1
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Taft JM, Tolley KA, Alexander GJ, Geneva AJ. De Novo Whole Genome Assemblies for Two Southern African Dwarf Chameleons (Bradypodion, Chamaeleonidae). Genome Biol Evol 2023; 15:evad182. [PMID: 37847614 PMCID: PMC10603767 DOI: 10.1093/gbe/evad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
A complete and high-quality reference genome has become a fundamental tool for the study of functional, comparative, and evolutionary genomics. However, efforts to produce high-quality genomes for African taxa are lagging given the limited access to sufficient resources and technologies. The southern African dwarf chameleons (Bradypodion) are a relatively young lineage, with a large body of evidence demonstrating the highly adaptive capacity of these lizards. Bradypodion are known for their habitat specialization, with evidence of convergent phenotypes across the phylogeny. However, the underlying genetic architecture of these phenotypes remains unknown for Bradypodion, and without adequate genomic resources, many evolutionary questions cannot be answered. We present de novo assembled whole genomes for Bradypodion pumilum and Bradypodion ventrale, using Pacific Biosciences long-read sequencing data. BUSCO analysis revealed that 96.36% of single copy orthologs were present in the B. pumilum genome and 94% in B. ventrale. Moreover, these genomes boast scaffold N50 of 389.6 and 374.9 Mb, respectively. Based on a whole genome alignment of both Bradypodion genomes, B. pumilum is highly syntenic with B. ventrale. Furthermore, Bradypodion is also syntenic with Anolis lizards, despite the divergence between these lineages estimated to be nearly 170 Ma. Coalescent analysis of the genomic data also suggests that historical changes in effective population size for these species correspond to notable shifts in the southern African environment. These high-quality Bradypodion genome assemblies will support future research on the evolutionary history, diversification, and genetic underpinnings of adaptation in Bradypodion.
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Affiliation(s)
- Jody M Taft
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
| | - Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anthony J Geneva
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University–Camden, Camden, New Jersey, USA
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2
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Pinto BJ, Gamble T, Smith CH, Wilson MA. A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. J Hered 2023; 114:445-458. [PMID: 37018459 PMCID: PMC10445521 DOI: 10.1093/jhered/esad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/03/2023] [Indexed: 04/07/2023] Open
Abstract
In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012 and 2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
- Bell Museum of Natural History, University of Minnesota, St Paul, MN, United States
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, United States
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3
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Pinto BJ, Gamble T, Smith CH, Wilson MA. A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524006. [PMID: 37034614 PMCID: PMC10081179 DOI: 10.1101/2023.01.20.524006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012-2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN USA
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ USA
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4
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Shylo NA, Smith SE, Price AJ, Guo F, McClain M, Trainor PA. Morphological changes and two Nodal paralogs drive left-right asymmetry in the squamate veiled chameleon ( C. calyptratus). Front Cell Dev Biol 2023; 11:1132166. [PMID: 37113765 PMCID: PMC10126504 DOI: 10.3389/fcell.2023.1132166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/23/2023] [Indexed: 04/29/2023] Open
Abstract
The ancestral mode of left-right (L-R) patterning involves cilia in the L-R organizer. However, the mechanisms regulating L-R patterning in non-avian reptiles remains an enigma, since most squamate embryos are undergoing organogenesis at oviposition. In contrast, veiled chameleon (Chamaeleo calyptratus) embryos are pre-gastrula at oviposition, making them an excellent organism for studying L-R patterning evolution. Here we show that veiled chameleon embryos lack motile cilia at the time of L-R asymmetry establishment. Thus, the loss of motile cilia in the L-R organizers is a synapomorphy of all reptiles. Furthermore, in contrast to avians, geckos and turtles, which have one Nodal gene, veiled chameleon exhibits expression of two paralogs of Nodal in the left lateral plate mesoderm, albeit in non-identical patterns. Using live imaging, we observed asymmetric morphological changes that precede, and likely trigger, asymmetric expression of the Nodal cascade. Thus, veiled chameleons are a new and unique model for studying the evolution of L-R patterning.
