1
|
Kosch TA, Torres-Sánchez M, Liedtke HC, Summers K, Yun MH, Crawford AJ, Maddock ST, Ahammed MS, Araújo VLN, Bertola LV, Bucciarelli G, Carné A, Carneiro CM, Chan KO, Chen Y, Crottini A, da Silva JM, Denton RD, Dittrich C, Themudo GE, Farquharson KA, Forsdick NJ, Gilbert E, Jing C, Katzenback BA, Kotharambath R, Levis NA, Márquez R, Mazepa G, Mulder KP, Müller H, O’Connell MJ, Orozco-terWengel P, Palomar G, Petzold A, Pfennig DW, Pfennig KS, Reichert MS, Robert J, Scherz MD, Siu-Ting K, Snead AA, Stöck M, Stuckert AMM, Stynoski JL, Tarvin RD, Valero KCW. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601086. [PMID: 39005434 PMCID: PMC11244923 DOI: 10.1101/2024.06.27.601086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.
Collapse
Affiliation(s)
- Tiffany A. Kosch
- One Health Research Group, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Werribee, Victoria, Australia
| | - María Torres-Sánchez
- Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Kyle Summers
- Biology Department, East Carolina University, Greenville, NC, USA 27858
| | - Maximina H. Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrew J. Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
- Museo de Historia Natural C.J. Marinkelle, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Simon T. Maddock
- School of Natural and Environmental Sciences, Newcastle University, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Seychelles
| | | | - Victor L. N. Araújo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Lorenzo V. Bertola
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, QLD 4810, Australia
| | - Gary Bucciarelli
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, USA
| | - Albert Carné
- Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Céline M. Carneiro
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kin O. Chan
- University of Kansas Biodiversity Institute and Natural History Museum, Lawrence, Kansas 66045, USA
| | - Ying Chen
- Biology Department, Queen’s University, Ontario, Canada
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169– 007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Jessica M. da Silva
- Evolutionary Genomics and Wildlife Management, Foundatonal Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute, Newlands 7735, Cape Town, South Africa
- Centre for Evolutionary Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, Johannesburg, South Africa
| | - Robert D. Denton
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Carolin Dittrich
- Rojas Lab, Konrad-Lorenz-Institute of Ethology, Department of Life Science, University of Veterinary Medicine, Vienna, Austria
| | - Gonçalo Espregueira Themudo
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos, Portugal
| | - Katherine A. Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Edward Gilbert
- School of Natural Sciences, The University of Hull, Hull, HU6 7RX, United Kingdom
- Energy and Environment Institute, The University of Hull, Hull, HU6 7RX, United Kingdom
| | - Che Jing
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | | | - Ramachandran Kotharambath
- Herpetology Lab, Dept. of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, 671320, India
| | - Nicholas A. Levis
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Roberto Márquez
- Department of Biological Sciences, Virginia Tech. Blacksburg, VA 24060, USA
| | - Glib Mazepa
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015, Switzerland
- Department of Ecology and Genetics, Evolutionary Biology, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Kevin P. Mulder
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Hendrik Müller
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, D-06108 Halle (Saale), Germany
| | - Mary J. O’Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Museum Avenue, CF10 3AX Cardiff, United Kingdom
| | - Gemma Palomar
- Department of Genetics, Physiology, and Microbiology; Faculty of Biological Sciences; Complutense University of Madrid, Madrid, Spain
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Alice Petzold
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Str.24-25, 14476 Potsdam, Germany
| | - David W. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karin S. Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael S. Reichert
- Department of Integrative Biology, Oklahoma State University, Stillwater OK, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Karen Siu-Ting
- School of Biological Sciences, Queen’s University Belfast, Belfast, BT7 1NN, Northern Ireland, United Kingdom
- Instituto Peruano de Herpetología, Ca. Augusto Salazar Bondy 136, Surco, Lima, Peru
- Herpetology Lab, The Natural History Museum, London, United Kingdom
| | - Anthony A Snead
- Department of Biology, New York University, New York, NY, USA
| | - Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany
| | - Adam M. M. Stuckert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204, USA
| | | | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | | | | |
Collapse
|
5
|
Ta AC, Huang LC, McKeown CR, Bestman JE, Van Keuren-Jensen K, Cline HT. Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles. G3-GENES GENOMES GENETICS 2021; 12:6423992. [PMID: 34751375 PMCID: PMC8728038 DOI: 10.1093/g3journal/jkab387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022]
Abstract
Amphibian metamorphosis is a transitional period that involves significant changes in the cell type populations and biological processes occurring in the brain. Analysis of gene expression dynamics during this process may provide insight into the molecular events underlying these changes. We conducted differential gene expression analyses of the developing X. laevis tadpole brain during this period in two ways: first, over stages of development in the midbrain, and second, across regions of the brain at a single developmental stage. We found that genes pertaining to positive regulation of neural progenitor cell proliferation as well as known progenitor cell markers were upregulated in the midbrain prior to metamorphic climax; concurrently, expression of cell cycle timing regulators decreased across this period, supporting the notion that cell cycle lengthening contributes to a decrease in proliferation by the end of metamorphosis. We also found that at the start of metamorphosis, neural progenitor populations appeared to be similar across the fore-, mid-, and hindbrain regions. Genes pertaining to negative regulation of differentiation were upregulated in the spinal cord compared to the rest of the brain, however, suggesting that a different program may regulate neurogenesis there. Finally, we found that regulation of biological processes like cell fate commitment and synaptic signaling follow similar trajectories in the brain across early tadpole metamorphosis and mid- to late-embryonic mouse development. By comparing expression across both temporal and spatial conditions, we have been able to illuminate cell type and biological pathway dynamics in the brain during metamorphosis.
Collapse
Affiliation(s)
- Aaron C Ta
- The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, 92037, USA
| | | | | | | | | | - Hollis T Cline
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| |
Collapse
|