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Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in snakes and caecilians

Vladimir Ovchinnikov, Marcela Uliano-Silva, Mark Wilkinson, Jonathan Wood, Michelle Smith, Karen Oliver, Ying Sims, James Torrance, Alexander Suh, View ORCID ProfileShane A. McCarthy, Richard Durbin, View ORCID ProfileMary J. O’Connell
doi: https://doi.org/10.1101/2022.02.23.481419
Vladimir Ovchinnikov
1Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Science, University of Nottingham, NG7 2RD, UK
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Marcela Uliano-Silva
2Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
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Mark Wilkinson
3Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
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Jonathan Wood
2Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
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Michelle Smith
4Scientific Operations, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
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Karen Oliver
4Scientific Operations, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
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Ying Sims
2Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
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James Torrance
2Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
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Alexander Suh
5School of Biological Sciences, University of East Anglia, NR4 7TU, Norwich, UK
6Department of Organismal Biology, Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden
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Shane A. McCarthy
2Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
7Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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  • ORCID record for Shane A. McCarthy
Richard Durbin
2Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
7Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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  • For correspondence: Mary.O’Connell@nottingham.ac.uk rd109@cam.ac.uk
Mary J. O’Connell
1Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Science, University of Nottingham, NG7 2RD, UK
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  • ORCID record for Mary J. O’Connell
  • For correspondence: Mary.O’Connell@nottingham.ac.uk rd109@cam.ac.uk
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Abstract

We present genome sequences for Geotrypetes seraphini (3.8Gb) and Microcaecilia unicolor (4.7Gb) caecilians, a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. We identify signatures of positive selection unique to caecilians in 1,150 orthogroups, with enrichment of functions for olfaction and detection of chemical signals. All our caecilian genomes are missing the ZRS enhancer of Sonic Hedgehog, shown by in vivo deletions to be required for limb development in mice and also absent in snakes, thus revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://zenodo.org/record/5780326/export/json#.YhTCq_XP0dc

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Posted February 25, 2022.
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Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in snakes and caecilians
Vladimir Ovchinnikov, Marcela Uliano-Silva, Mark Wilkinson, Jonathan Wood, Michelle Smith, Karen Oliver, Ying Sims, James Torrance, Alexander Suh, Shane A. McCarthy, Richard Durbin, Mary J. O’Connell
bioRxiv 2022.02.23.481419; doi: https://doi.org/10.1101/2022.02.23.481419
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Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in snakes and caecilians
Vladimir Ovchinnikov, Marcela Uliano-Silva, Mark Wilkinson, Jonathan Wood, Michelle Smith, Karen Oliver, Ying Sims, James Torrance, Alexander Suh, Shane A. McCarthy, Richard Durbin, Mary J. O’Connell
bioRxiv 2022.02.23.481419; doi: https://doi.org/10.1101/2022.02.23.481419

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