Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary sex classification of somatic tissues
- Max Planck Institute for Evolutionary Biology, Germany
- Biomedical Pioneering Innovation Center, Peking University, China
Figures
Figure 1
Relationship of the mouse taxa and numbers of sex-biased genes for each organ comparison.
The top left of the plot shows the phylogenetic relationships of the taxa in the study. The other plots show the numbers of sex-biased genes as bar plots, female-biased in red, male-biased in green. DOM = M. m. domesticus, MUS = M. m. musculus, SPR = M. spretus, SPI = M. spicilegus. The Y-axes show the number of genes. Note that there are two different Y-axis scales for the somatic organs and the gonadal organs. All numbers are provided in Figure 1—source data 1, full data are provided in Supplementary Data D1.
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Figure 1—source data 1
Numbers of sex-biased genes in mouse organs.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig1-data1-v1.xlsx
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Figure 1—source data 2
List of mouse samples included in the study.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig1-data2-v1.xlsx
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Figure 1—source data 3
Histograms of distributions of female/male sex-bias ratios for all mouse and human organ datasets.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig1-data3-v1.pdf
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Figure 1—source data 4
Scatterplots of F/M ratio values for all genes that show a significant sex-bias change in the respective tissue and mouse taxon pair comparison.
Based on the values provided in Supplementary Data D1, all plotted in log-scale.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig1-data4-v1.pdf
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Figure 1—source data 5
Numbers of shared genes between organs for each of the taxa.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig1-data5-v1.xlsx
Figure 2
Turnover of sex-biased gene expression between the taxa.
(A) Plots of percentages of genes shared as sex-biased across the four taxa for each organ comparison (including the Y-chromosomal genes for the male-biased gene sets). Numbers are normalized to ‘one taxon’ which represents the sum of all unique genes in at least one taxon (set to 100%), ‘two taxa’, ‘three taxa’, and ‘four taxa’ represent the percentages of the sums of shared genes for any pairwise comparison between the taxa for all sex-biased genes. Data for the figure are provided in Figure 2—source data 1. (B) Percentage turnover differences between sex-biased genes versus resampling averages from all genes as female gene swaps or male gene swaps in three groups of taxa comparisons. See text for further details. Note that standard deviations from the resampling were too small to show them in the graphic as error bars (all in the order of 0.015). Data for the figure are provided in Figure 2—source data 2 and for all data and statistics in Supplementary Data D2.
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Figure 2—source data 1
Numbers and percentages of sex-biased genes shared between taxa for each organ.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig2-data1-v1.xlsx
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Figure 2—source data 2
Comparative analysis of gene expression level turnover between the taxa.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig2-data2-v1.xlsx
Figure 3
Variances and positive selection on sex-biased genes.
(A) Variances of expression in sex-biased and non-biased genes for each organ. The ranges of relative variances (interquartile range [IQR]/median ratios for transcripts per million [TPM] counts) for the four taxa are displayed as box plots; note that these constitute all values from the four taxa. The ‘reciprocal’ values are for the orthologous genes that are sex-biased in one taxon, but not in the other for M. m. domesticus (DOM)-M. m. musculus (MUS) comparisons and M. spretus (SPR)-M. spicilegus (SPI) comparisons. The data for this sub-figure are provided in Figure 3—source data 1. Most pairwise comparisons are significant (p<<0.01), the ones which are not significant are marked with ‘x’ (all p-values are included in Figure 3—source data 1). (B) Results of the McDonald-Kreitman (MK) test for positive selection at coding positions for the sex-biased genes in DOM and MUS. The ‘reciprocal’ values are for the orthologous genes that are sex-biased in one taxon, but not in the other. Note that this corresponds to different gene sets in DOM and MUS, since they have different sets of sex-biased genes each. The alpha values represent the fraction of amino acid substitutions that are predicted to be driven by positive selection. The violin plots are derived from the range of alpha values obtained in 1000 bootstrap replications. The boxes show the averages and quartiles of the data distribution. The averages between all distributions are significantly different from each other (p<<0.01). All data, including the gene numbers in the analysis and statistical values, are provided in Figure 3—source data 2.