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Affiliation(s)
- Natalia A. Shylo
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Sarah E. Smith
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Andrew J. Price
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Melainia McClain
- Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, MO, United States
- *Correspondence: Paul A. Trainor,
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5
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Identification of Iguania Ancestral Syntenic Blocks and Putative Sex Chromosomes in the Veiled Chameleon ( Chamaeleo calyptratus, Chamaeleonidae, Iguania). Int J Mol Sci 2022; 23:ijms232415838. [PMID: 36555478 PMCID: PMC9779593 DOI: 10.3390/ijms232415838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
The veiled chameleon (Chamaeleo calyptratus) is a typical member of the family Chamaeleonidae and a promising object for comparative cytogenetics and genomics. The karyotype of C. calyptratus differs from the putative ancestral chameleon karyotype (2n = 36) due to a smaller chromosome number (2n = 24) resulting from multiple chromosome fusions. The homomorphic sex chromosomes of an XX/XY system were described recently using male-specific RADseq markers. However, the chromosomal pair carrying these markers was not identified. Here we obtained chromosome-specific DNA libraries of C. calyptratus by chromosome flow sorting that were assigned by FISH and sequenced. Sequence comparison with three squamate reptiles reference genomes revealed the ancestral syntenic regions in the C. calyptratus chromosomes. We demonstrated that reducing the chromosome number in the C. calyptratus karyotype occurred through two fusions between microchromosomes and four fusions between micro-and macrochromosomes. PCR-assisted mapping of a previously described Y-specific marker indicates that chromosome 5 may be the sex chromosome pair. One of the chromosome 5 conserved synteny blocks shares homology with the ancestral pleurodont X chromosome, assuming parallelism in the evolution of sex chromosomes from two basal Iguania clades (pleurodonts and acrodonts). The comparative chromosome map produced here can serve as the foundation for future genome assembly of chameleons and vertebrate-wide comparative genomic studies.
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6
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Pinto BJ, Keating SE, Nielsen SV, Scantlebury DP, Daza JD, Gamble T. Chromosome-Level Genome Assembly Reveals Dynamic Sex Chromosomes in Neotropical Leaf-Litter Geckos (Sphaerodactylidae: Sphaerodactylus). J Hered 2022; 113:272-287. [PMID: 35363859 PMCID: PMC9270867 DOI: 10.1093/jhered/esac016] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.
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Affiliation(s)
- Brendan J Pinto
- Address correspondence to B. J. Pinto at the address above, or e-mail:
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Stuart V Nielsen
- Department of Biological Sciences, Louisiana State University in Shreveport, Shreveport, LA 71115, USA,Division of Herpetology, Florida Museum of Natural History, Gainesville, FL 32611, USA
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI 53233, USA,Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA,Bell Museum of Natural History, University of Minnesota, St Paul, MN 55455, USA
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7
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Pfaff F, Rubbenstroth D. Two novel bornaviruses identified in colubrid and viperid snakes. Arch Virol 2021; 166:2611-2614. [PMID: 34128103 PMCID: PMC8321990 DOI: 10.1007/s00705-021-05138-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/26/2021] [Indexed: 12/04/2022]
Abstract
We present the complete genome sequences of Caribbean watersnake bornavirus (CWBV) and Mexican black-tailed rattlesnake bornavirus (MRBV), which we identified in archived raw transcriptomic read data of a Caribbean watersnake (Tretanorhinus variabilis) and a Mexican black-tailed rattlesnake (Crotalus molossus nigrescens), respectively. The genomes of CWBV and MRBV have a length of about 8,900 nucleotides and comprise the complete coding regions and the untranslated regions. The overall genomic makeup and predicted gene content is typical for members of the genus Orthobornavirus within the family Bornaviridae. Alternative splicing was detected for the L and M genes. Based on a phylogenetic analysis of all viral proteins, we consider both viruses to be members of a single novel species within the genus Orthobornavirus. Both viruses form a distinct outgroup to all currently known orthobornaviruses. Based on the novel virus genomes, we furthermore identified closely related endogenous bornavirus-like nucleoprotein sequences in transcriptomic data of veiled chameleons (Chamaeleo calyptratus) and a common lancehead (Bothrops atrox).
