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Cited by 44Developmental Biology and Gene RegulationChromosomal and Genetic VariationsGenomics and Chromatin Dynamics

Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages

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Roscito, Juliana Gusson, Sameith, Katrin, Kirilenko, Bogdan Mikhailovich, Hecker, Nikolai, Winkler, Sylke, Dahl, Andreas, Rodrigues, Miguel Trefaut, Hiller, Michael·2022·Cell Reports
DOI 10.1016/j.celrep.2021.110280
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Abstract

Loss of limbs evolved many times in squamate reptiles. Here we investigated the genomic basis of convergent limb loss in reptiles. We sequenced the genomes of a closely related pair of limbless-limbed gymnophthalmid lizards and performed a comparative genomic analysis including five snakes and the limbless glass lizard. Our analysis of these three independent limbless lineages revealed that signatures of shared sequence or transcription factor binding site divergence in individual limb regulatory elements are generally rare. Instead, shared divergence occurs more often at the level of signaling pathways, involving different regulatory elements associated with the same limb genes (such as Hand2 or Hox) and/or patterning mechanisms (such as Shh signaling). Interestingly, although snakes are known to have mutations in the Shh ZRS limb enhancer, this enhancer lacks relevant mutations in limbless lizards. Thus, different mechanisms could contribute to limb loss, and there are likely multiple evolutionary paths to limblessness in reptiles.

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  • TOGA enables phylogenomic analyses as well as screens for selection patterns and gene losses that are linked to relevant phenotypes.

    “First, by detecting inactivated genes and providing orthologous sequences for codon alignments, TOGA enables phylogenomic analyses as well as screens for selection patterns and gene losses that are linked to relevant phenotypes (6, 35–38).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [36]

    The Gene identification section says TOGA identifies orthologous gene loci, and Screen for gene losses says it detects gene-inactivating mutations in a search for limb-related gene losses. These passages support the orthology and phenotype-linked gene-loss parts of the claim, but do not establish that TOGA provides codon alignments or enables phylogenomic analyses and screens for selection patterns. Page numbers are unavailable in our copy. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 13

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Authors
Roscito, J. G., Sameith, K., Kirilenko, B. M., Hecker, N., Winkler, S., Dahl, A., Rodrigues, M. T., & Hiller, M.
Affiliations
  • Max Planck Institute for the Physics of Complex Systems (DE)
  • Goethe University Frankfurt (DE)
  • Max Planck Institute of Molecular Cell Biology and Genetics (DE)
  • DRESDEN-concept Genome Center (DE)
Corresponding author
  • Roscito, Juliana Gusson
  • Hiller, Michael
ORCID
Venue
Cell Reports
Publisher
Elsevier BV
Published
2022-01
Volume
38
Issue
3
Pages
110280
ISSN
2211-1247 (ISSN-L)
DOI
10.1016/j.celrep.2021.110280
OpenAlex
W4205919993
Cited by
44
References
8
Citations by year
2026: 12 · 2025: 10 · 2024: 11 · 2023: 9 · 2022: 2
FWCI
2.61
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Reports (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Lirias (KU Leuven) (submittedVersion, other-oa)
Funders
  • Max-Planck-Gesellschaft
  • Fundação de Amparo à Pesquisa do Estado de São Paulo (2012/01319-8, 2012/23360)
  • Hessisches Ministerium für Wissenschaft und Kunst
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
limb loss, convergent evolution, snakes, glass lizards, enhancer evolution, Hand2, Hox genes, Sonic hedgehog signaling, transcription factor binding sites, squamate reptiles
MeSH terms
Animals, Biological Evolution, Extremities, Phylogeny, Regulatory Sequences, Nucleic Acid, Reptiles, Genomics, Transcriptome

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