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Figure 3—source data 1
Data for expression variance across all four taxa.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig3-data1-v1.xlsx
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Figure 3—source data 2
Results of the McDonald-Kreitman (MK) test with 1000 bootstrap replications.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig3-data2-v1.xlsx
Figure 4
Module analysis on sex-biased genes.
The plots show for four somatic organs the fractions of total genes (row ‘all’ at the top - black color) that are assigned to modules in a weighted gene co-expression network analysis (WGCNA). The rows below represent the fraction differences of sex-biased genes for each taxon (DOM, MUS, SPR, SPI) compared to all genes. Positive values show an excess and negative values a deficiency compared to the fraction of all genes. Plotted in red are the differences for all sex-biased genes in the organ, in blue for the sex-biased genes that occur only in the respective taxon, i.e., can be considered as having a newly evolved sex-bias expression in this taxon. A maximum of 15–16 modules plus the 0 bin are plotted for each organ. Higher-numbered modules are plotted only when they include a difference of larger than 3% in at least one taxon. The full data are provided in Figure 4—source data 1. Note that the module numbers can only be compared within an organ, not between the organs. Bin number ‘0’ is the sum of all genes that cannot be assigned to one of the other modules. The brain is not included in this figure, since it has too few sex-biased genes to make the comparison meaningful. DOM, M. m. domesticus; MUS, M. m. musculus; SPR, M. spretus; SPI, M. spicilegus.
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Figure 4—source data 1
Data for module plots with normalized gene counts - reduced set, see text.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig4-data1-v1.xlsx
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Figure 4—source data 2
Scale independence and mean connectivity plots for the different organs for determining the soft threshold parameter β for the weighted gene co-expression network analysis (WGCNA) module assignments.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig4-data2-v1.pdf
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Figure 4—source data 3
Weighted gene co-expression network analysis (WGCNA) module lists for all genes in all somatic organs derived from analyses between 48 females.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig4-data3-v1.xlsx
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Figure 4—source data 4
Gene counts for each module class in all somatic organs.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig4-data4-v1.xlsx
Figure 5
Density plots of individual variation values of the sex-biased gene expression index (SBI) for mouse organs.
Plots for all organs are grouped according to organ for each taxon. Males are represented by blue shading, females by red shading. The taxon designations are on the top, the organ designations to the left. The Y-axis represents the density scale of the smoothed distribution; the X-axis represents the relative maleness <--> femaleness scores centered around zero. All individual SBI values are included in Figure 5—source data 1.
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Figure 5—source data 1
Sex-biased gene expression index (SBI) values for mouse tissues.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig5-data1-v1.xlsx
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Figure 5—source data 2
Spearman’s correlation test values between organ sex-biased gene expression indices (SBIs).
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig5-data2-v1.xlsx
Figure 6
Heatmap plots of sex-biased gene expression index (SBI) values for mice.
Each individual (numbered 1–9 for each sex) is represented by the normalized SBI values for the somatic organs organized in rows. The color scale represents the normalized SBI value in the range from 1 (maximal femaleness, dark red) to –1 (maximal maleness, dark blue). The mouse data are provided for the individuals from all four taxa. All individual SBI values are included in Figure 5—source data 1.
Figure 7
Sex-biased genes and sex-biased gene expression indices (SBIs) for data from human tissues.
(A) and (B) Bar plots representing the numbers of sex-biased genes in tissues that show at least five such genes per sex (excluding the Y-chromosomally encoded genes). Note the different Y-axis scale for the numbers of genes in (B). (C) SBI plots for the nine individuals of each sex based on the set of organs and genes shown in (A) and (B). The Y-axis represents the density scale; the X-axis represents the relative maleness <--> femaleness scores centered around zero. (D) SBI plots for the same individuals and organs as in (C), but based on the sex-biased gene lists from Oliva et al., 2020. Note that these authors have not included a comparison for OvaTes. All SBI values are listed in Figure 7—source data 1.
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Figure 7—source data 1
Sex-biased gene expression index (SBI) values for human tissues.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig7-data1-v1.xlsx
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Figure 7—source data 2
List of samples used for the analysis of sex-biased expression in humans.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig7-data2-v1.xlsx
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Figure 7—source data 3
Numbers of sex-biased genes found in the human organ samples.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig7-data3-v1.xlsx
Figure 8
Genes with conserved sex-biased gene expression between mice and humans.
