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 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.

Fig. 1

Flow chart reporting the bioinformatic pipeline used for the analyses. Input and output of the pipeline are reported inside the boxes, the software used for each pipeline step is reported above or between the boxes

Fig. 2

Phylogenomic inferences based on the concatenated supermatrix (a) and multispecies coalescent (b) approaches. The dataset was composed by 664 single-copy gene regions longer than 1 Kb (after alignment trimming with Gblocks). Topology mismatches between the phylogenies are highlighted by red dashed branch lines. Bootstrap support values lower than 100% are shown. Lichenothelia and Saxomyces clades are highlighted by orange boxes. Pink and green boxes alternatively delimit the other lineages, either represented by a single genus or by multiple genera

Fig. 3

Distribution of the 30 normalized RF distances from the reference topology for each of the five resampling efforts. Boxes are delimited by the distance between the 25th and 75th percentile; lines inside the boxes show the median value of the distribution; whiskers refer to 10th and 90th percentiles; outliers are marked with black dots. Letters (a, b, c, d) are used to label statistical significance; boxes with different letters are significantly different (p < 0.01) while the same letter indicates no statistical difference