Taming the beast: a revised classification of Cortinariaceae based on genomic data

Family Cortinariaceae currently includes only one genus, Cortinarius,
which is the largest Agaricales genus, with thousands of species
worldwide. The species are important ectomycorrhizal fungi and form
associations with many vascular plant genera from tropicals to arctic
regions. Genus Cortinarius contains a lot of morphological variation, and
its complexity has led many taxonomists to specialize in particular on
infrageneric groups. The previous attempts to divide Cortinarius have been
shown to be unnatural and the phylogenetic studies done to date have not
been able to resolve the higher-level classification of the group above
section level. Genomic approaches have revolutionized our view on fungal
relationships and provide a way to tackle difficult groups. We used both
targeted capture sequencing and shallow whole genome sequencing (WGS) to
produce data and to perform phylogenomic analyses of 75 single-copy genes
from 19 species. In addition, a wider 5-locus analysis of 245 species,
from the Northern and Southern Hemispheres, was also done. Based on our
results, a classification of the family Cortinariaceae into ten
genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius,
Cystinarius, Volvanarius, Hygronarius, Mystinarius, and
Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four
sections are described as new to science and five subgenera are introduced
as new combinations in a new rank. In addition, 41 section names and 514
species names are combined in new genera and four lecto- and epitypes
designated. The position of Stephanopus in suborder Agaricineae remains to
be studied. Targeted capture sequencing is used for the first time in
fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to
produce -omics data in species-rich groups. The -omics data was produced
from fungarium specimens up to 21 years old, demonstrating the value of
museum specimens in the study of the fungal tree of life. This study is
the first family revision in Agaricales based on genomics data and
hopefully many others will soon follow.