DOI: 10.5061/dryad.qrfj6q5tk
title: Sheltered load in fungal mating-type chromosomes revealed by fitness experiments

description: Sex chromosomes and mating-type chromosomes can carry large regions with
 suppressed recombination. As a result of a lower efficacy of selection,
 recessive deleterious mutations are expected to accumulate in these
 non-recombining regions. Multiple genomic analyses have indirectly
 inferred the presence of deleterious mutations in sex and mating-type
 chromosomes, but direct experimental evidence remains scarce. Here, we
 performed fitness assays in fungi with megabase-large and young
 non-recombining regions around the mating-type locus, using three
 Sordariales species, to test whether heterokaryons (diploid-like,
 heterozygous at the mating-type locus) exhibited a fitness advantage over
 homokaryons (haploid-like, with a single mating-type allele), in terms of
 spore germination dynamics or mycelium growth speed, under different
 conditions of light and temperature. We found a faster growth of
 heterokaryons compared to one of the homokaryons for Podospora anserina at
 18°C and for Schizothecium tetrasporum and Schizothecium tritetrasporum at
 22°C under light. These findings suggest the presence of a sheltered load,
 i.e., recessive deleterious mutations at the heterozygous state in or near
 non-recombining regions, associated to a specific mating-type allele.
 Genomic analyses indeed suggested that the non-recombining regions around
 the mating-type locus likely carries heterozygous deleterious mutations,
 while the rest of the genome was mostly homozygous. We also showed that
 the difference in growth rates did not result from different numbers or
 densities of nuclei between homokaryons and heterokaryons. Leveraging the
 experimental assets of fungi, allowing cultivating separately haploid-like
 and diploid-like life stages, our experiments provided one of the rare
 direct experimental evidence of sheltered load around mating-compatibility
 loci, which is crucial for our understanding of sex-related chromosome
 evolution.
description: # Sheltered load in fungal mating-type chromosomes revealed by fitness
 experiments ## Guyot_JEB_2025_vcffile.vcf Merged vcf file for the 13
 Schizothecium fungal genomes described in "Sheltered load in fungal
 mating-type chromosomes revealed by fitness experiments", Guyot et
 al, JEB 2025. Those are: CBS81571 PSN1070 PSN881 PSN829 PSN779 PSN777
 PSN710 PSN667 PSN571 PSN352 PSN1433 PSN1236 PSN1040. ".h"
 indicates that the genome was sequenced as a heterokaryon. ".p"
 and ".m" indicate that the genome was sequenced as a homokaryon,
 "m." is the MAT1_1 mating type and "p." is the
 "MAT1_2" mating type. "S1." indicates that the strain
 is from the S. tetrasporum species and "S3." indicates that the
 strain is from the S. tritetrasporum species. See Guyot et al, JEB 2025
 for a detailed description of filters. The info column contains SNPeff
 annotation as described in Guyot et al, JEB 2025. ##
 Guyot_JEB_2025_Photos_nuclei.zip Photos of the thallus of the *P.
 anserina* S strain when either homokaryotic or heterokaryotic. For each of
 the homokaryotic strains mat-1-1 (mat-), mat1-2 (mat+), and the
 heterokaryotic strain mat-1-1 / mat1-2 (mat-/mat+), three replicates have
 been analysed. The first number of the image files corresponds to the
 replicate number. Then, 7 photos (z-stacks) per replicate have been taken
 in the transmitted light channel (bright) and in the DAPI channel. To
 precisely observe the nuclei and the septa, the counting of nuclei has
 been done on the z-slices. Here, the Z-stacks have been transformed into
 z-projections, and they correspond to the .tiff files deposited. ##
 Guyot_JEB_2025_Photos_growth.zip Photos of mycelium used to measure growth
 speed, organized by species, growth conditions (light vs. dark or 18°C vs.
 37°C), batch (Batch1 vs. Batch2), and time points of measurement T1 and T2
 (Day 6 and Day 14 for *S. tritetrasporum* and *S. tetrasporum*; Day 2 and
 Day 6 for *P. anserina*). For each species and experimental condition or
 batch, photos sharing the same number in the T1 and T2 folders correspond
 to the same individual mycelium from a single Petri dish, photographed at
 two distinct time points. Correspondence between photo number, strain ID,
 and nuclear status is provided in the Guyot_JEB_2025_Growth.csv file.
 Note: The photo number is not unique across the dataset; it depends on the
 species, light condition, temperature, and/or batch. Some Petri dishes
 missing here were excluded from the analysis due to contamination, drying,
 or the presence of satellite colonies. ``` |- S_tetrasporum/ | |- Dark/ |
 | |- T1/ | | |- T2/ | |- Light | | |- T1/ | | |- T2/ |- S_tritetrasporum/
 | |- Batch1/ | | |- T1/ | | |- T2/ | |- Batch2/ | | |- T1/ | | |- T2/ |-
 P_anserina/ | |- 37C/ | | |- T1/ | | |- T2/ | |- 18C/ | | |- T1/ | | |-
 T2/ ``` ## Guyot_JEB_2025_Nuclei.zip Data on number of nuclei and their
 density per article in heterokaryotic and homokaryotic mycelium in the
 Podospora anserina S strain, with nuclear status of the mycelia (H:
 heterokaryon, MAT1-1: homokaryon of MAT1-1 mating type, MAT1-2: homokaryon
 of MAT1-2 mating type), Petri dish replicate number (replica), nuclei
 number in the article, article size (in μm). ## Guyot_JEB_2025_Growth.zip
 Data on growth speed, with species name (*Schizothecium tetrasporum*, *S.
 tritetrasporum*, or *Podospora anserina*), strain ID, nuclear status (H:
 heterokaryon, MAT1-1: homokaryon of MAT1-1 mating type, MAT1-2: homokaryon
 of MAT1-2 mating type), light exposure during growth, temperature of
 growth (in degrees Celsius), batch, corresponding photos number at the two
 time points (this number is not unique across the dataset and depends on
 the species, light exposure, temperature and/or batch), diameters measured
 (in millimeters) at the two time points (day 6 and day 14 for *S.
 triterasporum* and *S. tetrasporum*; day 2 and day 6 for *P. anserina*),
 number of plugs that remain heterokaryotic at the second time point
 (Nb_plug_H_T2), or that returned by PCR only the MAT1-1 mating type
 (Nb_plug_MAT1_1_T2) or MAT1-2 mating type (Nb_plug_MAT1_2_T2). When
 "NA" are present in the cells in the last three columns, it
 means that no PCR were run for these samples. ##
 Guyot_JEB_2025_Germination.zip Data on germination dynamics for
 Schizothecium tetrasporum, with strain ID, spore size (small or large,
 indicating mostly homokaryotic versus heterokaryotic spores), day of
 measure, total number of tracked spores, number of germinated spores, and
 batch.