Male reproductive system

The male reproductive system includes the testes, epididymis and accessory reproductive glands, which together support sperm production, maturation, transport and the secretion of seminal fluid. Although these functions are conserved across mammals, the anatomy, organization and relative development of the accessory glands differ considerably between species, reflecting differences in reproductive physiology.

Samples from the testis, epididymis, prostate and seminal vesicle are available in human and all four mammalian species, enabling direct cross-species comparisons. However, the prostate differs substantially in anatomical organization, particularly in rodents, where distinct prostatic lobes are present. Samples from the anterior and ventral prostate are grouped into one main tissue type for the tissue specificity analysis, while individual samples can be explored in the sample details.

The mammalian datasets also include additional tissues, such as the bulbourethral gland, ductus deferens and penis, which are not represented in the human RNA data. These tissues provide valuable information about specialized reproductive functions, including sperm transport and the production of secretions that contribute to seminal fluid. Due to their overlapping secretory functions and gene expression profiles, the accessory reproductive glands are also grouped into a broader male glands category for tissue specificity analysis. Although direct comparisons with human are limited for these additional tissues, their inclusion enables investigation of tissue-specific expression patterns and reproductive specializations across mammalian species.

Figure 1. Tissue sample overview and the hierarchy of grouped tissues representing male tissues

Comparative transcriptomics of the mammalian endocrine tissues

The transcriptomic data is used to identify genes with elevated expression in individual tissues or groups of tissues, classified into three categories:

Tissue enriched: Genes with elevated expression in a single tissue compared with all other tissues.
Group enriched: Genes with elevated expression in a limited group of tissues compared with the remaining tissues.
Tissue enhanced: Genes with elevated expression in one or more tissues compared with the average expression across tissues (gap ratio ≥2)

Tissue specificity is evaluated at two levels: first, within each species using all available tissue types, and second, using only tissues that can be directly compared between the species and human. This distinction makes it possible to explore both tissue-specific expression within each species and the conservation of expression patterns across evolution.

The results can be explored for individual genes on the gene summary pages or searched to identify genes with specific expression patterns. To assess evolutionary conservation, pairwise overlap analysis compares each species individually with human, identifying genes that share the same tissue specificity classification in corresponding tissues and quantifying the extent of overlap between species.

Tissue	Species	Elevated	Human elevated overlap
Tissue	Species	Elevated	Complete overlap	Partial overlap
Ductus deferens	Macaque	71	n/a	n/a
	Mouse	86	n/a	n/a
	Rat	92	n/a	n/a
	Pig	49	n/a	n/a
Epididymis	Macaque	235	71	37
	Mouse	258	49	23
	Rat	184	38	25
	Pig	270	39	29
Male glands	Macaque	137	n/a	n/a
	Mouse	619	n/a	n/a
	Rat	388	n/a	n/a
	Pig	536	n/a	n/a
Penis	Macaque	17	n/a	n/a
	Mouse	74	n/a	n/a
	Rat	48	n/a	n/a
	Pig	29	n/a	n/a
Testis	Macaque	1664	683	333
	Mouse	1915	661	291
	Rat	1784	601	301
	Pig	1180	518	257

Testis

The testis contains seminiferous tubules in which sperm develop, supported by Sertoli cells, while interstitial Leydig cells produce testosterone. Although spermatogenesis is broadly conserved, the organization and relative abundance of germ cell populations vary between species, reflecting differences in reproductive physiology and the duration of sperm development.

Species coverage

Epididymis

The epididymis supports sperm maturation, storage and transport through regionally specialized epithelial cells that modify the luminal environment. Its segmentation and epithelial organization differ across mammals, with particularly pronounced regional specialization in rodents, potentially contributing to differences in secreted proteins and sperm maturation-related gene expression.

Species coverage

Male glands

Seminal vesicle

The seminal vesicles produce secretions containing proteins and other molecules that support sperm function and contribute to seminal fluid. Their size, glandular architecture and secretory composition vary considerably between mammals, with particularly large and highly folded seminal vesicles in rodents.

Prostate

The prostate produces secretions that contribute to seminal fluid, but its anatomical organization differs substantially across mammals. Humans and macaques have relatively compact prostates, whereas rats and mice possess distinct prostate lobes, including anterior, dorsal, lateral and ventral regions, with different glandular structures and secretory profiles. These differences are particularly important when comparing tissue-level expression of prostate-associated genes.

Bulbourethral gland

The bulbourethral glands produce mucus-rich secretions that lubricate and protect the urethra during reproduction. Their size and secretory activity differ substantially between species, being particularly prominent in pigs, where they contribute extensively to the seminal plasma and gel fraction.

Species coverage

Uretheral gland

The urethral glands produce mucus-rich secretions that lubricate and protect the urethral lining. In this dataset, the urethral gland was sampled only in pig, providing additional insight into the specialized secretory functions of the male reproductive tract.

Male preputial gland

Preputial glands are specialized sebaceous glands associated with the genital region and are particularly well developed in rodents. Their secretions contain lipid-rich compounds involved in chemical communication, including social and reproductive signaling, making them an example of a tissue with pronounced species-specific specialization.

Ductus deferens

The ductus deferens transports sperm from the epididymis towards the urethra through contractions of its muscular wall. Its epithelial and muscular organization is broadly conserved, although differences in wall thickness, glandular structures and regional anatomy occur between species.

Species coverage

Penis

The penis consists of erectile tissue, smooth muscle, blood vessels and abundant connective tissue, supporting its reproductive and urinary functions. Samples were collected as cross-sections of the penile shaft, where the substantial connective tissue component may influence the overall gene expression profile and contribute to similarities with other connective tissue-rich organs in tissue clustering analyses.