Eye

Eyes are responsible for the detection of light and its subsequent conversion of visual stimuli to neuronal signals that are transported to the visual centers of the brain. Protein expression of selected genes with literature indicating function related to different structures in the eye, excluding retina, were analyzed by using the whole section of the eye. Human representation of the eye and retinal proteomes are already described in the Tissue Resource.

Here, we summarize and describe the samples representing other mammalian species (macaque, rat, mouse and pig) included in the Evolutionary Resource. Retina, cornea and lens were sampled in all four species. The Harderian gland (a secretory gland located behind the eye) is additionally represented in rat and mouse, reflecting its greater prominence in rodents compared with macaque and pig.

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

Crystallin beta B2 (CRYBB2) is a major structural protein of the eye lens, contributing to its transparency and refractive properties. CRYBB2 shows conserved lens-enriched expression across the investigated mammalian species, consistent with its known function in lens fibre cells. Although RNA detection in human sample is missing it is confirmed at protein level (by IHC, in figure 2) that it is specific to human lens.

Figure 2. Immunohistochemical staining of human eye using an antibody toward CRYBB2 shows strong positivity in lens.

Comparative transcriptomics of the mammalian eye

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
Cornea	Macaque	99	n/a	n/a
	Mouse	93	n/a	n/a
	Rat	111	n/a	n/a
	Pig	156	n/a	n/a
Harderian gland	Mouse	327	n/a	n/a
Harderian gland	Rat	253	n/a	n/a
Lens	Macaque	377	n/a	n/a
	Mouse	305	n/a	n/a
	Rat	381	n/a	n/a
	Pig	825	n/a	n/a
Retina	Macaque	405	161	120
	Mouse	597	149	121
	Rat	400	132	96
	Pig	381	126	89

Retina

The retina is the light-sensitive tissue at the back of the eye, containing rod and cone photoreceptors that convert light into electrical signals for visual processing. Rods support vision in dim light, while cones enable colour vision and the perception of fine details.

The organization and distribution of photoreceptors differ considerably between species. Humans and macaques have a cone-rich fovea specialized for high-acuity vision and three cone types, whereas pigs have a cone-rich visual streak and two cone types. Rats and mice have strongly rod-dominated retinas without a fovea, with regional differences in the distribution of cone photoreceptors.

Species coverage

Lens

The lens is a transparent, flexible structure that focuses light onto the retina. Changes in its shape allow the eye to adjust focus for objects at different distances. The lens has a highly conserved structure across mammals, consisting of densely packed, transparent fibre cells that maintain optical clarity. However, lens shape, size and accommodative ability differ between species, with humans and macaques having more developed accommodation than rodents, whose lenses are relatively spherical and less flexible.

Species coverage

Cornea

The cornea is the transparent front surface of the eye, protecting the underlying structures and providing much of the eye's focusing power. Its transparency is maintained by the highly organized collagen-rich stroma and specialized epithelial and endothelial cell layers.

Although the overall corneal structure is conserved across mammals, differences exist in thickness and histological organization. The pig cornea is generally thicker than the human cornea and lacks a clearly defined Bowman's layer, a structure present beneath the corneal epithelium in humans and macaques.

Species coverage

Harderian gland

The Harderian gland is a large orbital gland located behind the eye and is particularly well developed in rats and mice. It produces lipid-rich secretions and contributes to ocular lubrication and protection. It is not exclusively found in rodents; it occurs in several other mammalian groups. However, it is generally absent or vestigial in adult primates, including humans. and in this dataset it is ony sampled in mouse and rat. Rodent Harderian glands also have distinctive secretory properties, including the accumulation of porphyrins, and their epithelial composition differs from that of human lacrimal glands.