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Affiliation(s)
- Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493, Greifswald, Riems, Germany.
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493, Greifswald, Riems, Germany
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8
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Pinto BJ, Weis JJ, Gamble T, Ode PJ, Paul R, Zaspel JM. A chromosome-level genome assembly of the parasitoid wasp, Cotesia glomerata (Hymenoptera: Braconidae). J Hered 2021; 112:558-564. [PMID: 34043785 DOI: 10.1093/jhered/esab032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet under-studied hymenopterans, are parasitoid wasps in the family Braconidae. Among this under-studied group are braconid wasps in the genus Cotesia; a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing technologies, including Oxford Nanopore, whole-genome shotgun sequencing, and 3-D chromatin contact information (Hi-C). Our assembly is one of the most contiguous, complete, and publicly available hymenopteran genomes, represented by 3,355 scaffolds with a scaffold N50 of ~28Mb and a BUSCO score of ~99%. Given the genome sizes found in closely related species, our genome assembly was ~50% larger than expected, which was apparently induced by runaway amplification of three types of repetitive elements: simple repeats, Long Terminal Repeats (LTRs), and Long Interspersed Nuclear Elements (LINEs). This assembly is another step forward for genomics across this hyper-diverse, yet understudied, order of insects. The assembled genomic data and metadata files are publicly available via Figshare (https://doi.org/10.6084/m9.figshare.13010549).
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Affiliation(s)
- Brendan J Pinto
- Department of Integrative Biology, University of Texas at Austin, TX, USA.,Milwaukee Public Museum, Milwaukee, WI, USA
| | | | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.,Bell Museum of Natural History, University of Minnesota, St Paul, MN, USA
| | - Paul J Ode
- Colorado State University, Ft. Collins, CO, USA
| | - Ryan Paul
- Colorado State University, Ft. Collins, CO, USA
| | - Jennifer M Zaspel
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
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9
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Dash S, Trainor PA. The development, patterning and evolution of neural crest cell differentiation into cartilage and bone. Bone 2020; 137:115409. [PMID: 32417535 DOI: 10.1016/j.bone.2020.115409] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022]
Abstract
Neural crest cells are a vertebrate-specific migratory, multipotent cell population that give rise to a diverse array of cells and tissues during development. Cranial neural crest cells, in particular, generate cartilage, bone, tendons and connective tissue in the head and face as well as neurons, glia and melanocytes. In this review, we focus on the chondrogenic and osteogenic potential of cranial neural crest cells and discuss the roles of Sox9, Runx2 and Msx1/2 transcription factors and WNT, FGF and TGFβ signaling pathways in regulating neural crest cell differentiation into cartilage and bone. We also describe cranioskeletal defects and disorders arising from gain or loss-of-function of genes that are required for patterning and differentiation of cranial neural crest cells. Finally, we discuss the evolution of skeletogenic potential in neural crest cells and their function as a conduit for intraspecies and interspecies variation, and the evolution of craniofacial novelties.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO, 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, KS, USA.
