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

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

doi:10.1186/s43008-019-0018-2

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

IMA Fungus. 2019 Oct 30:10:19. doi: 10.1186/s43008-019-0018-2. eCollection 2019.

Authors

Claudio G Ametrano¹, Felix Grewe², Pedro W Crous³, Stephen B Goodwin⁴, Chen Liang⁵, Laura Selbmann^{6

7}, H Thorsten Lumbsch², Steven D Leavitt⁸, Lucia Muggia¹

Affiliations

¹ Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy.
² Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA.
³ Westerdijk Fungal Biodiversity Institute, P.O. Box 85176, 3508 AD Utrecht, The Netherlands.
⁴ USDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA.
⁵ College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China.
⁶ Department of Ecological and Biological Sciences, University of Tuscia, Largo dell' Università, 01100 Viterbo, Italy.
⁷ Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy.
⁸ Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602 USA.

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.