101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens
| Autor: | Hee-Jin Park, Kurt LaButti, Scott E. Baker, L.-H. Zwiers, Anna Lipzen, David Ezra, Charles H. Cannon, B. H. Bluhm, François Lutzoni, Hui Sun, Joseph W. Spatafora, David E. Culley, B.G. Turgeon, Igor V. Grigoriev, Alan Kuo, Bernard Henrissat, Raúl Castanera, Pedro W. Crous, Robin A. Ohm, Christopher Daum, R. Albert, Gerald F. Bills, Manuel Alfaro, M. Binder, Yuko Yoshinaga, Bill Andreopoulos, Jon K. Magnuson, Kerrie Barry, J. Bloem, Lucía Ramírez, Andrew Tritt, Matt Nolan, Stephen J. Mondo, Asaf Salamov, Stephen B. Goodwin, C. Liang, J.B. González, Jasmyn Pangilinan, Sajeet Haridas |
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| Přispěvatelé: | Dpt of Geosciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Evonik Nutrition&Care, Abbott GmbH & Co. KG, Alterra, Wageningen University and Research [Wageningen] (WUR), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdulaziz University, United States Department of Energy (DOE) DE-AC02-05CH11231 National Science Foundation (NSF) DEB-1354625 IOS-1456958JGI Community Sequencing Project 662, Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa. IMAB - Institute for Multidisciplinary Research in Applied Biology, Sub Molecular Microbiology, Molecular Microbiology, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Lineolataceae Crous
Spatafora Haridas & Grigoriev Genome evolution Aulographales Crous Lineolatales Crous Mycology & Parasitology Genome Microbiology 030308 mycology & parasitology 03 medical and health sciences Coniosporiaceae Crous New taxa Phylogenetics Genetics Spatafora Rhizodiscinaceae Crous lcsh:QH301-705.5 Machine-learning 2. Zero hunger Ecological niche 0303 health sciences Biomass (ecology) biology 030306 microbiology Human Genome Dothideomycetes 15. Life on land biology.organism_classification Agricultural and Biological Sciences (miscellaneous) Genome-based prediction Haridas & Grigoriev lcsh:Biology (General) 13. Climate action Evolutionary biology Rhizodiscinaceae Crous Spatafora Haridas & Grigoriev Evolutionary ecology Eremomycetales Crous Fungal evolution Adaptation Coniosporiales Crous Lineolataceae Crous Coniosporiaceae Crous Spatafora Haridas & Grigoriev [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology |
| Zdroj: | Studies in Mycology Studies in Mycology, Centraalbureau voor Schimmelcultures, 2020, 96, pp.141-153. ⟨10.1016/j.simyco.2020.01.003⟩ Studies in Mycology, Vol 96, Iss, Pp 141-153 (2020) Studies in mycology, vol 96, iss 96 Studies in Mycology, 96, 141. Centraalbureau voor Schimmelculturen Academica-e: Repositorio Institucional de la Universidad Pública de Navarra Universidad Pública de Navarra Studies in Mycology, 96, 141-153. Westerdijk Fungal Biodiversity Institute Studies in Mycology, 2020, 96, pp.141-153. ⟨10.1016/j.simyco.2020.01.003⟩ Academica-e. Repositorio Institucional de la Universidad Pública de Navarra instname |
| ISSN: | 0166-0616 1872-9797 |
| DOI: | 10.1016/j.simyco.2020.01.003⟩ |
| Popis: | Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species. This manuscript has been authored by an author at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231 with the U.S. Department of Energy. R. A. and I. V. G. were supported by the NSF grants DEB-1354625 and IOS-1456958. Sequencing of Dothideomycetes genomes were conducted as part of the 1000 Fungal Genomes Project supported by the JGI Community Sequencing Project #662. |
| Databáze: | OpenAIRE |
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