High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa
By Daniel Wibberg, M. Stadler, C. Lambert, Boyke Bunk, C. Spröer, C. Rückert, Jörn Kalinowski, Russell John Cox, E. Kuhnert. Fungal diversity, 2020
84 citations recorded by the source corpus.
The Hypoxylaceae (Xylariales, Ascomycota) is a diverse family of mainly saprotrophic fungi, which commonly occur in angiosperm-dominated forests around the world. Despite their importance in forest and plant ecology as well as a prolific source of secondary metabolites and enzymes, genome sequences of related taxa are scarce and usually derived from environmental isolates. To address this lack of knowledge thirteen taxonomically well-defined representatives of the family and one member of the closely related Xylariaceae were genome sequenced using combinations of Illumina and Oxford nanopore technologies or PacBio sequencing. The workflow leads to high quality draft genome sequences with an average N50 of 3.0 Mbp. A backbone phylogenomic tree was calculated based on the amino acid sequences of 4912 core genes reflecting the current accepted taxonomic concept of the Hypoxylaceae. A Percentage of Conserved Proteins (POCP) analysis revealed that 70% of the proteins are conserved within the family, a value with potential application for the definition of family boundaries within the order Xylariales. Also, Hypomontagnella spongiphila is proposed as a new marine derived lineage of Hypom. monticulosa based on in-depth genomic comparison and morphological differences of the cultures. The results showed that both species share 95% of their genes corresponding to more than 700 strain-specific proteins. This difference is not reflected by standard taxonomic assessments (morphology of sexual and asexual morph, chemotaxonomy, phylogeny), preventing species delimitation based on traditional concepts. Genetic changes are likely to be the result of environmental adaptations and selective pressure, the driving force of speciation. These data provide an important starting point for the establishment of a stable phylogeny of the Xylariales; they enable studies on evolution, ecological behavior and biosynthesis of natural products; and they significantly advance the taxonomy of fungi.
Subfields: Cell Biology, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/8c34a9fe47e791b74b5cbc131e8d26ece38a3304
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Cell Biology
In Plant Science
Citations in the corpus
- Morphological approaches in studying fungi: collection, examination, isolation, sporulation and preservation (2020, methodology): “Modern mycotaxonomy has moved forward using morphology with a combination of chemotaxonomy, phylogeny, genetics, ecology and molecular biology (Senanayake et al. 2017b, 2018, Manawasinghe et al. 2019, Hyde et al. 2020a, Phukhamsakda et al. 2020a, Samarakoon et al. 2020, Wibberg et al. 2020).”