Sheltered load in fungal mating-type chromosomes revealed by fitness experiments
Data files
Jul 17, 2025 version files 3.82 GB
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Guyot_JEB_2025_Photos_nuclei.zip
859.05 MB
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Guyot_JEB_2025_Photos_growth.zip
2.87 GB
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Guyot_JEB_2025_Germination.zip
648 B
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Guyot_JEB_2025_Growth.zip
8.14 KB
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Guyot_JEB_2025_Nuclei.zip
1.54 KB
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Guyot_JEB_2025_vcffile.vcf
93.11 MB
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README.md
4.51 KB
Abstract
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.
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.