Sex-biased gene expression at single-cell resolution: Cause and consequence of sexual dimorphism

Abstract

Gene expression differences between males and females are thought to be key for the evolution of sexual dimorphism, and sex-biased genes are often used to study the molecular footprint of sex-specific selection. However, gene expression is often measured from complex aggregations of diverse cell types, making it difficult to distinguish between sex differences in expression that are due to regulatory rewiring within similar cell types and those that are simply a consequence of developmental differences in cell type abundance. To determine the role of regulatory versus developmental differences underlying sex-biased gene expression, we use single-cell transcriptomic data from multiple somatic and reproductive tissues of male and female guppies, a species which exhibits extensive phenotypic sexual dimorphism. Our analysis of gene expression at single-cell resolution demonstrates that non-isometric scaling between the cell populations within each tissue and heterogeneity in cell type abundance between the sexes can influence inferred patterns of sex-biased gene expression by increasing both the false-positive and false-negative rates. Moreover, we show that at the bulk level, the subset of sex-biased genes that are the product of sex differences in cell type abundance can significantly confound patterns of coding-sequence evolution. Taken together, our results offer a unique insight into the evolution of sex-biased gene expression and highlight the power of single-cell RNA-sequencing in disentangling between genes that are a cause as opposed to a consequence of sexual dimorphism.

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

“…Several species have been observed to exhibit rapid evolutionary rates of sequences on sex chromosomes compared to autosomes, which has been related to the evolutionary theories of fast-X or fast-Z (Meisel and Connallon, 2013; Hough et al, 2014; Wright et al, 2015; Charlesworth et al, 2018; Darolti et al, 2023). Furthermore, the quantification of gene expression by bulk RNA-seq technology, relative to single-cell transcriptome analysis, has been shown to potentially obfuscate true signals in the evolution of sex-biased gene expression in complex aggregations of diverse cell types (Darolti and Mank, 2023; Tosto et al, 2023). Additionally, our samples were relatively small, and may provide low power to detect differential expression and evolutionary analysis.…”

Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary classification of sexes

“…All SBI values are listed in suppl. Table S6 Sex-biased expression in human single-cell data Gene expression in organs is measured from complex aggrega-ons of diverse cell types, making it difficult to dis-nguish between sex differences in expression that are due to regulatory rewiring within similar cell types and those that are simply a consequence of developmental differences in cell-type abundance (Darol-& Mank, 2023). It has actually been shown that only a subset of cells in a given -ssue may express the sex-biased genes (Rodríguez-Montes et al, 2023).…”

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

“…Several species have been observed to exhibit rapid evolutionary rates of sequences on sex chromosomes compared to autosomes, which has been related to the evolutionary theories of fast-X or fast-Z (Hough et al, 2014 ;Wright et al, 2015 ;Charlesworth et al, 2018a ). Furthermore, the quantification of gene expression by bulk RNA-seq technology, relative to single-cell transcriptome analysis, has been shown to potentially obfuscate true signals in the evolution of sex-biased gene expression in complex aggregations of diverse cell types (Darolti and Mank, 2023 ;Tosto et al, 2023 ). However, investigation of these interesting issues related to sexbiased gene evolution in T. pilosa can only be conducted when whole genome sequences become available in the near future.…”