Saccharomycetaceae : delineation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies

作者：Fei Liu, Z-D Hu, Andrey Yurkov, X-H Chen, W-J Bao, Qinghua Ma, W-N Zhao, Shan-Shan Pan, X-M Zhao, J.-H. Liu, Q.-M. Wang, Teun Boekhout · 发表于：Persoonia - Molecular Phylogeny and Evolution of Fungi · 年份：2024 · DOI：10.3767/persoonia.2024.52.01 · 被引用次数：31 · 研究领域：Plant Pathogens and Fungal Diseases、Yeasts and Rust Fungi Studies、Mycorrhizal Fungi and Plant Interactions

A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence- absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae , namely Eremothecium , Grigorovia , Kazachstania , Kluyveromyces , Lachancea , Nakaseomyces , Naumovozyma , Saccharomyces , Tetrapisispora , Torulaspora , Vanderwaltozyma , Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania , Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed ana...