High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa

authored by

Daniel Wibberg, Marc Stadler, Christopher Lambert, Boyke Bunk, Cathrin Spröer, Christian Rückert, Jörn Kalinowski, Russell J. Cox, Eric Kuhnert

Abstract

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.

Organisation(s)

Institute of Organic Chemistry

External Organisation(s)

Bielefeld University
Helmholtz Centre for Infection Research (HZI)
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures

Type

Article

Journal

Fungal diversity

Volume

106

Pages

7-28

No. of pages

22

ISSN

1560-2745

Publication date

01.2021

Publication status

Published

Peer reviewed

Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics, Ecology

Sustainable Development Goals

SDG 14 - Life Below Water

Electronic version(s)

https://doi.org/10.1007/s13225-020-00447-5 (Access: Open)