Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant

Lei Zhao
Wei Zhou
Jun He
De-Zhu Li author has email address
Hong-Tao Li author has email address

Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China

https://doi.org/10.7554/eLife.89941.4

Open access
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Figures and data

Floral buds and flowers at anthesis of females (A, B) and males (C) in Trichosanthes pilosa.

Sex-biased gene expression for floral buds and flowers at anthesis in males and females of Trichosanthes pilosa. Volcano plots of average expression between female-biased, male-biased and unbiased genes in floral buds (A) and flowers at anthesis (B). M1 and F1 indicate male and female floral buds; M2 and F2 indicate male and female flowers at anthesis. The value of y coordinate represents -log₁₀(FDR), and the value of x coordinate represents log₂(Fold Change) identified by DESeq2. Heatmap of sex-biased gene expression (C) using hierarchical clustering analysis. Hierarchical gene clustering is based on Euclidean distance with an average of log₂(FPKM) for differentially expressed genes. The color gradient represents from high to low (from red to green) gene expression.

The overlap between sex-biased and tissue-biased genes in two types of sexes and tissues. Male-biased genes in floral buds (M1BGs) (A) or flowers at anthesis (M2BGs) (B) overlapped with tissue-biased genes in floral buds (M1TGs) and flowers at anthesis (M2TGs). Female-biased genes in floral buds (F1BGs) (C) or flowers at anthesis (F2BGs) (D) overlapped with tissue-biased genes in floral buds (F1TGs) and flowers at anthesis (F2TGs).

Violin plots of d_N/d_S values (0 < ω < 2) of female-biased, male-biased and unbiased genes in floral buds and flowers at anthesis of Trichosanthes pilosa. White dot indicates the median of d_N/d_S values for sex-biased and unbiased genes. Wilcoxon rank sum tests are used to test for significant differences (***P < 0.0005, **P < 0.005 and *P < 0.05). The distributions of d_N/d_S values for female-biased, male-biased and unbiased genes in floral buds (A) and flowers at anthesis (B) using ‘two-ratio’ branch model. The distributions of d_N/d_S values for female-biased, male-biased and unbiased genes in floral buds (C) and flowers at anthesis (D) using ‘free-ratio’ branch model.

Venn diagrams of male-biased genes detected to be under positive selection using aBSREL, BUSTED, CodeML and RELAX in floral buds.

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