A haplotype-resolved chromosomal reference genome for the porcini mushroom Boletus edulis

Brejon Lamartinière, Etienne ORCID: https://orcid.org/0000-0001-9632-8788; Tremble, Keaton; Dentinger, Bryn T M; Dasmahapatra, Kanchon K; Hoffman, Joseph I. ORCID: https://orcid.org/0000-0001-5895-8949. 2025 A haplotype-resolved chromosomal reference genome for the porcini mushroom Boletus edulis. G3: Genes, Genomes, Genetics, jkaf069. 11, pp. 10.1093/g3journal/jkaf069

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Official URL: https://doi.org/10.1093/g3journal%2Fjkaf069

Abstract/Summary

Haplotype-resolved chromosomal reference genomes are increasingly available for many fungi, offering insights into the evolution of pathogenic and symbiotic lifestyles. However, these resources remain scarce for ectomycorrhizal fungi, which play crucial roles in forest ecosystems. Here, we used a combination of chromatin conformation capture and PacBio sequencing to construct a haplotype-resolved chromosomal genome assembly for Boletus edulis, a prized edible fungus and emerging model for ectomycorrhizal fungal research. Our new reference assembly, “BolEdBiel_h2,” derives from a B. edulis sporocarp sampled in Bielefeld, Germany. The genome assembly spans 41.8 Mb, with a scaffold N50 of 4.1 Mb, and includes 11 chromosome-level scaffolds, achieving near telomere-to-telomere coverage across multiple chromosomes. We annotated a total of 15,406 genes, with a Benchmarking Universal Single-Copy Orthologs score of 96.2%. Key genomic features such as mating loci, carbohydrate-active enzymes, and effector proteins, were identified. As a first application of this new genomic resource, we mapped whole-genome resequencing data from 53 genets to investigate the population structure and genetic diversity of the European lineage of B. edulis. We identified 2 distinct genetic clusters and found that high-latitude populations from Iceland and Fennoscandia exhibited greater nucleotide diversity than populations from the United Kingdom and Central Europe. Additionally, we discovered a 0.4-Mb inversion on chromosome 3 and identified several regions of locally elevated nucleotide diversity, which may represent candidates for ecological adaptation. This genomic resource will facilitate a deeper understanding of this ecologically and commercially important wild fungus.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1093/g3journal/jkaf069
ISSN:	2160-1836
Additional Keywords:	Boletus edulis; ectomycorrhizal fungi (EMF); reference genome assembly; Hi-C; population structure
Date made live:	06 May 2025 13:20 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/539371

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.1093/g3journal/jkaf069

ISSN:

2160-1836

Additional Keywords:

Boletus edulis; ectomycorrhizal fungi (EMF); reference genome assembly; Hi-C; population structure

Date made live:

06 May 2025 13:20 +0 (UTC)

URI:

https://nora.nerc.ac.uk/id/eprint/539371