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Juchem DP, Schimani K, Holzinger A, Permann C, Abarca N, Skibbe O, Zimmermann J, Graeve M, Karsten U. Lipid degradation and photosynthetic traits after prolonged darkness in four Antarctic benthic diatoms, including the newly described species Planothidium wetzelii sp. nov. Front Microbiol 2023; 14:1241826. [PMID: 37720158 PMCID: PMC10500929 DOI: 10.3389/fmicb.2023.1241826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
In polar regions, the microphytobenthos has important ecological functions in shallow-water habitats, such as on top of coastal sediments. This community is dominated by benthic diatoms, which contribute significantly to primary production and biogeochemical cycling while also being an important component of polar food webs. Polar diatoms are able to cope with markedly changing light conditions and prolonged periods of darkness during the polar night in Antarctica. However, the underlying mechanisms are poorly understood. In this study, five strains of Antarctic benthic diatoms were isolated in the field, and the resulting unialgal cultures were identified as four distinct species, of which one is described as a new species, Planothidium wetzelii sp. nov. All four species were thoroughly examined using physiological, cell biological, and biochemical methods over a fully controlled dark period of 3 months. The results showed that the utilization of storage lipids is one of the key mechanisms in Antarctic benthic diatoms to survive the polar night, although different fatty acids were involved in the investigated taxa. In all tested species, the storage lipid content declined significantly, along with an ultrastructurally observable degradation of the chloroplasts. Surprisingly, photosynthetic performance did not change significantly despite chloroplasts decreasing in thylakoid membranes and an increased number of plastoglobules. Thus, a combination of biochemical and cell biological mechanisms allows Antarctic benthic diatoms to survive the polar night.
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Affiliation(s)
- Desirée P. Juchem
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Katherina Schimani
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Andreas Holzinger
- Department of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, Austria
| | - Charlotte Permann
- Department of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, Austria
| | - Nélida Abarca
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Oliver Skibbe
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Jonas Zimmermann
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Martin Graeve
- Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research, Ecological Chemistry, Bremerhaven, Germany
| | - Ulf Karsten
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
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Levesque-Beaudin V, Miller ME, Dikow T, Miller SE, Prosser SW, Zakharov EV, McKeown JT, Sones JE, Redmond NE, Coddington JA, Santos BF, Bird J, deWaard JR. A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections. Biodivers Data J 2023; 11:e100677. [PMID: 38327333 PMCID: PMC10848567 DOI: 10.3897/bdj.11.e100677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/20/2023] [Indexed: 02/09/2024] Open
Abstract
Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.
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Affiliation(s)
- Valerie Levesque-Beaudin
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Meredith E. Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Jaclyn T.A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jayme E. Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Niamh E Redmond
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jonathan A. Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Bernardo F. Santos
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jessica Bird
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
- School of Environmental Sciences, University of Guelph, Guelph, CanadaSchool of Environmental Sciences, University of GuelphGuelphCanada
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3
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Santos BF, Miller ME, Miklasevskaja M, McKeown JTA, Redmond NE, Coddington JA, Bird J, Miller SE, Smith A, Brady SG, Buffington ML, Chamorro ML, Dikow T, Gates MW, Goldstein P, Konstantinov A, Kula R, Silverson ND, Solis MA, deWaard SL, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Sones JE, Zakharov EV, deWaard JR. Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History. Biodivers Data J 2023; 11:e100904. [PMID: 38327288 PMCID: PMC10848724 DOI: 10.3897/bdj.11.e100904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 02/09/2024] Open
Abstract
The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian's National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximise sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,737 determined species in 3,886 genera and 205 families distributed in 137 countries. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximise output and minimise cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.
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Affiliation(s)
- Bernardo F. Santos
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UAParisFrance
| | - Meredith E. Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Margarita Miklasevskaja
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jaclyn T. A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Niamh E. Redmond
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jonathan A. Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jessica Bird
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Ashton Smith
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Seán G. Brady
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Matthew L. Buffington
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - M. Lourdes Chamorro
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Michael W. Gates
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Paul Goldstein
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Alexander Konstantinov
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Robert Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Nicholas D. Silverson
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - M. Alma Solis
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Stephanie L. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jayme E. Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Jeremy R. deWaard
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- School of Environmental Sciences, University of Guelph, Guelph, CanadaSchool of Environmental Sciences, University of GuelphGuelphCanada
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4
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Angeles NAC, Catap ES. Challenges on the Development of Biodiversity Biobanks: The Living Archives of Biodiversity. Biopreserv Biobank 2023; 21:5-13. [PMID: 35133889 DOI: 10.1089/bio.2021.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Biodiversity biobanks or ex situ biodiversity biorepositories tend to receive less attention compared with their biomedical counterparts. In this review, we highlight the necessity for these biorepositories by presenting their significant role in health, biodiversity, linking of big data, other translational research, and biodiversity conservation efforts. Moreover, the significant challenges in developing and maintaining biodiversity biobanks based on successful biobanks in some megadiverse developing countries are examined to provide insights into what needs to be done and what can be improved by up-and-coming biodiversity biobanks. These challenges include lack of financial support and political will; availability of experts; development of standard policies; and information management system. In addition, issues regarding access and benefit sharing and Digital Sequence Information must be addressed by biodiversity biobanks.
