Cross-species comparative single-cell transcriptomics highlights the molecular evolution and genetic basis of male infertility

In male animals, spermatogonia in testes differentiate into sperm, one of the most diverse cell types across species. Despite the evolutionary retention of key genes essential for spermatogenesis, the extent of their conservation remains unclear. To explore the genetic basis of spermatogenesis under strong selective pressure, we compare single-cell RNA sequencing (scRNA-seq) datasets from the testes of humans, mice, and fruit flies. Our analysis identifies conserved genes involved in key molecular programs, such as post-transcriptional regulation, meiosis, and energy metabolism. We perform gene knockout experiments of 20 candidate genes, three of which, when mutated in fruit flies, result in reduced male fertility, emphasizing the conservation of sperm centriole and steroid lipid processes across mammals and Drosophila. Additionally, deep-learning analysis uncovers potential transcriptional mechanisms driving gene-expression evolution. These findings establish a core genetic foundation for spermatogenesis, offering insights into sperm-phenotype evolution and the underlying mechanisms of male infertility.