Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)
Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently gene...
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BMC
2019-10-01
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| Series: | IMA Fungus |
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| Online Access: | http://link.springer.com/article/10.1186/s43008-019-0018-2 |
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| author | Claudio G. Ametrano Felix Grewe Pedro W. Crous Stephen B. Goodwin Chen Liang Laura Selbmann H. Thorsten Lumbsch Steven D. Leavitt Lucia Muggia |
| author_facet | Claudio G. Ametrano Felix Grewe Pedro W. Crous Stephen B. Goodwin Chen Liang Laura Selbmann H. Thorsten Lumbsch Steven D. Leavitt Lucia Muggia |
| author_sort | Claudio G. Ametrano |
| collection | DOAJ |
| description | Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class. |
| format | Article |
| id | doaj-art-278dc1c66a664d2e86fc1d0cdf2d6392 |
| institution | Kabale University |
| issn | 2210-6359 |
| language | English |
| publishDate | 2019-10-01 |
| publisher | BMC |
| record_format | Article |
| series | IMA Fungus |
| spelling | doaj-art-278dc1c66a664d2e86fc1d0cdf2d63922025-02-02T09:15:24ZengBMCIMA Fungus2210-63592019-10-0110111210.1186/s43008-019-0018-2Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)Claudio G. Ametrano0Felix Grewe1Pedro W. Crous2Stephen B. Goodwin3Chen Liang4Laura Selbmann5H. Thorsten Lumbsch6Steven D. Leavitt7Lucia Muggia8Department of Life Sciences, University of TriesteGrainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural HistoryWesterdijk Fungal Biodiversity InstituteUSDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, Purdue UniversityCollege of Plant Health and Medicine, Qingdao Agricultural UniversityDepartment of Ecological and Biological Sciences, University of Tuscia, Largo dell’ UniversitàGrainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural HistoryDepartment of Biology and M.L. Bean Life Science Museum, Brigham Young UniversityDepartment of Life Sciences, University of TriesteAbstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.http://link.springer.com/article/10.1186/s43008-019-0018-2LichenotheliaPhylogenomicsSaxomycesSpecies treeSupermatrixSupertree |
| spellingShingle | Claudio G. Ametrano Felix Grewe Pedro W. Crous Stephen B. Goodwin Chen Liang Laura Selbmann H. Thorsten Lumbsch Steven D. Leavitt Lucia Muggia Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) IMA Fungus Lichenothelia Phylogenomics Saxomyces Species tree Supermatrix Supertree |
| title | Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) |
| title_full | Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) |
| title_fullStr | Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) |
| title_full_unstemmed | Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) |
| title_short | Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) |
| title_sort | genome scale data resolve ancestral rock inhabiting lifestyle in dothideomycetes ascomycota |
| topic | Lichenothelia Phylogenomics Saxomyces Species tree Supermatrix Supertree |
| url | http://link.springer.com/article/10.1186/s43008-019-0018-2 |
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