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Affiliation(s)
- Nestly Anne C Angeles
- Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines.,Department of Science and Technology-Science Education Institute, Taguig, Philippines
| | - Elena S Catap
- Functional Bioactivity Screening Lab, Institute of Biology, College of Science National Science Complex, University of the Philippines-Diliman, Quezon City, Philippines
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5
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González-Toral C, Cires E. Relevance of DNA preservation for future botany and ecology. Mol Ecol 2022; 31:5125-5131. [PMID: 36214196 DOI: 10.1111/mec.16652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/20/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
The use of molecular methods in plant systematics and taxonomy has increased during the last decades; however, the accessibility of curated genetic samples and their metadata is a bottleneck for DNA-based genetic studies in botany. Plant biodiversity DNA banks and DNA-friendly collections could be critical suppliers of curated genetic material for researchers in the current context of plant biodiversity loss. Here, we aimed to understand the potential of plant DNA banks and DNA-friendly collections to enhance the growth and openness of scientific knowledge. The preservation of genetic material should become part of a natural collection's process for the generation of extended specimens enabling the preservation of both the phenotype and genotype and contributing to the generation of data networks which cross-fertilize other fields. These curated collections are advantageous in endangered species research, detecting processes related to extinction, giving a genetic dimension to IUCN assessments or completing the Leipzig Catalogue of Vascular Plants. Therefore, DNA collections are fundamental in producing FAIR data, responsible research and innovation (RRI) and meeting the goals of international conservation programmes. The completion of natural collections is important for current research efforts and furthermore vital to support future research in an era of ongoing plant biodiversity loss.
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Affiliation(s)
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain.,Institute of Natural Resources and Territorial Planning (INDUROT), Mieres, Spain
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6
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Toh EC, Liu KL, Tsai S, Lin C. Cryopreservation and Cryobanking of Cells from 100 Coral Species. Cells 2022; 11:cells11172668. [PMID: 36078076 PMCID: PMC9454506 DOI: 10.3390/cells11172668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
When coral species become extinct, their genetic resources cannot be recovered. Coral cryobanks can be employed to preserve coral samples and thereby maintain the availability of the samples and increase their potential to be restocked. In this study, we developed a procedure to determine coral species-specific requirements for cryobank freezing through determining suitable cryoprotective agents (CPAs), CPA concentrations, equilibration times, holding durations, viability rates, and cell amounts for banked coral cells, and we established the first ever coral cell cryobank. Coral cells, including supporting and gland cells, epidermal nematocysts, Symbiodiniaceae and symbiotic endoderm cells (SEC) were found from the extracted protocol. Approximately half of the corals from the experimental corals consisted of spindle and cluster cells. Gastrodermal nematocysts were the least common. The overall concentration of Symbiodiniaceae in the coral cells was 8.6%. Freezing using DMSO as a CPA was suitable for approximately half of the corals, and for the other half of species, successful cell cryopreservation was achieved using MeOH and EG. EG and DMSO had similar suitabilities for Acanthastrea, Euphyllia, Favites, Lobophyllia, Pavona, Seriatopora, and Turbinaria, as did EG and MeOH for Acropora, Echinopyllia, and Sinularia and MeOH and DMSO for Platygyra after freezing. At least 14 straws from each species of coral were cryobanked in this study, totaling more than 1884 straws (0.5 mL) with an average concentration of 6.4 × 106 per mL. The results of this study may serve as a framework for cryobanks worldwide and contribute to the long-term conservation of coral reefs.
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Affiliation(s)
- En-Chun Toh
- Institute of Marine Biology, National Dong Hwa University, Pingtung 944401, Taiwan
| | - Kuan-Lin Liu
- Institute of Marine Biology, National Dong Hwa University, Pingtung 944401, Taiwan
| | - Sujune Tsai
- Department of Post Modern Agriculture, Mingdao University, Peetow, Changhua 52345, Taiwan
- Correspondence: (S.T.); (C.L.); Tel.: +886-925750025 (S.T.); +886-08-88825036 (C.L.)
| | - Chiahsin Lin
- Institute of Marine Biology, National Dong Hwa University, Pingtung 944401, Taiwan
- National Museum of Marine Biology & Aquarium, Checheng, Pingtung 944, Taiwan
- Correspondence: (S.T.); (C.L.); Tel.: +886-925750025 (S.T.); +886-08-88825036 (C.L.)
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7
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Waterhouse RM, Adam-Blondon AF, Agosti D, Baldrian P, Balech B, Corre E, Davey RP, Lantz H, Pesole G, Quast C, Glöckner FO, Raes N, Sandionigi A, Santamaria M, Addink W, Vohradsky J, Nunes-Jorge A, Willassen NP, Lanfear J. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR. F1000Res 2022; 10. [PMID: 35999898 PMCID: PMC9360911 DOI: 10.12688/f1000research.73825.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 12/03/2022] Open
Abstract
Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.