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10
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Hampl M, Dumkova J, Kavkova M, Dosedelova H, Bryjova A, Zahradnicek O, Pyszko M, Macholan M, Zikmund T, Kaiser J, Buchtova M. Polarized Sonic Hedgehog Protein Localization and a Shift in the Expression of Region-Specific Molecules Is Associated With the Secondary Palate Development in the Veiled Chameleon. Front Cell Dev Biol 2020; 8:572. [PMID: 32850780 PMCID: PMC7399257 DOI: 10.3389/fcell.2020.00572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Secondary palate development is characterized by the formation of two palatal shelves on the maxillary prominences, which fuse in the midline in mammalian embryos. However, in reptilian species, such as turtles, crocodilians, and lizards, the palatal shelves of the secondary palate develop to a variable extent and morphology. While in most Squamates, the palate is widely open, crocodilians develop a fully closed secondary palate. Here, we analyzed developmental processes that underlie secondary palate formation in chameleons, where large palatal shelves extend horizontally toward the midline. The growth of the palatal shelves continued during post-hatching stages and closure of the secondary palate can be observed in several adult animals. The massive proliferation of a multilayered oral epithelium and mesenchymal cells in the dorsal part of the palatal shelves underlined the initiation of their horizontal outgrowth, and was decreased later in development. The polarized cellular localization of primary cilia and Sonic hedgehog protein was associated with horizontal growth of the palatal shelves. Moreover, the development of large palatal shelves, supported by the pterygoid and palatine bones, was coupled with the shift in Meox2, Msx1, and Pax9 gene expression along the rostro-caudal axis. In conclusion, our results revealed distinctive developmental processes that contribute to the expansion and closure of the secondary palate in chameleons and highlighted divergences in palate formation across amniote species.
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Affiliation(s)
- Marek Hampl
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jana Dumkova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Michaela Kavkova
- Laboratory of Computed Tomography, Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Hana Dosedelova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | - Anna Bryjova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Oldrich Zahradnicek
- Department of Developmental Biology, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia.,Department of Radiation Dosimetry, Nuclear Physics Institute, Czech Academy of Sciences, Prague, Czechia
| | - Martin Pyszko
- Department of Anatomy, Histology, and Embryology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia
| | - Milos Macholan
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
| | - Tomas Zikmund
- Laboratory of Computed Tomography, Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Jozef Kaiser
- Laboratory of Computed Tomography, Central European Institute of Technology, Brno University of Technology, Brno, Czechia
| | - Marcela Buchtova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
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11
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Pinto BJ, Nielsen SV, Gamble T. Transcriptomic data support a nocturnal bottleneck in the ancestor of gecko lizards. Mol Phylogenet Evol 2019; 141:106639. [PMID: 31586687 DOI: 10.1016/j.ympev.2019.106639] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 11/17/2022]
Abstract
Gecko lizards are a species-rich clade of primarily-nocturnal squamate reptiles. In geckos, adaptations to nocturnality have dramatically reshaped the eye. Perhaps the most notable change is the loss of rod cells in the retina and subsequent "transmutation" of cones into a rod-like morphology and physiology. While many studies have noted the absence of some rod-specific genes, such as the visual pigment Rhodopsin (RH1), these studies have focused on just a handful of species that are nested deep in the gecko phylogeny. Thus, it is not clear whether these changes arose through convergence, are homologous and ubiquitous across geckos, or restricted to a subset of species. Here, we used de novo eye transcriptomes from five gecko species, and genomes from two additional gecko species, representing the breadth of extant gecko diversity (i.e. 4 of the 7 gecko families, spanning the deepest divergence of crown Gekkota), to show that geckos lost expression of almost the entire suite of necessary rod-cell phototransduction genes in the eye, distinct from all other squamate reptiles. Geckos are the first vertebrate group to have lost their complete rod-cell expression pathway, not just the visual pigment. In addition, all sampled species have also lost expression of the cone-opsin SWS2 visual pigment. These results strongly suggest a single loss of rod cells and subsequent cone-to-rod transmutation that occurred prior to the diversification of extant geckos.
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Affiliation(s)
- Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA; Milwaukee Public Museum, Milwaukee, WI, USA.
| | - Stuart V Nielsen
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA; Milwaukee Public Museum, Milwaukee, WI, USA; Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA.
