1
|
Overcast I, Noguerales V, Meramveliotakis E, Andújar C, Arribas P, Creedy TJ, Emerson BC, Vogler AP, Papadopoulou A, Morlon H. Inferring the ecological and evolutionary determinants of community genetic diversity. Mol Ecol 2023; 32:6093-6109. [PMID: 37221561 DOI: 10.1111/mec.16958] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species within a community, unlocking a new axis of data to potentially unveil the origins and maintenance of biodiversity at local scales. Here, we present a new eco-evolutionary simulation model for investigating community assembly dynamics using metabarcoding data. The model makes joint predictions of species abundance, genetic variation, trait distributions and phylogenetic relationships under a wide range of parameter settings (e.g. high speciation/low dispersal or vice versa) and across a range of community states, from pristine and unmodified to heavily disturbed. We first demonstrate that parameters governing metacommunity and local community processes leave detectable signatures in simulated biodiversity data axes. Next, using a simulation-based machine learning approach we show that neutral and non-neutral models are distinguishable and that reasonable estimates of several model parameters within the local community can be obtained using only community-scale genetic data, while phylogenetic information is required to estimate those describing metacommunity dynamics. Finally, we apply the model to soil microarthropod metabarcoding data from the Troodos mountains of Cyprus, where we find that communities in widespread forest habitats are structured by neutral processes, while high-elevation and isolated habitats act as an abiotic filter generating non-neutral community structure. We implement our model within the ibiogen R package, a package dedicated to the investigation of island, and more generally community-scale, biodiversity using community-scale genetic data.
Collapse
Affiliation(s)
- Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Víctor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| |
Collapse
|
2
|
Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [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: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
Collapse
Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| |
Collapse
|
3
|
Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [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: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
Collapse
Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
| | | |
Collapse
|
4
|
Nishimura O, Rozewicki J, Yamaguchi K, Tatsumi K, Ohishi Y, Ohta T, Yagura M, Niwa T, Tanegashima C, Teramura A, Hirase S, Kawaguchi A, Tan M, D'Aniello S, Castro F, Machado A, Koyanagi M, Terakita A, Misawa R, Horie M, Kawasaki J, Asahida T, Yamaguchi A, Murakumo K, Matsumoto R, Irisarri I, Miyamoto N, Toyoda A, Tanaka S, Sakamoto T, Semba Y, Yamauchi S, Yamada K, Nishida K, Kiyatake I, Sato K, Hyodo S, Kadota M, Uno Y, Kuraku S. Squalomix: shark and ray genome analysis consortium and its data sharing platform. F1000Res 2022; 11:1077. [PMID: 36262334 PMCID: PMC9561540 DOI: 10.12688/f1000research.123591.1] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.
Collapse
Affiliation(s)
- Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - John Rozewicki
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Tazro Ohta
- Joint Support-Center for Data Science Research, Database Center for Life Science, Mishima, Shizuoka, 411-8540, Japan
| | - Masaru Yagura
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Taiki Niwa
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Akinori Teramura
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Akane Kawaguchi
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Filipe Castro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal
| | - André Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Ryo Misawa
- Japan Fisheries Research and Education Agency, Hachinohe, Aomori, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Junna Kawasaki
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Takashi Asahida
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Atsuko Yamaguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
| | | | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature-Zoology, Hamburg, 20146, Germany
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sho Tanaka
- School of Marine Science and Technology, Tokai University, Shizuoka, Shizuoka, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi, Japan., Okayama, Japan
| | - Yasuko Semba
- Highly Migratory Resources Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shizuoka, Shizuoka, Japan
| | | | - Kazuyuki Yamada
- Marine Science Museum, Tokai University, Shizuoka, Shizuoka, Japan
| | | | | | - Keiichi Sato
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo,, Kashiwa, Chiba, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan,
| |
Collapse
|
5
|
Feron R, Waterhouse RM. Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes. Gigascience 2022; 11:6537158. [PMID: 35217859 PMCID: PMC8881204 DOI: 10.1093/gigascience/giac006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 10/27/2021] [Revised: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. FINDINGS Here we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets. CONCLUSIONS These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.
Collapse
Affiliation(s)
- Romain Feron
- Department of Ecology and Evolution, Le Biophore UNIL-Sorge, University of Lausanne, Lausanne 1015, Switzerland.,Evolutionary-Functional Genomics Group, L'Amphipole UNIL-Sorge, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Le Biophore UNIL-Sorge, University of Lausanne, Lausanne 1015, Switzerland.,Evolutionary-Functional Genomics Group, L'Amphipole UNIL-Sorge, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| |
Collapse
|
6
|
Tsuchiya MTN, Dikow RB, Cassin-Sackett L. First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague. Genome Biol Evol 2021; 12:618-625. [PMID: 32277812 PMCID: PMC7250503 DOI: 10.1093/gbe/evaa069] [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] [Accepted: 04/05/2020] [Indexed: 12/30/2022] Open
Abstract
Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America's grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison's prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels.
