NB: In the 2017-2020 IUCN period the Genome Resources Working Group has been split into two separate Working Groups (WGs), a Genomics WG and a Biobanking WG. The Chair/Co-Chairs for the new WGs are Caren Helbing (Genomics WG), Gina Della Togna and Natalie Calatayud (Biobanking WG). The information below refers to the 2013-2016 Genome Resources WG, but will be updated to reflect the new arrangements in the coming months.
Group Facilitators: Caren Helbing & Craig Hassapakis
ASG Secretariat Lead Contact: Jos Kielgast (jkielgast[at]amphibians.org)
Vision
To create a historically permanent record and resource (publicly accessible in sustainable repositories) of bioinformatics and tissue for amphibian species conservation and research.*
Target Areas
A) Bioinformatics of amphibian genomes: Sequence, assemble, and annotate representative nuclear genomes from each family of Amphibia and make them publicly available in curated databases.
B) Biodiversity preservation of tissues representing all amphibian species: Cryopreserve tissues. Promote assisted reproductive technologies. Develop and use cell/tissue culture in amphibian species, particularly those in immediate danger of being lost.
Goals
Part A. Bioinformatics of amphibian genomes
- Nuclear Genomes: Sequence, assemble, and annotate representative genomes from each family of Amphibia (Anura: 55, Caudata: 10, Gymnophiona: 10)—total 75, to enable initiatives such as evaluation of biological responses to pollutants, infectious diseases, climate change, habitat stress/loss using transcriptomics, proteomics, and metabolomics approaches, identification of antimicrobial peptides, etc. Promote the development of non-lethal molecular health assessment tools.
- Resource Accessibility: Promote the deposition of genome, microbiome, and related data into curated public databases to facilitate their widespread accessibility and use.
Part B. Preservation of amphibian tissues
- Collection and Discoverability: Determine existing worldwide amphibian genome, tissue, and cell culture resource availability and making these resources known and accessible. Collect (germ, somatic cells and other tissues), cataloging, and cryodeposition in publically accessible repositories, first, representing all genera of amphibians (Anura: 445 genera (6,630 sp.); Caudata: 68 genera (682 sp.); Gymnophiona: 33 genera (205 sp.)—total: 546, and the completion of all species worldwide within 10 years (7,517 sp.: March 4, 2016, AmphibiaWeb).
- Priorities: Collect, store, and catalogue cryobanked tissues of all amphibian species, but most importantly, those in immediate danger of being lost forever. Facilitate Assisted Reproductive Technologies (ART) and development of cell/tissue culture techniques and resources.
- Education and Standards: Generate and integrate operating ethics and standards for cryopreservation of tissue, proper storage, and depositing in publicly accessible venues practices routine. Promote the use of standard procedures.
Current Priority Actions
| Major Constraints To Effective Conservation | Mid-term Priorities (1–5 years) | Short-term Targets (6–12 months) |
|---|---|---|
| Part A. Critical gaps in basic knowledge, funding, and resources | ||
| Knowledge: Genetic diversity of amphibian species; linkage of genetic makeup, physiology, and phenotype at various life stages; impact of pollutants, toxicants, infectious disease, climate change; role of microbiomes in amphibian health and disease. | Support: Facilitate and support large scale efforts to sequence, assemble, and annotate high quality amphibian genomes that will be made publicly available. Support initiatives using genomic (including microbiomes), transcriptomics, proteomics, and/or metabolomics-based approaches. | Priorities: Motivate a synergistic community effort towards transparency, communication and coordination among large scale sequencing projects. Create prioritized list of target species for genome sequencing. Engage appropriate sequencing and bioinformatics partners. |
| Tools: Lack of conservation-friendly, minimally invasive tools to determine amphibian health and reliable distribution and estimated population sizes of species. | Training: Invest in the training and support of students and highly qualified personnel in creating and using molecular resources/tools and bioinformatics. | Support: Support funding initiatives, formation and interactions of research consortia aimed at amphibian genome sequencing, assembly, and annotation as well as developing and using these molecular tools and approaches. |
| Education: Promote data acquisition and dissemination relevant to environmental regulatory agencies e.g., linking molecular indicators to deleterious outcomes. | Infrastructure & Policy: Identify sustainable informatics structure for providing public access to genome information. | |
| Dissemination: Encourage the scientific community to take data-based recommendations for reducing threats to amphibians to policy makers, industry, and the public at international, national, regional, and local levels. | Education & Financial: Identify and interact with potential donors and funding partners. Set up funding structures. | |
| Research & Development: Promote and support the development of high quality minimally invasive molecular assays for animal health and population distribution assessments (e.g., eDNA from water samples; swab or biopsy techniques followed by biomolecular assays). | ||
| Part B. Critical gaps in basic knowledge, funding, and agreement within the amphibian conservation community | ||
| Knowledge: Lack of technical ability for female gamete cryopreservation and specific parameters for male gamete cryopreservation conditions for all known amphibian species. | Support: Facilitate and support large scale efforts to collect, store, and catalogue cryopreserved amphibian tissues, assistive reproduction technologies, and development of cell/tissue culture techniques and resources for research, experimentation, and conservation purposes. | Priorities: Create prioritized list of species and areas for tissue collection and cryopreservation (determine types of tissue collected: somatic, reproductive, blood, etc.) taking action before it is too late for certain areas and species. |
| Agreement: Shortfall in understanding and agreement within the amphibian conservation community of how to best protect and preserve amphibian species worldwide. | Training: Invest in the training and support of students and highly qualified personnel for amphibian tissue cryopreservation collection, storage, and maintenance. | Activities: Support funding initiatives, formation, and interactions of research consortia (e.g., Global Genome Biodiversity Network [GGBN]) aimed specifically at amphibian tissue collection, cryopreservation, and cataloging. |
| Stakeholder Challenges: National politics; intellectual property rights agreement; lack of curation infrastructure for tissue collection and storage; lack of complete support and agreement (e.g., MOUs, collecting permits) for effective cooperation toward amphibian cryopreservation goals; and lack of funding to develop and implement urgent action(s). | Financial: Develop long term financial and institutional support specific for amphibian tissue cryopreservation technology and development. | Funding: Identify and interact with potential donors and funding partners specific to further amphibian tissue cryopreservation worldwide. |
| Education & Publication: Development of technical manuals, protocols, hands on training, and public awareness campaigns for amphibian tissue acquisition and storage in multiply conservation specific countries, areas, and languages. | Research: Construct a list of research topics which urgently need to be addressed (e.g., female gamete cryopreservation technology and development, bioinformatics, reproductive technologies) and actively promote participation within educational systems (M.Sc., Ph.D., and Postdoctoral programs) worldwide. | |
| Education/Agreement: Sign MOUs with stakeholders. |
ACAP Related Chapter
Chapter 11. Bioresource Banking Efforts in Support of Amphibian Conservation (O.A. Ryder). Read the whole ACAP here.
*This resource impacts many aspects of amphibian conservation including infectious diseases, trade & policy, climate change, ecotoxicology, assessing the success of species conservation strategies, reintroductions, & management, habitat loss & restoration, invasive alien species, surveys & monitoring, taxonomy & systematics, education & awareness, and politics. Ongoing promotion of integration genome resources into larger initiatives encompassing broader organismal groups e.g., mammals, reptiles, microorganisms, plants, etc. is essential.