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Shylo NA, Price AJ, Robb S, Kupronis R, Méndez IAG, DeGraffenreid D, Gamble T, Trainor PA. Chamaeleo calyptratus (veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.03.611012. [PMID: 39282430 PMCID: PMC11398420 DOI: 10.1101/2024.09.03.611012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
The family Chamaeleonidae comprises 228 species, boasting an extensive geographic spread and an array of evolutionary novelties and adaptations, but a paucity of genetic and molecular analyses. Veiled chameleon (Chamaeleo calyptratus) has emerged as a tractable research organism for the study of squamate early development and evolution. Here we report a chromosomal-level assembly and annotation of the veiled chameleon genome. We note a remarkable chromosomal conservation across squamates, but comparisons to more distant genomes reveal GC peaks correlating with ancestral chromosome fusion events. We subsequently identified the XX/XY region on chromosome 5, confirming environmental-independent sex determination in veiled chameleons. Furthermore, our analysis of the Hox gene family indicates that veiled chameleons possess the most complete set of 41 Hox genes, retained from an amniote ancestor. Lastly, the veiled chameleon genome has retained both ancestral paralogs of the Nodal gene, but is missing Dand5 and several other genes, recently associated with the loss of motile cilia during the establishment of left-right patterning. Thus, a complete veiled chameleon genome provides opportunities for novel insights into the evolution of reptilian genomes and the molecular mechanisms driving phenotypic variation and ecological adaptation.
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Affiliation(s)
| | - Andrew J Price
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sofia Robb
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Irán Andira Guzmán Méndez
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Institute of Marine Sciences and Limnology (El Carmen Station), National Autonomous University of Mexico, Ciudad del Carmen, Campeche, Mexico
| | | | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Missouri, USA
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Shylo NA, Trainor PA. Decrypting the phylogenetics history of EGF-CFC proteins Cripto and Cryptic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610562. [PMID: 39257814 PMCID: PMC11383694 DOI: 10.1101/2024.08.30.610562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
EGF-CFC proteins are obligate coreceptors for Nodal signaling and are thus required for gastrulation and left-right patterning. Species with multiple family members show evidence of specialization. For example, mouse Cripto is required for gastrulation, whereas Cryptic is involved in left-right patterning. However, the members of the family across model organisms have little sequence conservation beyond the EGF-CFC domain, posing challenges for determining their evolutionary history and functional conservation. In this study we outline the evolutionary history of the EGF-CFC family of proteins. We traced the EGF-CFC gene family from a single gene in the deuterostome ancestor through its expansion and functional specialization in tetrapods, and subsequent gene loss and translocation in eutherian mammals. Mouse Cripto and Cryptic, zebrafish Tdgf1, and all three Xenopus EGF-CFC genes (Tdgf1, Tdgf1.2 and Cripto.3) and are all descendants of the ancestral Tdgf1 gene. We propose that subsequent to the family expansion in tetrapods, Tdgf1B (Xenopus Tdgf1.2) acquired specialization in the left-right patterning cascade, and after its translocation in eutherians to a different chromosomal location, Cfc1/Cryptic has maintained that specialization.
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Affiliation(s)
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Missouri, USA
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Banavar SP, Fowler EW, Nelson CM. Biophysics of morphogenesis in the vertebrate lung. Curr Top Dev Biol 2024; 160:65-86. [PMID: 38937031 DOI: 10.1016/bs.ctdb.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Morphogenesis is a physical process that sculpts the final functional forms of tissues and organs. Remarkably, the lungs of terrestrial vertebrates vary dramatically in form across species, despite providing the same function of transporting oxygen and carbon dioxide. These divergent forms arise from distinct physical processes through which the epithelium of the embryonic lung responds to the mechanical properties of its surrounding mesenchymal microenvironment. Here we compare the physical processes that guide folding of the lung epithelium in mammals, birds, and reptiles, and suggest a conceptual framework that reconciles how conserved molecular signaling generates divergent mechanical forces across these species.
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Affiliation(s)
- Samhita P Banavar
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ, United States
| | - Eric W Fowler
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ, United States
| | - Celeste M Nelson
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ, United States; Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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Kuraku S. Enigmatic Nodal and Lefty gene repertoire discrepancy: Latent evolutionary history revealed by vertebrate-wide phylogeny. Dev Dyn 2024. [PMID: 38647085 DOI: 10.1002/dvdy.710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Homology in vertebrate body plans is traditionally ascribed to the high-level conservation of regulatory components within the genetic programs governing them, particularly during the "phylotypic stage." However, advancements in embryology and molecular phylogeny have unveiled the dynamic nature of gene repertoires responsible for early development. Notably, the Nodal and Lefty genes, members of the transforming growth factor-beta superfamily producing intercellular signaling molecules and crucial for left-right (L-R) symmetry breaking, exhibit distinctive features within their gene repertoires. These features encompass among-species gene repertoire variations resulting from gene gain and loss, as well as gene conversion. Despite their significance, these features have been largely unexplored in a phylogenetic context, but accumulating genome-wide sequence information is allowing the scrutiny of these features. It has exposed hidden paralogy between Nodal1 and Nodal2 genes resulting from differential gene loss in amniotes. In parallel, the tandem cluster of Lefty1 and Lefty2 genes, which was thought to be confined to mammals, is observed in sharks and rays, with an unexpected phylogenetic pattern. This article provides a comprehensive review of the current understanding of the origins of these vertebrate gene repertoires and proposes a revised nomenclature based on the elucidated history of vertebrate genome evolution.
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Affiliation(s)
- Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Shizuoka, Japan
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