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Affiliation(s)
- Robert M. Waterhouse
- Department of Ecology and Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Vaud, 1015, Switzerland
| | | | | | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Praha, 142 20, Czech Republic
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, 70126, Italy
| | - Erwan Corre
- CNRS/Sorbonne Université, Station Biologique de Roscoff, Roscoff, 29680, France
| | | | - Henrik Lantz
- Department of Medical Biochemistry and Microbiology/NBIS, Uppsala University, Uppsala, Sweden
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, 70126, Italy
- Department of Biosciences. Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Bari, 70126, Italy
| | - Christian Quast
- Life Sciences & Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| | - Frank Oliver Glöckner
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremerhaven, 27570, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Bremerhaven, 27570, Germany
| | - Niels Raes
- NLBIF - Netherlands Biodiversity Information Facility, Naturalis Biodiversity Center, Leiden, 2300 RA, The Netherlands
| | | | - Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, 70126, Italy
| | - Wouter Addink
- DiSSCo - Distributed System of Scientific Collections, Naturalis Biodiversity Center, Leiden, 2300 RA, The Netherlands
| | - Jiri Vohradsky
- Laboratory of Bioinformatics, Institute of Microbiology, Prague, 142 20, Czech Republic
| | | | | | - Jerry Lanfear
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
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8
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Prelle LR, Schmidt I, Schimani K, Zimmermann J, Abarca N, Skibbe O, Juchem D, Karsten U. Photosynthetic, Respirational, and Growth Responses of Six Benthic Diatoms from the Antarctic Peninsula as Functions of Salinity and Temperature Variations. Genes (Basel) 2022; 13:genes13071264. [PMID: 35886047 PMCID: PMC9324188 DOI: 10.3390/genes13071264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
Temperature and salinity are some of the most influential abiotic parameters shaping biota in aquatic ecosystems. In recent decades, climate change has had a crucial impact on both factors—especially around the Antarctic Peninsula—with increasing air and water temperature leading to glacial melting and the accompanying freshwater increase in coastal areas. Antarctic soft and hard bottoms are typically inhabited by microphytobenthic communities, which are often dominated by benthic diatoms. Their physiology and primary production are assumed to be negatively affected by increased temperatures and lower salinity. In this study, six representative benthic diatom strains were isolated from different aquatic habitats at King George Island, Antarctic Peninsula, and comprehensively identified based on molecular markers and morphological traits. Photosynthesis, respiration, and growth response patterns were investigated as functions of varying light availability, temperature, and salinity. Photosynthesis−irradiance curve measurements pointed to low light requirements, as light-saturated photosynthesis was reached at <70 µmol photons m−2 s−1. The marine isolates exhibited the highest effective quantum yield between 25 and 45 SA (absolute salinity), but also tolerance to lower and higher salinities at 1 SA and 55 SA, respectively, and in a few cases even <100 SA. In contrast, the limnic isolates showed the highest effective quantum yield at salinities ranging from 1 SA to 20 SA. Almost all isolates exhibited high effective quantum yields between 1.5 °C and 25 °C, pointing to a broad temperature tolerance, which was supported by measurements of the short-term temperature-dependent photosynthesis. All studied Antarctic benthic diatoms showed activity patterns over a broader environmental range than they usually experience in situ. Therefore, it is likely that their high ecophysiological plasticity represents an important trait to cope with climate change in the Antarctic Peninsula.
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Affiliation(s)
- Lara R. Prelle
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
| | - Ina Schmidt
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
| | - Katherina Schimani
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Jonas Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Nelida Abarca
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Oliver Skibbe
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Desiree Juchem
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
| | - Ulf Karsten
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
- Correspondence:
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9
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Salim JA, Saraiva AM, Zermoglio PF, Agostini K, Wolowski M, Drucker DP, Soares FM, Bergamo PJ, Varassin IG, Freitas L, Maués MM, Rech AR, Veiga AK, Acosta AL, Araujo AC, Nogueira A, Blochtein B, Freitas BM, Albertini BC, Maia-Silva C, Nunes CEP, Pires CSS, dos Santos CF, Queiroz EP, Cartolano EA, de Oliveira FF, Amorim FW, Fontúrbel FE, da Silva GV, Consolaro H, Alves-dos-Santos I, Machado IC, Silva JS, Aleixo KP, Carvalheiro LG, Rocca MA, Pinheiro M, Hrncir M, Streher NS, Ferreira PA, de Albuquerque PMC, Maruyama PK, Borges RC, Giannini TC, Brito VLG. Data standardization of plant-pollinator interactions. Gigascience 2022; 11:6593428. [PMID: 35639882 PMCID: PMC9154084 DOI: 10.1093/gigascience/giac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing. Results Here we present a vocabulary of terms and a data model for sharing plant–pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant–pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant–pollinator interactions. Conclusions The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant–pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant–pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of terms.
