TY - JOUR

T1 - High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa

AU - Wibberg, Daniel

AU - Stadler, Marc

AU - Lambert, Christopher

AU - Bunk, Boyke

AU - Spröer, Cathrin

AU - Rückert, Christian

AU - Kalinowski, Jörn

AU - Cox, Russell J.

AU - Kuhnert, Eric

N1 - Funding information: Open Access funding provided by Projekt DEAL. This work was funded by the DFG (Deutsche Forschungsgemeinschaft) priority program “Taxon-Omics: New Approaches for Discovering and Naming Biodiversity” (SPP 1991). The bioinformatics support of the BMBF-funded project ‘Bielefeld-Gießen Center for Microbial Bioinformatics; BiGi (Grant Number 031A533)’ within the German Network for Bioinformatics Infrastructure (de.NBI) is gratefully acknowledged. The authors also would like to thank Dr. Mark Sumarah for providing the Hypom. submonticulosa strain and Dr. Jamal Ouazzani for providing the Hypom. spongiphila strain. In this regard we thank the French and French-Polynesian governments for their support in the sponge survey from French Polynesia (project Biopolyval). We are grateful to Dr. Esteban B. Sir for help in morphological descriptions. Dongsong Tian and Sen Yin are acknowledged for support in DNA and RNA isolation. Prof. Theresia Stradal is thanked for providing computational power for phylogenetic calculations. Open Access funding provided by Projekt DEAL. This work was funded by the DFG (Deutsche Forschungsgemeinschaft) priority program ?Taxon-Omics: New Approaches for Discovering and Naming Biodiversity? (SPP 1991). The bioinformatics support of the BMBF-funded project ?Bielefeld-Gie?en Center for Microbial Bioinformatics; BiGi (Grant Number 031A533)? within the German Network for Bioinformatics Infrastructure (de.NBI) is gratefully acknowledged. The authors also would like to thank Dr. Mark Sumarah for providing the Hypom. submonticulosa strain and Dr. Jamal Ouazzani for providing the Hypom. spongiphila strain. In this regard we thank the French and French-Polynesian governments for their support in the sponge survey from French Polynesia (project Biopolyval). We are grateful to Dr. Esteban B. Sir for help in morphological descriptions. Dongsong Tian and Sen Yin are acknowledged for support in DNA and RNA isolation. Prof. Theresia Stradal is thanked for providing computational power for phylogenetic calculations.

PY - 2021/1

Y1 - 2021/1

N2 - 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.

AB - 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.

KW - AAI

KW - ANI

KW - Cazyme

KW - Oxford nanopore

KW - Phylogenomics

KW - POCP

KW - Xylariales

UR - http://www.scopus.com/inward/record.url?scp=85085372001&partnerID=8YFLogxK

U2 - 10.1007/s13225-020-00447-5

DO - 10.1007/s13225-020-00447-5

M3 - Article

AN - SCOPUS:85085372001

VL - 106

SP - 7

EP - 28

JO - Fungal diversity

JF - Fungal diversity

SN - 1560-2745

IS - 1

ER -