Collapse
Affiliation(s)
- Mirian T N Tsuchiya
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
| | | |
Collapse
|
7
|
Whibley A. Genome insights give cause for optimism in the ongoing battle to save the vaquita. Mol Ecol Resour 2021; 21:1005-1007. [PMID: 33539649 DOI: 10.1111/1755-0998.13345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 11/28/2022]
Abstract
Whilst the global threat to biodiversity is accelerating, recent advances in sequencing and assembly technologies, along with decreasing costs, are ushering in a golden age for biodiversity genomics. In a From the Cover article in this issue of Molecular Ecology Resources, Morin et al. report an exceptionally high-quality draft genome assembly of the vaquita (Phocoena sinus), a porpoise first described in 1958 and currently numbering fewer than 20 individuals in the wild. On the brink of extinction and described as critically endangered by the International Union for the Conservation of Nature (IUCN), a precipitous population decline since the 1990 s has been due to bycatch in gillnets in the Upper Gulf of California.
Collapse
Affiliation(s)
- Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| |
Collapse
|
8
|
Olsen LK, Heckenhauer J, Sproul JS, Dikow RB, Gonzalez VL, Kweskin MP, Taylor AM, Wilson SB, Stewart RJ, Zhou X, Holzenthal R, Pauls SU, Frandsen PB. Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera). Genome Biol Evol 2021; 13:6121109. [PMID: 33501983 PMCID: PMC7936034 DOI: 10.1093/gbe/evab013] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. Although Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving ∼275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least 3-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages.
Collapse
Affiliation(s)
- Lindsey K Olsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - John S Sproul
- Department of Biology, University of Rochester, New York, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Matthew P Kweskin
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Adam M Taylor
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Seth B Wilson
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA
| | - Russell J Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ralph Holzenthal
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, USA
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Department of Terrestrial Zoology, Entomology III, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany.,Institute of Insect Biotechnology, Justus-Liebig University, Gießen, Germany
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, USA.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| |
Collapse
|
9
|
Bohling J. Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets. Ecol Evol 2020; 10:7585-7601. [PMID: 32760550 PMCID: PMC7391306 DOI: 10.1002/ece3.6483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/24/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/29/2022] Open
Abstract
The advent of high-throughput sequencing (HTS) has made genomic-level analyses feasible for nonmodel organisms. A critical step of many HTS pipelines involves aligning reads to a reference genome to identify variants. Despite recent initiatives, only a fraction of species has publically available reference genomes. Therefore, a common practice is to align reads to the genome of an organism related to the target species; however, this could affect read alignment and bias genotyping. In this study, I conducted an experiment using empirical RADseq datasets generated for two species of salmonids (Actinopterygii; Teleostei; Salmonidae) to address these questions. There are currently reference genomes for six salmonids of varying phylogenetic distance. I aligned the RADseq data to all six genomes and identified variants with several different genotypers, which were then fed into population genetic analyses. Increasing phylogenetic distance between target species and reference genome reduced the proportion of reads that successfully aligned and mapping quality. Reference genome also influenced the number of SNPs that were generated and depth at those SNPs, although the affect varied by genotyper. Inferences of population structure were mixed: increasing reference genome divergence reduced estimates of differentiation but similar patterns of population relationships were found across scenarios. These findings reveal how the choice of reference genome can influence the output of bioinformatic pipelines. It also emphasizes the need to identify best practices and guidelines for the burgeoning field of biodiversity genomics.
Collapse
Affiliation(s)
- Justin Bohling
- Abernathy Fish Technology Center US Fish and Wildlife Service Longview WA USA
| |
Collapse
|
10
|
Seberg O, Droege G, Barker K, Coddington JA, Funk V, Gostel M, Petersen G, Smith PP. Global Genome Biodiversity Network: saving a blueprint of the Tree of Life - a botanical perspective. Ann Bot 2016; 118:393-9. [PMID: 27328683 PMCID: PMC4998982 DOI: 10.1093/aob/mcw121] [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] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/19/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples. SCOPE The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on 'harvesting' the Tree of Life for vascular plant taxa to enable genome-level studies. CONCLUSION While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic material from at least one species from each of the approx. 460 vascular plant families and one species from half of the approx. 15 000 vascular plant genera.
Collapse
Affiliation(s)
- O Seberg
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307 Copenhagen, Denmark
| | - G Droege
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14195 Berlin, Germany
| | - K Barker
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - J A Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - V Funk
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - M Gostel
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - G Petersen
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Sølvgade 83, opg. S, DK-1307 Copenhagen, Denmark
| | - P P Smith
- Botanic Gardens Conservation International, 199 Kew Road, Richmond TW9 3BW, Surrey, UK
| |
Collapse
|