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Affiliation(s)
- José A Salim
- Correspondence authors. José A. Salim. Universidade Estadual de Campinas Instituto de Biologia Departamento de Biologia Vegetal Rua Monteiro Lobato, 255, Phone +55 (19) 3521-6166. E-mail:
| | - Antonio M Saraiva
- Correspondence authors. Antonio M. Saraiva. Laboratório de Automação Agrícola - Escola Politécnica da USP Av. Prof. Luciano Gualberto, travessa 3, nº 158, sala C2-56 Edifício de Engenharia Elétrica Cidade Universitária - São Paulo - SP CEP 05508-900 Fone: +55 (11) 3091-5366 Fax: +55 (11) 3091-5294. E-mail:
| | - Paula F Zermoglio
- Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Kayna Agostini
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Rodovia Anhanguera km 174, Araras, São Paulo, Caixa Postal 153. CEP 13600-970, Brazil
| | - Marina Wolowski
- Instituto de Ciências da Natureza, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva 700, Alfenas, Minas Gerais, 37130-001, Brazil
| | - Debora P Drucker
- Embrapa Agricultura Digital, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Campinas, SP, Brazil
| | - Filipi M Soares
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Pedro J Bergamo
- Jardim Botânico do Rio de Janeiro, R. Pacheco Leão 915, Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - Isabela G Varassin
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Leandro Freitas
- Jardim Botânico do Rio de Janeiro, R. Pacheco Leão 915, Rio de Janeiro, Rio de Janeiro, 22460-030, Brazil
| | - Márcia M Maués
- Laboratório de Entomologia, Embrapa Amazônia Oriental, Trav. Dr. Enéas Pinheiro, s/n°, Bairro do Marco, Belém, Pará, 66095-903, Brazil
| | - Andre R Rech
- Faculdade Interdisciplinar de Humanidades, Centro Multiusuário de Pesquisa em Ciência Florestal (MULTIFLOR), Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, 39100-000, Brazil
| | - Allan K Veiga
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Andre L Acosta
- Instituto Tecnológico Vale. Rua Boaventura da Silva, 955, 66055-900, Belém, Pará, Brazil
| | - Andréa C Araujo
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Anselmo Nogueira
- Laboratório de Interações Plant-Animal (LIPA), Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC, Alameda da Universidade, s/nº, Anchieta, São Bernardo do Campo, São Paulo, Brazil
| | - Betina Blochtein
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 90619-900, Brazil
| | - Breno M Freitas
- Departamento de Zootecnia, Campus Universitário do Pici, Universidade Federal do Ceará, Centro de Ciências Agrárias, Fortaleza, CE, Brazil
| | - Bruno C Albertini
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Camila Maia-Silva
- Departamento de Biociências, Universidade Federal Rural do Semi-Árido, Av. Francisco Mota, n° 572, Presidente Costa e Silva, Mossoró, RN, 59625-900, Brazil
| | - Carlos E P Nunes
- Department of Biological and Environmental Sciences, Cottrell Building, University of Stirling, Stirling FK9 4LA, Scotland, United Kingdom
| | - Carmen S S Pires
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
| | - Charles F dos Santos
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, 90619-900, Brazil
| | - Elisa P Queiroz
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Etienne A Cartolano
- Escola Politécnica, Universidade de São Paulo, São Paulo, SP, 05508-010, Brazil
| | - Favízia F de Oliveira
- Laboratório de Bionomia, Biogeografia e Sistemática de Insetos (BIOSIS), Instituto de Biologia (IBIO), Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Felipe W Amorim
- Laboratório de Ecologia da Polinização e Interações (LEPI), Programa de Pós-graduação em Botânica, Programa de Pós-graduação em Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Francisco E Fontúrbel
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Gleycon V da Silva
- Programa de Pós-Graduação em Ecologia / INPA-V8 - Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, 69067-375, Manaus - AM, Brazil
| | - Hélder Consolaro
- Instituto de Biotecnologia, Universidade Federal de Catalão, Catalão, Goiás, Brazil
| | - Isabel Alves-dos-Santos
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Isabel C Machado
- Programa de Pós-Graduação em Biologia Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil
| | - Juliana S Silva
- Instituto Federal de Educação Ciência e Tecnologia de Mato Grosso, Avenida Sen. Filinto Müller, 953 - CEP: 78043-400 - Cuiabá, MT, Brazil
| | - Kátia P Aleixo
- Associação Brasileira de Estudos das Abelhas (A.B.E.L.H.A.), São Paulo, SP, 04535-001, Brazil
| | - Luísa G Carvalheiro
- Departamento de Ecologia, Universidade Federal de Goiás, Campus Samambaia, Goiânia, Brazil Centre for Ecology, Evolution and Environmental Changes (cE3c), University of Lisboa, Lisbon, Portugal
| | - Márcia A Rocca
- Departamento de Ecologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Sergipe, Avenida Marechal Rondon s/n, São Cristóvão, Sergipe, 49100-000, Brazil
| | - Mardiore Pinheiro
- Universidade Federal da Fronteira Sul, R. Major Antônio Cardoso 590, Cerro Largo, Rio Grande do Sul, 97900-000, Brazil
| | - Michael Hrncir
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 321, Travessa 14, São Paulo, São Paulo, 05508-900, Brazil
| | - Nathália S Streher
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA,15260, United States of America
| | - Patricia A Ferreira
- Environmental Sciences Department, Federal University of São Carlos, São Paulo, Brazil
| | | | - Pietro K Maruyama
- Centro de Síntese Ecológica e Conservação, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafael C Borges
- Instituto Tecnológico Vale. Rua Boaventura da Silva, 955, 66055-900, Belém, Pará, Brazil
| | - Tereza C Giannini
- Instituto Tecnológico Vale. Rua Boaventura da Silva, 955, 66055-900, Belém, Pará, Brazil
| | - Vinícius L G Brito
- Instituto de Biologia, Universidade Federal de Uberlândia, Rua Ceará sn, Uberlândia, Minas Gerais, 38.405-302, Brazil
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10
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Kress WJ, Soltis DE, Kersey PJ, Wegrzyn JL, Leebens-Mack JH, Gostel MR, Liu X, Soltis PS. Green plant genomes: What we know in an era of rapidly expanding opportunities. Proc Natl Acad Sci U S A 2022; 119:e2115640118. [PMID: 35042803 PMCID: PMC8795535 DOI: 10.1073/pnas.2115640118] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.
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Affiliation(s)
- W John Kress
- National Museum of Natural History, Smithsonian Institution, Department of Botany, Washington, DC 20013-7012;
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
- Arnold Arboretum, Harvard University, Boston, MA 02130
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
- Department of Biology, University of Florida, Gainesville, FL 32611
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, Institute for Systems Genomics: Computational Biology Core, University of Connecticut, Storrs, CT 06269-3214
| | - James H Leebens-Mack
- Department of Plant Biology, 2101 Miller Plant Sciences, University of Georgia, Athens, GA 30602-7271
| | - Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, TX 76107-3400
| | - Xin Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
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11
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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12
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de Santana CD, Parenti LR, Dillman CB, Coddington JA, Bastos DA, Baldwin CC, Zuanon J, Torrente-Vilara G, Covain R, Menezes NA, Datovo A, Sado T, Miya M. The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes. Sci Rep 2021; 11:18159. [PMID: 34518574 PMCID: PMC8438044 DOI: 10.1038/s41598-021-97128-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.