The different organs analyzed are listed to the left. The analysis of conserved mouse genes is included in Figure 8—source data 1. The green boxes designate sex-biased expression in the respective tissues.
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Figure 8—source data 1
Mouse sets of sex-biased genes that occur across all four taxa for each organ.
- https://cdn.elifesciences.org/articles/99602/elife-99602-fig8-data1-v1.xlsx
Tables
Table 1
Numbers of genes with sex-biased expression in human single-cell data.
| Female-biased | Male-biased* | ||||||
|---|---|---|---|---|---|---|---|
| Cell type | MTG | DLPFC | Overlap | MTG | DLPFC | Overlap | |
| Astrocyte | 4 | 7 | 4 | 2+4 | 0+4 | 4 | |
| L2_3_IT | 4 | 1 | 1 | 0+4 | 1+4 | 4 | |
| L4_IT | 1 | 1 | 1 | 0+5 | 0+5 | 4 | |
| L5_IT | 1 | 1 | 1 | 0+5 | 0+4 | 4 | |
| L6_IT | 1 | 2 | 1 | 0+4 | 2+4 | 4 | |
| Lamp5_Lhx6 | 2 | 1 | 1 | 0+5 | 0+5 | 5 | |
| Microglia-PVM | 5 | 10 | 4 | 1+6 | 7+6 | 6 | |
| Oligodendrocyte | 4 | 6 | 3 | 1+4 | 0+4 | 4 | |
| OPC | 7 | 3 | 2 | 0+5 | 0+5 | 5 | |
| Pvalb | 2 | 1 | 1 | 0+5 | 0+5 | 5 | |
| Sst | 1 | 7 | 1 | 0+5 | 0+5 | 5 | |
| Vip | 1 | 1 | 1 | 0+5 | 0+5 | 5 | |
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*
Non-Y-chromosomal+Y-chromosomal.
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Table 1—source data 1
Comparison of genes shared in the single-cell data between the two brain tissues, dorsolateral prefrontal cortex (DLPFC) and middle temporal gyrus (MTG).
Additional tabs include lists of sex-biased genes for the cell types in DLPFC samples and MTG samples.
- https://cdn.elifesciences.org/articles/99602/elife-99602-table1-data1-v1.xlsx
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological sample (Mus musculus domesticus) | Somatic and gonadal organs | MPI for Evolutionary Biology, Plön | FRA | Freshly dissected from animals |
| Biological sample (Mus musculus musculus) | Somatic and gonadal organs | MPI for Evolutionary Biology, Plön | KAZ | Freshly dissected from animals |
| Biological sample (Mus spretus) | Somatic and gonadal organs | MPI for Evolutionary Biology, Plön | SPR | Freshly dissected from animals |
| Biological sample (Mus spicilegus) | Somatic and gonadal organs | MPI for Evolutionary Biology, Plön | SPI | Freshly dissected from animals |
| Commercial assay or kit | RNeasy 96 Universal Tissue Kit | QIAGEN | Catalog no. 74881 | |
| Commercial assay or kit | TruSeq Stranded mRNA Kit | Illumina | 2×150 bp | Used in sequencing center Kiel |
| Software/algorithm | asymptoticMK (downloaded on 2023-2-20) | Haller and Messer, 2017; Haller and Leinweber, 2017 | https://github.com/MesserLab/asymptoticMK | |
| Software/algorithm | snpEff (4.3t) | Cingolani et al., 2012a; Cingolani et al., 2012b | https://pcingola.github.io/SnpEff/ | |
| Software/algorithm | Trimmomatic (0.38) | Bolger et al., 2014; Bolger et al., 2021 | https://www.usadellab.org/cms/?page=trimmomatic | |
| Software/algorithm | HISAT2 (2.2.1) | Kim et al., 2015; Kim et al., 2019 | https://daehwankimlab.github.io/hisat2/download/ | |
| Software/algorithm | featureCounts (2.0.3) | Liao et al., 2014; Liao et al., 2021 | https://subread.sourceforge.net/featureCounts.html | |
| Software/algorithm | WGCNA (1.71) | Langfelder and Horvath, 2008; Langfelder et al., 2022 | https://edo98811.github.io/WGCNA_official_documentation/ |
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Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary sex classification of somatic tissues
eLife 13:RP99602.
https://doi.org/10.7554/eLife.99602.4
