Conserved and lineage-specific mechanisms drive chromatophore differentiation in reptiles
Ontology highlight
ABSTRACT:
ORGANISM(S): Pogona vitticeps Pantherophis guttatus
PROVIDER: GSE303854 | GEO | 2026/05/28
REPOSITORIES: GEO
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Project description:<p><strong>BACKGROUND:</strong> Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved.</p><p><strong>RESULTS:</strong> We investigate color morph-enriched Asian vine snakes (<em>Ahaetulla prasina</em>), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77 Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in <em>SMARCE1</em>, which may be involved in the regulation of chromatophore development initiated from neural crest cells. <em>SMARCE1</em> knockdown in zebrafish and immunofluorescence verify the interactions among <em>SMARCE1</em>, iridophores, and <em>tfec</em>, which may determine color variations in the Asian vine snake.</p><p><strong>CONCLUSIONS:</strong> This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.</p>
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Project description:Background: Snakes exhibit a broad variety of adaptive colours and colour patterns, generated by the spatial arrangement of chromatophores, but little is known of the mechanisms responsible for these spectacular traits. Here, we investigate a monolocus trait with two recessive alleles that cause pattern aberrations in the corn snake: the motley and striped alleles. Results: We use mapping-by-sequencing to identify the genomic interval where the causal mutations reside. With our differential gene expression analyses, we find that CLCN2 (Chloride Voltage-Gated Channel 2), a gene within the genomic interval, is significantly downregulated in Motley embryonic skin. Furthermore, the insertion of a retrotransposon in CLCN2 results in a disruptive mutation in Stripe. We confirm the involvement of CLCN2 in colour pattern formation by producing knock-out snakes that present a phenotype similar to the Stripe one. In humans and mice, the disruption of CLCN2 results in leukoencephalopathy, as well as retinal and testes degeneration. Our single-cell transcriptomic analyses reveal that CLCN2 is indeed expressed in chromatophores during embryogenesis and in the adult brain. Although, we observe signs of vacuolation in the Stripe adult brain, the retina of Motley and Stripe animals is intact, and no fertility issues are reported for the carriers of both alleles. Conclusions: Our genomic, transcriptomic and functional analyses identify a plasma membrane anion channel to be involved in colour pattern development in Squamate reptiles and show that an active LTR-retrotransposon might be a key driver of trait diversification in corn snakes.
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