DOI: 10.5061/dryad.fxpnvx0t4
title: Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection

description: Balancing selection, an evolutionary force that retains genetic diversity,
 has been detected in multiple genes and organisms, such as the sexual
 mating loci in fungi. However, to quantify the strength of balancing
 selection and define the mating-related genes require a large number of
 strains. In tetrapolar basidiomycete fungi, sexual type is determined by
 two unlinked loci, MATA and MATB. Genes in both loci define mating type
 identity, control successful mating and completion of the life cycle.
 These loci are usually highly diverse. Previous studies have speculated,
 based on culture crosses, that species of the non-model genus Trichaptum
 (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with
 multiple alleles. Here, we sequenced a hundred and eighty strains of three
 Trichaptum species. We characterized the chromosomal location of MATA and
 MATB, the molecular structure of MAT regions and their allelic richness.
 The sequencing effort was sufficient to molecularly characterize multiple
 MAT alleles segregating before the speciation event of Trichaptum species.
 Analyses suggested that long-term balancing selection has generated
 trans-species polymorphisms. Mating sequences were classified in different
 allelic classes based on an amino acid identity (AAI) threshold supported
 by phylogenetics. 17,550 mating types were predicted based on the allelic
 classes. In vitro crosses allowed us to support the degree of allelic
 divergence needed for successful mating. Even with the high amount of
 divergence, key amino acids in functional domains are conserved. We
 conclude that the genetic diversity of mating loci in Trichaptum is due to
 long-term balancing selection, with limited recombination and duplication
 activity. The large number of sequenced strains highlighted the importance
 of sequencing multiple individuals from different species to detect the
 mating-related genes, the mechanisms generating diversity and the
 evolutionary forces maintaining them.
description: Description of methods included in the manuscript
description: Additional information can be found in the dedicated GitHub
 webpage: https://perisd.github.io/TriMAT/
description: # Large-scale fungal strain sequencing unravels the molecular diversity in
 mating loci maintained by long-term balancing selection publication in
 Plos Genetics 2022
 [https://doi.org/10.5061/dryad.fxpnvx0t4](https://doi.org/10.5061/dryad.fxpnvx0t4) Additional information is described in the dedicated [GitHub page](https://perisd.github.io/TriMAT/) ## Information about data in the dryad repository ### iWGS\_SPAdes\_Assemblies.tar.gz: Compressed file with genome assemblies for individuals sequenced by Illumina technology. Additional information about these assemblies can be found in Supplementary Table 1 of the manuscript. ### CrossingPictures.rar: Compressed picture files related with experimental crosses. ### IndividualGeneAlignments\_trimmed.zip: Compressed file with trimmed alignments for the coding sequences (*CDS*) and amino acid sequences (*aa*) ### MATA.zip: Assembled MATA regions (.fas) and annotations (.gff) for each specimen. ### MATB.zip: Assembled MATB regions (.fas) and annotations (.gff) for each specimen. ### SourceData.rar: Compressed file with raw data to generate figures and tables in the manuscript: * IQTree_logFiles.tar.gz: IQTree log files with information to replicate the phylogenetic reconstruction represented in iTOL. * AllvsAll_distances.meg: Converted Average Nucleotide Identity (ANI) used for reconstructing a Neighbour-Joining tree * BUSCO_MAT_info.csv: BUSCO annotation statistics and location on TA10106M1 genome * dxy.csv: Absolute divergence statitstic for BUSCO and MAT genes * Fst.csv: Relative divergence statitstic for BUSCO and MAT genes * MKT.csv: Multilocus Hudson–Kreitman–Aguadé (HKA) test performed with HKAdirect 0.7b * paml.csv: Average number of synonymous substitutions per synonymous sites (dS) and non-synonymous substitutions per non-synonymous sites (dN) for BUSCO and MAT genes * pi.csv: Nucleotide diversity values for BUSCO and MAT genes * tajimaD.csv: Tajima’s D values for BUSCO and MAT genes ### Annotation\_Tabietinum\_10106M1.zip: Compressed file with annotation files for TA10106M individual. * TA10106M1_BUSCO.gff: annotation file with the coordinates of BUSCO genes for the genome TA10106M1. * TA10106M1_nuclearV2.gff: MAKER pipeline annotation file with the coordinates of genes, CDS and other features for the genome TA10106M1. It also includes Interproscan, Blastp and KEGG (GenomeMaple KAAS) annotations. * TA10106M1_RepeatMasker.gff: annotation file with the coordinates of features annotated by RepeatMasker.