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12
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Griffing AH, Sanger TJ, Daza JD, Nielsen SV, Pinto BJ, Stanley EL, Gamble T. Embryonic development of a parthenogenetic vertebrate, the mourning gecko (
Lepidodactylus lugubris
). Dev Dyn 2019; 248:1070-1090. [DOI: 10.1002/dvdy.72] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Aaron H. Griffing
- Department of Biological SciencesMarquette University Milwaukee Wisconsin
| | - Thomas J. Sanger
- Department of BiologyLoyola University in Chicago Chicago Illinois
| | - Juan D. Daza
- Department of Biological SciencesSam Houston State University Huntsville Texas
| | - Stuart V. Nielsen
- Department of HerpetologyFlorida Museum of Natural History Gainesville Florida
| | - Brendan J. Pinto
- Department of Biological SciencesMarquette University Milwaukee Wisconsin
| | - Edward L. Stanley
- Department of HerpetologyFlorida Museum of Natural History Gainesville Florida
| | - Tony Gamble
- Department of Biological SciencesMarquette University Milwaukee Wisconsin
- Milwaukee Public Museum Milwaukee Wisconsin
- Bell Museum of Natural HistoryUniversity of Minnesota Saint Paul Minnesota
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Primary myogenesis in the sand lizard (Lacerta agilis) limb bud. Dev Genes Evol 2019; 229:147-159. [PMID: 31214772 PMCID: PMC6867991 DOI: 10.1007/s00427-019-00635-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/02/2019] [Indexed: 11/23/2022]
Abstract
Our studies conducted on reptilian limb muscle development revealed, for the first time, early forelimb muscle differentiation at the morphological and molecular level. Sand lizard skeletal muscle differentiation in the early forelimb bud was investigated by light, confocal, and transmission electron microscopy as well as western blot. The early forelimb bud, filled with mesenchymal cells, is surrounded by monolayer epithelium cells. The immunocytochemical analysis revealed the presence of Pax3- and Lbx-positive cells in the vicinity of the ventro-lateral lip (VLL) of the dermomyotome, suggesting that VLL is the source of limb muscle progenitor cells. Furthermore, Pax3- and Lbx-positive cells were observed in the dorsal and ventral myogenic pools of the forelimb bud. Skeletal muscle development in the early limb bud is asynchronous, which is manifested by the presence of myogenic cells in different stages of differentiation: multinucleated myotubes with well-developed contractile apparatus, myoblasts, and mitotically active premyoblasts. The western blot analysis revealed the presence of MyoD and Myf5 proteins in all investigated developmental stages. The MyoD western blot analysis showed two bands corresponding to monomeric (mMyoD) and dimeric (dMyoD) fractions. Two separate bands were also detected in the case of Myf5. The observed bands were related to non-phosphorylated (Myf5) and phosphorylated (pMyf5) fractions of Myf5. Our investigations on sand lizard forelimb myogenesis showed that the pattern of muscle differentiation in the early forelimb bud shares many features with rodents and chicks.
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Franz-Odendaal TA, Hockman D. Non-model organisms and unique approaches are needed for the future of evo-devo. Dev Dyn 2019; 248:618-619. [PMID: 31215704 DOI: 10.1002/dvdy.71] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Diaz RE, Shylo NA, Roellig D, Bronner M, Trainor PA. Filling in the phylogenetic gaps: Induction, migration, and differentiation of neural crest cells in a squamate reptile, the veiled chameleon (Chamaeleo calyptratus). Dev Dyn 2019; 248:709-727. [DOI: 10.1002/dvdy.38] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
- Raul E. Diaz
- Department of Biological Sciences, Southeastern Louisiana University Hammond Louisiana
- Natural History Museum of Los Angeles CountyDivision of Herpetology Los Angeles California
| | | | - Daniela Roellig
- Division of Biology and Biological Engineering, California Institute of Technology Pasadena California
| | - Marianne Bronner
- Division of Biology and Biological Engineering, California Institute of Technology Pasadena California
| | - Paul A. Trainor
- Stowers Institute for Medical Research Kansas City Missouri
- Department of Anatomy and Cell Biology, University of Kansas Medical Center Kansas City Kansas
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