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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.
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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
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Ortega-Jimenez VM, Jusufi A, Brown CE, Zeng Y, Kumar S, Siddall R, Kim B, Challita EJ, Pavlik Z, Priess M, Umhofer T, Koh JS, Socha JJ, Dudley R, Bhamla MS. Air-to-land transitions: from wingless animals and plant seeds to shuttlecocks and bio-inspired robots. BIOINSPIRATION & BIOMIMETICS 2023; 18:051001. [PMID: 37552773 DOI: 10.1088/1748-3190/acdb1c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/02/2023] [Indexed: 08/10/2023]
Abstract
Recent observations of wingless animals, including jumping nematodes, springtails, insects, and wingless vertebrates like geckos, snakes, and salamanders, have shown that their adaptations and body morphing are essential for rapid self-righting and controlled landing. These skills can reduce the risk of physical damage during collision, minimize recoil during landing, and allow for a quick escape response to minimize predation risk. The size, mass distribution, and speed of an animal determine its self-righting method, with larger animals depending on the conservation of angular momentum and smaller animals primarily using aerodynamic forces. Many animals falling through the air, from nematodes to salamanders, adopt a skydiving posture while descending. Similarly, plant seeds such as dandelions and samaras are able to turn upright in mid-air using aerodynamic forces and produce high decelerations. These aerial capabilities allow for a wide dispersal range, low-impact collisions, and effective landing and settling. Recently, small robots that can right themselves for controlled landings have been designed based on principles of aerial maneuvering in animals. Further research into the effects of unsteady flows on self-righting and landing in small arthropods, particularly those exhibiting explosive catapulting, could reveal how morphological features, flow dynamics, and physical mechanisms contribute to effective mid-air control. More broadly, studying apterygote (wingless insects) landing could also provide insight into the origin of insect flight. These research efforts have the potential to lead to the bio-inspired design of aerial micro-vehicles, sports projectiles, parachutes, and impulsive robots that can land upright in unsteady flow conditions.
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Affiliation(s)
- Victor M Ortega-Jimenez
- School of Biology and Ecology, University of Maine, Orono, ME 04469, United States of America
| | - Ardian Jusufi
- Soft Kinetic Group, Engineering Sciences Department, Empa Swiss Federal Laboratories for Materials Science and Technology, Ueberlandstrasse 129, Dübendorf 8600, Switzerland
- University of Zurich, Institutes for Neuroinformatics and Palaeontology, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Macquarie University, Sydney, NSW 2109, Australia
| | - Christian E Brown
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Science Center 110, Tampa, FL 33620, United States of America
| | - Yu Zeng
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Science Center 110, Tampa, FL 33620, United States of America
- Department of Integrative Biology, University of California, Berkeley, CA 94720, United States of America
| | - Sunny Kumar
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, United States of America
| | - Robert Siddall
- Aerial Robotics Lab, Imperial College of London, London, United Kingdom
| | - Baekgyeom Kim
- Department of Mechanical Engineering, Ajou University, Gyeonggi-do 16499, Republic of Korea
| | - Elio J Challita
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, United States of America
| | - Zoe Pavlik
- School of Biology and Ecology, University of Maine, Orono, ME 04469, United States of America
| | - Meredith Priess
- School of Biology and Ecology, University of Maine, Orono, ME 04469, United States of America
| | - Thomas Umhofer
- School of Biology and Ecology, University of Maine, Orono, ME 04469, United States of America
| | - Je-Sung Koh
- Department of Mechanical Engineering, Ajou University, Gyeonggi-do 16499, Republic of Korea
| | - John J Socha
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, United States of America
| | - Robert Dudley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Science Center 110, Tampa, FL 33620, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - M Saad Bhamla
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, United States of America
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Andrade P, Lyra ML, Zina J, Bastos DFO, Brunetti AE, Baêta D, Afonso S, Brunes TO, Taucce PPG, Carneiro M, Haddad CFB, Sequeira F. Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana. G3 (BETHESDA, MD.) 2022; 12:jkac270. [PMID: 36205610 PMCID: PMC9713437 DOI: 10.1093/g3journal/jkac270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 12/05/2022]
Abstract
Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Mariana L Lyra
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Juliana Zina
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, Brazil
| | - Deivson F O Bastos
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, Brazil
| | - Andrés E Brunetti
- Laboratory of Evolutionary Genetics, Institute of Subtropical Biology, National University of Misiones (UNaM-CONICET) Posadas N3300LQH, Misiones, Argentina
| | - Délio Baêta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Tuliana O Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Pedro P G Taucce
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
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