IMA Fungus 10(1): e33861, doi: 10.1186/s43008-019-0018-2

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

Claudio G. Ametrano^‡, Lucia Muggia, Pedro W. Crous^§, Stephen B. Goodwin^|, Chen Liang^¶, Laura Selbmann^#, H. Thorsten Lumbsch^¤, Steven D. Leavitt^«, Lucia Muggia

‡ University of Trieste, Department of Life Sciences, Trieste, Italy§ CBS-KNAW Fungal Biodiversity Centre, Utrecht| Purdue University, USDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, West Lafayette¶ Qingdao Agricultural University, College of Plant Health and Medicine, Qingdao, China# University of Tuscia, Largo dell’ Università, Department of Ecological and Biological Sciences, Viterbo, Italy¤ Grainger Bioinformatics Center, Field Museum, Department of Science and Education, Chicago« Brigham Young University, Department of Biology and M.L. Bean Life Science Museum, Provo

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Citation: Ametrano CG, Muggia L, Crous PW, Goodwin SB, Liang C, Selbmann L, Lumbsch HT, Leavitt SD, Muggia L (2019) Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 10(1): e33861. https://doi.org/10.1186/s43008-019-0018-2

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.

Keywords

Lichenothelia, Phylogenomics, Saxomyces, Species tree, Supermatrix, Supertree