Year: 2021
Type: preprint
Abstract: Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis , along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui , Engystomops pustulosus and Hymenochirus boettgeri . Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (HiC) data for all species. Abundant satellite repeats occupy the unusually long (∼20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl configuration similar to the “bouquet” structure of meiotic cells. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
Authors: Jessen V. Bredeson, Austin B. Mudd, Sofia Medina-Ruiz, Therese Mitros, Owen K. Smith, Kelly E. Miller, Jessica B. Lyons, Sanjit S. Batra, Joseph Park, Kodiak C. Berkoff, Christopher Plott, Jane Grimwood, Jeremy Schmutz, Guadalupe Aguirre-Figueroa, Mustafa K. Khokha, Maura Lane, Isabelle Philipp, Mara Laslo, James Hanken, Gwenneg Kerdivel, Nicolas Buisine, Laurent M. Sachs, Daniel R. Buchholz, Taejoon Kwon, Heidi Smith-Parker, Marcos Gridi-Papp, Michael J. Ryan, Robert D. Denton, John H. Malone, John B. Wallingford, Aaron F. Straight, Rebecca Heald, Dirk Hockemeyer, Richard M. Harland, Daniel S. Rokhsar
Institutions: University of California, Berkeley, Stanford Medicine, Stanford University, Innovative Genomics Institute, HudsonAlpha Institute for Biotechnology, Yale University, Harvard University, Centre National de la Recherche Scientifique, Muséum national d'Histoire naturelle, Evolution des Régulations Endocriniennes, University of Cincinnati, Ulsan National Institute of Science and Technology, The University of Texas at Austin, University of the Pacific, University of Connecticut, Chan Zuckerberg Biohub San Francisco, Okinawa Institute of Science and Technology Graduate University
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: green
Funders: National Science Foundation, Smithsonian Institution, U.S. Department of Energy, Oklahoma Medical Research Foundation, National Energy Research Scientific Computing Center, National Research Foundation, Ulsan National Institute of Science and Technology, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Institute for Basic Science, National Institutes of Health, Directorate for Biological Sciences, Office of Science, Smithsonian Tropical Research Institute, National Human Genome Research Institute, National Institute of General Medical Sciences, Division of Integrative Organismal Systems, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awards: Dissertation Research: Evaluating the role of thyroid hormone in embryonic limb development in direct-developing frogs, Control of collective cell movement by planar cell polarity signaling, Postgraduate Training Program in Genetics, G122673668, G1286236842, G138947319, G1677143136, Pacific Biosciences PacBio RS Single Molecule Real Time Sequencer, G1863003419, G3056906889, G3083819904, A system approach to the analysis of Heterotaxy Candidate Genes, G3549828030, G382641700, G392543403, Acquisition of Covaris E220 and Sciclone G3 systems for high throughput sequencin, G419881185, G42916606, Systematic improvement of Xenopus gene annotations and reference genomes, G4501827968, G498139845, G5076365615, G6447494072, Molecular Pharmacology Training Grant, Comparative Genetics and Genomics of Xenopus, DISSERTATION RESEARCH: Sperm Competition and the Evolution of Alternative Reproductive Strategies, G8276097517, A genome assembly for Xenopus laevis, Berkeley Training Program in Genomics and Computational Biology, Mechanisms of Kinetochore Assembly, Mechanisms of mitosis and size control in Xenopus, Mapping the ciliary interactome, an extensive protein interaction network underlying human ciliopathies, Gene Expression in Amphibian Development, G969889393, Digitization TCN: Collaborative Research: oVert: Open Exploration of Vertebrate Diversity in 3D
OpenAlex ID: W3206483751