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

Claudio G Ametrano,Lucia Muggia,Felix Grewe,Steven D Leavitt,Laura Selbmann,H Thorsten Lumbsch,Stephen B Goodwin,Pedro W Crous,Chen Liang

doi:10.1186/s43008-019-0018-2

Claudio G Ametrano, Lucia Muggia + Show 7 more

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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.

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Dothideomycetes is the largest and most diverse fungal class of ascomycetes, comprised of c. 20,000 species (Jaklitsch et al 2016) classified into 105 families (Hyde et al 2013) and 32 orders (Liu et al 2017)
Statistics and completeness of the genomes After quality filtering, total numbers of PE reads for each species were 39.4 million for Lichenothelia convexa L1844, 9.7 million for L. intermixta L2282, 8.6 million for Saxomyces alpinus Culture Collection of Fungi from Extreme Environments (CCFEE) 5470 and 9.9 million for S. americanus L1853
The mean and standard deviation for the entire assembly dataset of the 242 Dothideomycetes is 96.3 ± 6

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Dothideomycetes is the largest and most diverse fungal class of ascomycetes, comprised of c. 20,000 species (Jaklitsch et al 2016) classified into 105 families (Hyde et al 2013) and 32 orders (Liu et al 2017). Schoch et al 2006, Schoch et al 2009; Nelsen et al 2009; Ruibal et al 2009; Hyde et al 2013; Muggia et al 2015; Liu et al 2017; Ametrano et al 2019) These analyses usually considered wide taxon sampling and were based on combinations. Species of Lichenothelia and Saxomyces are widespread worldwide, occurring on exposed rocks, often in extreme environments, and having evolved lifestyles on nutrient-poor substrates. Because they can survive in harsh environments characterized by high solar radiation, very high and very low temperatures, and drought stress, they have been recognized within the group of polyextremotolerant fungi (Gostinčar et al 2012). More information from Lichenothelia and Saxomyces genomes is required to better understand their genetic diversity and evolutionary relationships with other closely related dothideomycetous taxa with varying lifestyles

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