Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians

Ovchinnikov, Vladimir; Uliano-Silva, Marcela; Wilkinson, Mark; Wood, Jonathan; Smith, Michelle; Oliver, Karen; Sims, Ying; Torrance, James; Suh, Alexander; McCarthy, Shane A; Durbin, Richard; O’Connell, Mary J

Abstract

We present genome sequences for the caecilians Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons being the most abundant. We identify 1,150 orthogroups that are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception, and immunity amongst others. We discover that caecilian genomes are missing the zone of polarizing activity regulatorysequence (ZRS) enhancer of Sonic Hedgehog which is also mutated in snakes. In vivo deletions have shown ZRS is required for limb development in mice, thus, revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.

Citation

Ovchinnikov, V., Uliano-Silva, M., Wilkinson, M., Wood, J., Smith, M., Oliver, K., Sims, Y., Torrance, J., Suh, A., McCarthy, S. A., Durbin, R., & O’Connell, M. J. (2023). Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians. Molecular Biology and Evolution, 40(5), 1-11. https://doi.org/10.1093/molbev/msad102

• Journal Article Type: Article
• Acceptance Date: May 2, 2023
• Online Publication Date: May 18, 2023
• Publication Date: May 2, 2023
• Deposit Date: Nov 4, 2024
• Publicly Available Date: Nov 6, 2024
• Journal: Molecular Biology and Evolution
• Print ISSN: 0737-4038
• Electronic ISSN: 1537-1719
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 40
• Issue: 5
• Article Number: msad102
• Pages: 1-11
• DOI: https://doi.org/10.1093/molbev/msad102
• Keywords: Gymnophiona, amphibia, vertebrate comparative genomics, limblessness
• Public URL: https://nottingham-repository.worktribe.com/output/20841739
• Publisher URL: https://academic.oup.com/mbe/article/40/5/msad102/7166927?login=false