DOI: 10.5061/dryad.0p2ngf238
title: Taming the beast: a revised classification of Cortinariaceae based on genomic data

description: 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.
description: Our goal was to design a 20,000-probe custom myBaits® enrichment
 panel for target capture of phylogenetically-informative, single-copy
 nuclear orthologs. Four out of nine <em>Cortinarius</em>
 species (<em>C. victoriaensis, C. neofurvolaesus, C.
 scaurus</em>, and <em>C. typicus</em>), for which most
 single-copy orthologs recovered by exonorate and representing different
 lineages across <em>Cortinariaceae</em>, were selected for
 probe design. The size of the dataset exceeded the limits of the 20,000
 probe enrichment panel and we therefore discarded 20 target genes with the
 most missing data from all four species. The final dataset included 188
 targets, from those identified by Dentinger et al. (2016), with the
 addition of the currently used loci (RPB1<em>,
 </em>RPB2<em>, </em>MCM7<em>, </em>GPD, and
 TEF1), resulting in a total of 193 targets. For the probe design,
 nucleotide sequences containing both intron and exon regions were used.
 Based on the visual inspection of the alignments of each target, the
 intron regions were generally short (&lt; 50 bp) and largely conserved
 within the family making it possible to include them in the enrichment
 panel. The design and production of the probes was done by Arbor
 Biosciences (Ann Arbor, Michigan, USA) based on the sequence data
 provided. The probes were 120 nucleotides long and designed with ~2x
 tiling density.
description: DNA sequences used to design the enrichment panel probes.