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Affiliation(s)
- C David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.
| | - Lynne R Parenti
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Casey B Dillman
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Douglas A Bastos
- Programa de Pós-Graduação em Ciências Biológicas (BADPI), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Carole C Baldwin
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Gislene Torrente-Vilara
- Instituto do Mar, Universidade Federal de São Paulo, Campus Baixada Santista, Santos, São Paulo, Brazil
| | - Raphaël Covain
- Museum of Natural History, Department of Herpetology and Ichthyology, route de Malagnou 1, PO Box 6434, 1211, Geneva 6, Switzerland
| | - Naércio A Menezes
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - Aléssio Datovo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - T Sado
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
| | - M Miya
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
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13
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Guo X, Chen F, Gao F, Li L, Liu K, You L, Hua C, Yang F, Liu W, Peng C, Wang L, Yang X, Zhou F, Tong J, Cai J, Li Z, Wan B, Zhang L, Yang T, Zhang M, Yang L, Yang Y, Zeng W, Wang B, Wei X, Xu X. CNSA: a data repository for archiving omics data. Database (Oxford) 2021; 2020:5875523. [PMID: 32705130 PMCID: PMC7377928 DOI: 10.1093/database/baaa055] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/31/2020] [Accepted: 06/25/2020] [Indexed: 12/16/2022]
Abstract
With the application and development of high-throughput sequencing technology in life and health sciences, massive multi-omics data brings the problem of efficient management and utilization. Database development and biocuration are the prerequisites for the reuse of these big data. Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its further analyzed results which are organized into six objects, namely Project, Sample, Experiment, Run, Assembly and Variation at present. Moreover, CNSA has created a correlation model of living samples, sample information and analytical data on some projects. Both living samples and analytical data are directly correlated with the sample information. From either one, information or data of the other two can be obtained, so that all data can be traced throughout the life cycle from the living sample to the sample information to the analytical data. Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for storing, managing and sharing of omics data. We will continue to improve the data standards and provide free access to open-data resources for worldwide scientific communities to support academic research and the bio-industry. Database URL: https://db.cngb.org/cnsa/.
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Affiliation(s)
- Xueqin Guo
- China National GeneBank, Shenzhen 518120, China
| | | | - Fei Gao
- China National GeneBank, Shenzhen 518120, China
| | - Ling Li
- China National GeneBank, Shenzhen 518120, China
| | - Ke Liu
- China National GeneBank, Shenzhen 518120, China
| | - Lijin You
- China National GeneBank, Shenzhen 518120, China
| | - Cong Hua
- China National GeneBank, Shenzhen 518120, China
| | - Fan Yang
- China National GeneBank, Shenzhen 518120, China
| | | | | | - Lina Wang
- China National GeneBank, Shenzhen 518120, China
| | | | - Feiyu Zhou
- China National GeneBank, Shenzhen 518120, China
| | - Jiawei Tong
- China National GeneBank, Shenzhen 518120, China
| | - Jia Cai
- China National GeneBank, Shenzhen 518120, China
| | - Zhiyong Li
- China National GeneBank, Shenzhen 518120, China
| | - Bo Wan
- China National GeneBank, Shenzhen 518120, China
| | - Lei Zhang
- China National GeneBank, Shenzhen 518120, China
| | - Tao Yang
- China National GeneBank, Shenzhen 518120, China
| | | | - Linlin Yang
- China National GeneBank, Shenzhen 518120, China
| | - Yawen Yang
- China National GeneBank, Shenzhen 518120, China
| | - Wenjun Zeng
- China National GeneBank, Shenzhen 518120, China
| | - Bo Wang
- China National GeneBank, Shenzhen 518120, China
| | | | - Xun Xu
- China National GeneBank, Shenzhen 518120, China.,BGI-Shenzhen, Shenzhen 518083, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
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14
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Dimitrova M, Meyer R, Buttigieg PL, Georgiev T, Zhelezov G, Demirov S, Smith V, Penev L. A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers. Gigascience 2021; 10:6275150. [PMID: 33983435 PMCID: PMC8117446 DOI: 10.1093/gigascience/giab034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 11/30/2020] [Accepted: 04/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer review and increases the impact of datasets by enhancing their visibility, accessibility, and reusability. Objective We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivize researchers to publish well-described datasets, we created a prototype workflow for streamlined import of genomics metadata from the European Nucleotide Archive directly into a data paper manuscript. Methods An omics data paper template was designed by defining key article sections that encourage the description of omics datasets and methodologies. A metadata import workflow, based on REpresentational State Transfer services and Xpath, was prototyped to extract information from the European Nucleotide Archive, ArrayExpress, and BioSamples databases. Findings The template and workflow for automatic import of standard-compliant metadata into an omics data paper manuscript provide a mechanism for enhancing existing metadata through publishing. Conclusion The omics data paper structure and workflow for import of genomics metadata will help to bring genomic and other omics datasets into the spotlight. Promoting enhanced metadata descriptions and enforcing manuscript peer review and data auditing of the underlying datasets brings additional quality to datasets. We hope that streamlined metadata reuse for scholarly publishing encourages authors to create enhanced metadata descriptions in the form of data papers to improve both the quality of their metadata and its findability and accessibility.
