preference for the cold, they are potentially equipped to survive even when temperatures rise due to the global warming. 18 páginas.- 5 figuras.- 2 tablas.- referencias.- Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s13225-024-00533-y Class-wide genomic tendency throughout specific extremes in black fungi 10.1007/s13225-024-00533-y 702057