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Affiliation(s)
- Mariya Dimitrova
- Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria.,Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Acad. G. Bonchev St., Block 25A, 1113 Sofia, Bulgaria
| | - Raïssa Meyer
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Pier Luigi Buttigieg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Teodor Georgiev
- Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria
| | - Georgi Zhelezov
- Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria
| | | | - Vincent Smith
- The Natural History Museum, Cromwell Rd, South Kensington, SW7 5BD London, UK
| | - Lyubomir Penev
- Pensoft Publishers, Prof. Georgi Zlatarski Street 12, 1700 Sofia, Bulgaria.,Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin St., 1113 Sofia, Bulgaria
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15
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Blom MPK. Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing. Mol Ecol 2021; 30:5935-5948. [PMID: 33786900 DOI: 10.1111/mec.15909] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.
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Affiliation(s)
- Mozes P K Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
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16
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Collins JE, Rabone M, Vanagt T, Amon DJ, Gobin J, Huys I. Strengthening the global network for sharing of marine biological collections: recommendations for a new agreement for biodiversity beyond national jurisdiction. ICES J Mar Sci 2021; 78:305-314. [PMID: 33814897 PMCID: PMC7988798 DOI: 10.1093/icesjms/fsaa227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/28/2020] [Accepted: 11/04/2020] [Indexed: 11/13/2022]
Abstract
Biological collections are fundamental to marine scientific research and understanding of biodiversity at various scales. Despite their key importance, sample collections and the institutes that house them are often underfunded and receive comparatively little attention in the discussions associated with global biodiversity agreements. Furthermore, access to collections can be limited by inadequate systems, infrastructure, and networks. With negotiations underway for a new implementing agreement on biodiversity beyond national jurisdiction, marine genetic resources (MGR), including questions on the sharing of benefits, remains the most debated and contentious element. Disparities remain between States regarding access to and utilization of marine biological samples (including MGR) from areas beyond national jurisdiction. Addressing capacity gaps related to collections could provide a point of agreement during negotiations and enhance global inclusivity in access to and utilization of MGR. Here, we examine both existing capacity and regional gaps in marine collections. We propose the strengthening of a distributed network of marine biological collections, building on existing initiatives and emphasizing best practices to bridge regional gaps. Our recommendations include: promoting scientific best practice for the curation of collections; alignment with ocean observing, and sampling initiatives; a potential pairing scheme for collections in developing and developed States; raising awareness of collections and benefits to marine science including through a global registry/directory; and promoting sustainable funding mechanisms to support collections and sustain global generation of contributors and users.
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Affiliation(s)
- Jane Eva Collins
- ABSint, Bruges, Belgium
- Faculty of Pharmaceutical Sciences, Clinical Pharmacology and Pharmacotherapy, KU Leuven, Leuven, Belgium
| | - Muriel Rabone
- Life Sciences Department, Natural History Museum, London, UK
| | | | - Diva J Amon
- Life Sciences Department, Natural History Museum, London, UK
| | - Judith Gobin
- Department of Life Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Isabelle Huys
- Faculty of Pharmaceutical Sciences, Clinical Pharmacology and Pharmacotherapy, KU Leuven, Leuven, Belgium
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17
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Lopez L, Turner KG, Bellis ES, Lasky JR. Genomics of natural history collections for understanding evolution in the wild. Mol Ecol Resour 2020; 20:1153-1160. [DOI: 10.1111/1755-0998.13245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Lua Lopez
- Department of Biology California State University San Bernardino San Bernardino CaliforniaUSA
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
| | - Kathryn G. Turner
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
- Department of Biological Sciences Idaho State University Pocatello IdahoUSA
| | - Emily S. Bellis
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
- Arkansas Biosciences Institute & Department of Computer Science Arkansas State University Jonesboro ArkansasUSA
| | - Jesse R. Lasky
- Department of Biology Pennsylvania State University University Park PennsylvaniaUSA
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18
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Fitak RR, Antonides JD, Baitchman EJ, Bonaccorso E, Braun J, Kubiski S, Chiu E, Fagre AC, Gagne RB, Lee JS, Malmberg JL, Stenglein MD, Dusek RJ, Forgacs D, Fountain-Jones NM, Gilbertson MLJ, Worsley-Tonks KEL, Funk WC, Trumbo DR, Ghersi BM, Grimaldi W, Heisel SE, Jardine CM, Kamath PL, Karmacharya D, Kozakiewicz CP, Kraberger S, Loisel DA, McDonald C, Miller S, O'Rourke D, Ott-Conn CN, Páez-Vacas M, Peel AJ, Turner WC, VanAcker MC, VandeWoude S, Pecon-Slattery J. The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise. J Hered 2020; 110:261-274. [PMID: 31067326 DOI: 10.1093/jhered/esz001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 01/08/2019] [Indexed: 12/14/2022] Open
Abstract
The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented "Big Data" tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural "Genomics of Disease in Wildlife" workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) "Improving communication," 2) "Methodological and analytical advancements," 3) "Translation into practice," 4) "Integrating landscape ecology and genomics," and 5) "Emerging new questions." Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.
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Affiliation(s)
| | - Jennifer D Antonides
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN
| | - Eric J Baitchman
- The Zoo New England Division of Animal Health and Conservation, Boston, MA
| | - Elisa Bonaccorso
- The Instituto BIOSFERA and Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, vía Interoceánica y Diego de Robles, Quito, Ecuador
| | - Josephine Braun
- The Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Steven Kubiski
- The Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Elliott Chiu
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Anna C Fagre
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Roderick B Gagne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Justin S Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Jennifer L Malmberg
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Robert J Dusek
- The U. S. Geological Survey, National Wildlife Health Center, Madison, WI
| | - David Forgacs
- The Interdisciplinary Graduate Program of Genetics, Texas A&M University, College Station, TX
| | | | - Marie L J Gilbertson
- The Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN
| | | | - W Chris Funk
- The Department of Biology, Colorado State University, Fort Collins, CO
| | - Daryl R Trumbo
- The Department of Biology, Colorado State University, Fort Collins, CO
| | | | | | - Sara E Heisel
- The Odum School of Ecology, University of Georgia, Athens, GA
| | - Claire M Jardine
- The Department of Pathobiology, Canadian Wildlife Health Cooperative, University of Guelph, Guelph, Ontario, Canada
| | - Pauline L Kamath
- The School of Food and Agriculture, University of Maine, Orono, ME
| | | | | | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
| | - Dagan A Loisel
- The Department of Biology, Saint Michael's College, Colchester, VT
| | - Cait McDonald
- The Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY (McDonald)
| | - Steven Miller
- The Department of Biology, Drexel University, Philadelphia, PA
| | | | - Caitlin N Ott-Conn
- The Michigan Department of Natural Resources, Wildlife Disease Laboratory, Lansing, MI
| | - Mónica Páez-Vacas
- The Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, Ecuador
| | - Alison J Peel
- The Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Wendy C Turner
- The Department of Biological Sciences, University at Albany, State University of New York, Albany, NY
| | - Meredith C VanAcker
- The Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY
| | - Sue VandeWoude
- The College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Jill Pecon-Slattery
- The Center for Species Survival, Smithsonian Conservation Biology Institute-National Zoological Park, Front Royal, VA
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19
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Bakker FT, Antonelli A, Clarke JA, Cook JA, Edwards SV, Ericson PGP, Faurby S, Ferrand N, Gelang M, Gillespie RG, Irestedt M, Lundin K, Larsson E, Matos-Maraví P, Müller J, von Proschwitz T, Roderick GK, Schliep A, Wahlberg N, Wiedenhoeft J, Källersjö M. The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ 2020; 8:e8225. [PMID: 32025365 PMCID: PMC6993751 DOI: 10.7717/peerj.8225] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/15/2019] [Indexed: 12/27/2022] Open
Abstract
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.
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Affiliation(s)
- Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Julia A Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, United States of America
| | - Joseph A Cook
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Nuno Ferrand
- Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Magnus Gelang
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Rosemary G Gillespie
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Kennet Lundin
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Johannes Müller
- Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Ted von Proschwitz
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - George K Roderick
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alexander Schliep
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | | | - John Wiedenhoeft
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | - Mari Källersjö
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Botanical Garden, Göteborg, Sweden
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20
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Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O'Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford) 2020; 2020:baaa062. [PMID: 32761142 PMCID: PMC7408187 DOI: 10.1093/database/baaa062] [Citation(s) in RCA: 615] [Impact Index Per Article: 153.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/04/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022]
Abstract
The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy.
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Affiliation(s)
- Conrad L Schoch
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Stacy Ciufo
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Mikhail Domrachev
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Carol L Hotton
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Sivakumar Kannan
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Rogneda Khovanskaya
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Detlef Leipe
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard Mcveigh
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Kathleen O'Neill
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Barbara Robbertse
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Shobha Sharma
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Vladimir Soussov
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - John P Sullivan
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Lu Sun
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Seán Turner
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
| | - Ilene Karsch-Mizrachi
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD 20892, USA
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21
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deWaard JR, Ratnasingham S, Zakharov EV, Borisenko AV, Steinke D, Telfer AC, Perez KHJ, Sones JE, Young MR, Levesque-Beaudin V, Sobel CN, Abrahamyan A, Bessonov K, Blagoev G, deWaard SL, Ho C, Ivanova NV, Layton KKS, Lu L, Manjunath R, McKeown JTA, Milton MA, Miskie R, Monkhouse N, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Radulovici AE, Steinke C, Warne CP, Hebert PDN. A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples. Sci Data 2019; 6:308. [PMID: 31811161 PMCID: PMC6897906 DOI: 10.1038/s41597-019-0320-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
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Affiliation(s)
- Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Alex V Borisenko
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Arusyak Abrahamyan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kara K S Layton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ocean Frontier Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Norm Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Connor P Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.
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22
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Petersen M, Glöckler F, Hoffmann J. Harmonizing plot data with collection data. RIO 2019. [DOI: 10.3897/rio.5.e33509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although plot or monitoring data are quite often associated with objects collected in the plot and stored in specific collections, controlled vocabularies currently available do not cover both disciplines. This situation limits the possibility to publish common data sets and consequently brings a loss of significant information by combining plot-based research with collection object associated data. To facilitate the exchange and publication of these important data sets, experts in natural history collection data, ecological research, and environmental science met for a one-day workshop in Berlin. The participants discussed data standards and ontologies relevant for each discipline and collected requirements for a first application schema covering terms important for both, collection object related data and plot-based research.
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23
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Rambold G, Yilmaz P, Harjes J, Klaster S, Sanz V, Link A, Glöckner FO, Triebel D. Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research. Database (Oxford) 2019; 2019:5303972. [PMID: 30715273 PMCID: PMC6354027 DOI: 10.1093/database/baz002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
With the advent of advanced molecular meta-omics techniques and methods, a new era commenced for analysing and characterizing historic collection specimens, as well as recently collected environmental samples. Nucleic acid and protein sequencing-based analyses are increasingly applied to determine the origin, identity and traits of environmental (biological) objects and organisms. In this context, the need for new data structures is evident and former approaches for data processing need to be expanded according to the new meta-omics techniques and operational standards. Existing schemas and community standards in the biodiversity and molecular domain concentrate on terms important for data exchange and publication. Detailed operational aspects of origin and laboratory as well as object and data management issues are frequently neglected. Meta-omics Data and Collection Objects (MOD-CO) has therefore been set up as a new schema for meta-omics research, with a hierarchical organization of the concepts describing collection samples, as well as products and data objects being generated during operational workflows. It is focussed on object trait descriptions as well as on operational aspects and thereby may serve as a backbone for R&D laboratory information management systems with functions of an electronic laboratory notebook. The schema in its current version 1.0 includes 653 concepts and 1810 predefined concept values, being equivalent to descriptors and descriptor states, respectively. It is published in several representations, like a Semantic Media Wiki publication with 2463 interlinked Wiki pages for concepts and concept values, being grouped in 37 concept collections and subcollections. The SQL database application DiversityDescriptions, a generic tool for maintaining descriptive data and schemas, has been applied for setting up and testing MOD-CO and for concept mapping on elements of corresponding schemas.
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Affiliation(s)
- Gerhard Rambold
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany
| | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany
| | - Janno Harjes
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany
| | - Sabrina Klaster
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany
| | - Veronica Sanz
- University of Bayreuth, Universitätsstraße 30, Bayreuth, Germany.,SNSB IT Center, Menzinger Straße 67, München, Germany
| | - Anton Link
- SNSB IT Center, Menzinger Straße 67, München, Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, Bremen, Germany.,Jacobs University, Campus Ring 1, Bremen, Germany
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Dormontt EE, van Dijk KJ, Bell KL, Biffin E, Breed MF, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill PG, Shapcott A, Young JM, Waycott M, Lowe AJ. Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00134] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP, Goldstein MM, Grigoriev IV, Hackett KJ, Haussler D, Jarvis ED, Johnson WE, Patrinos A, Richards S, Castilla-Rubio JC, van Sluys MA, Soltis PS, Xu X, Yang H, Zhang G. Earth BioGenome Project: Sequencing life for the future of life. Proc Natl Acad Sci U S A 2018; 115:4325-33. [PMID: 29686065 DOI: 10.1073/pnas.1720115115] [Citation(s) in RCA: 406] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.
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Abstract
With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.
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Affiliation(s)
- Andrew Edward Z Short
- Department of Ecology and Evolutionary Biology; and Division of Entomology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA;
| | - Torsten Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA;
| | - Corrie S Moreau
- Department of Science and Education, Field Museum of Natural History, Chicago, Illinois 60605, USA;
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Sharma S, Ciufo S, Starchenko E, Darji D, Chlumsky L, Karsch-Mizrachi I, Schoch CL. The NCBI BioCollections Database. Database (Oxford) 2018; 2018:4904552. [PMID: 29688360 PMCID: PMC5824777 DOI: 10.1093/database/bay006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 11/13/2022]
Abstract
The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses. The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections
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Affiliation(s)
- Shobha Sharma
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
| | - Elena Starchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
| | - Dakshesh Darji
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
| | - Larry Chlumsky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
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Abstract
Androgen receptor plays a pivotal role in prostate cancer progression, and androgen deprivation therapy to intercept androgen receptor signal pathway is an indispensable treatment for most advanced prostate cancer patients to delay cancer progression. However, the emerging of castration-resistant prostate cancer reminds us the alteration of androgen receptor, which includes androgen receptor mutation, the formation of androgen receptor variants, and androgen receptor distribution in cancer cells. In this review, we introduce the process of androgen receptor and also its variants' formation, translocation, and function alteration by protein modification or interaction with other pathways. We dissect the roles of androgen receptor in prostate cancer from molecular perspective to provide clues for battling prostate cancer, especially castration-resistant prostate cancer.
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Affiliation(s)
- Jieping Hu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Gongxian Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Mulcahy DG, Macdonald KS, Brady SG, Meyer C, Barker KB, Coddington J. Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA. PeerJ 2016; 4:e2528. [PMID: 27761327 DOI: 10.7287/peerj.preprints.2202v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/04/2016] [Indexed: 05/26/2023] Open
Abstract
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples-and their quantifiable metadata-preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall "genome-quality" DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA "greater than X kb" as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards ("DNA Threshold" and "Percent above Threshold") introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.
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Affiliation(s)
- Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution , Washingtion, DC , USA
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Katharine B Barker
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Jonathan Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washingtion, DC, USA
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31
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Mulcahy DG, Macdonald KS, Brady SG, Meyer C, Barker KB, Coddington J. Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA. PeerJ 2016; 4:e2528. [PMID: 27761327 PMCID: PMC5068448 DOI: 10.7717/peerj.2528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/04/2016] [Indexed: 12/02/2022] Open
Abstract
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall “genome-quality” DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA “greater than X kb” as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (“DNA Threshold” and “Percent above Threshold”) introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.
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Affiliation(s)
- Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution , Washingtion, DC , USA
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Katharine B Barker
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Jonathan Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washingtion, DC, USA
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