Skip to main content
SpringerLink
Log in

MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems

  • Protocol
  • First Online:
DNA Barcoding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2744))

Abstract

The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.

This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases (https://metazoogene.org).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bucklin A, Lindeque PK, Rodriguez-Ezpeleta N, Albaina A, Lehtiniemi M (2016) Metabarcoding of marine zooplankton: Progress, prospects and pitfalls. J Plankton Res 38:393–400. https://doi.org/10.1093/plankt/fbw023

    Article  CAS  Google Scholar 

  2. Bucklin A, Peijnenburg KTCA, Kosobokova KN, O’Brien TD, Blanco-Bercial L, Cornils A, Falkenhaug T, Hopcroft RR, Hosia A, Laakmann S, Li C, Martell L, Questel JM, Wall-Palmer D, Wang M, Wiebe PH, Weydmann-Zwolicka A (2021) Toward a global reference database of COI barcodes for marine zooplankton. Mar Biol 168(78). https://doi.org/10.1007/s00227-021-03887-y

  3. Machida RJ, Leray M, Ho S-L, Knowlton N (2017) Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Sci Data 4:170027. https://doi.org/10.1038/sdata.2017.27

  4. Taberlet P, Bonin A, Zinger L, Coissac E (2018) References databases. In: Environmental DNA: for biodiversity research and monitoring. Oxford University Press, pp 21–27. https://doi.org/10.1093/oso/9780198767220.001.0001

    Chapter  Google Scholar 

  5. Bucklin A, Steinke D, Blanco-Bercial L (2011) DNA barcoding of marine metazoa. Annu Rev Mar Sci 3:471–508. https://doi.org/10.1146/annurev-marine-120308-080950

    Article  Google Scholar 

  6. Pinheiro HT, Moreau CS, Daly M, Rocha LA (2019) Will DNA barcoding meet taxonomic needs? Science 365:873–874

    Article  CAS  PubMed  Google Scholar 

  7. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al (2009) Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Caporaso J, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Gonzalez Peña A et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Callahan B, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. https://doi.org/10.1038/nmeth.3869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Closek CJ, Santora JA, Starks HA, Schroeder ID, Andruszkiewicz EA, Sakuma KM, Bograd SJ, Hazen EL, Field JC, Boehm AB (2019) Marine vertebrate biodiversity and distribution within the Central California current using environmental DNA (eDNA) metabarcoding and ecosystem surveys. Front Mar Sci 6:732. https://doi.org/10.3389/fmars.2019.00732

    Article  Google Scholar 

  11. Govindarajan AF, Francolini RD, Jech JM, Lavery AC, Llopiz JK, Wiebe PH, Zhang W (2021) Exploring the use of environmental DNA (eDNA) to detect animal taxa in the mesopelagic zone. Front Ecol Evol 9:574877. https://doi.org/10.3389/fevo.2021.574877

    Article  Google Scholar 

  12. Andres KJ, Lambert TD, Lodge DM, Andrés J, Jackson JR (2023) Combining sampling gear to optimally inventory species highlights the efficiency of eDNA metabarcoding. Environ DNA 5:146–157. https://doi.org/10.1002/edn3.366

    Article  CAS  Google Scholar 

  13. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2012) GenBank Nuc Acids Res 41:D36–D42. https://www.ncbi.nlm.nih.gov/genbank/

    Article  Google Scholar 

  14. Ratnasingham S, Hebert PD (2007) BOLD: the barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes 7: 355–364. https://www.boldsystems.org/

  15. Leray M, Knowlton N, Machida RJ (2022) MIDORI2: a collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environ DNA 4:894–907. http://www.reference-midori.info/

    Article  CAS  Google Scholar 

  16. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res 41(D1):D590–D596. https://www.arb-silva.de/

    Article  CAS  PubMed  Google Scholar 

  17. Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C et al (2013) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res 41:D597–D604. https://pr2-database.org/

    Article  CAS  PubMed  Google Scholar 

  18. Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W (2018) MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Mol Biol Evol 35:1553–1555. http://mitofish.aori.u-tokyo.ac.jp/

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. O’Brien TD, Lorenzoni L, Isensee K, Valdés L (2017) What are marine ecological time series telling us about the ocean: a status report. IOC Tech Ser 129:1–297

    Google Scholar 

  20. Smith WH, Sandwell DT (1997) Global Sea floor topography from satellite altimetry and ship depth soundings. Science 277:1956–1962

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This review results from the collaborative efforts of members and colleagues of Working Group 157 (WG157), MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases, sponsored by the Scientific Committee on Oceanic Research (SCOR). The authors acknowledge contributions from the Working Group on Integrated Morphological and Molecular Taxonomy (WGIMT) of the International Council for the Exploration of the Sea (ICES). Funding was provided by SCOR and a grant to SCOR from the U.S. National Science Foundation (OCE-1840868).

Author information

Authors and Affiliations

  1. NOAA Fisheries, Office of Science & Technology, Silver Spring, MD, USA

    Todd D. O’Brien

  2. Bermuda Institute of Ocean Sciences, Arizona State University, St. George’s, Bermuda

    Leocadio Blanco-Bercial

  3. College of Fisheries & Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA

    Jennifer M. Questel

  4. Department of Marine Sciences, University of Connecticut, Groton, CT, USA

    Paola G. Batta-Lona & Ann Bucklin

Authors
  1. Todd D. O’Brien
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Leocadio Blanco-Bercial
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jennifer M. Questel
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Paola G. Batta-Lona
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ann Bucklin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ann Bucklin .

Editor information

Editors and Affiliations

  1. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA

    Robert DeSalle

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

O’Brien, T.D., Blanco-Bercial, L., Questel, J.M., Batta-Lona, P.G., Bucklin, A. (2024). MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems. In: DeSalle, R. (eds) DNA Barcoding. Methods in Molecular Biology, vol 2744. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3581-0_28

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3581-0_28

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3580-3

  • Online ISBN: 978-1-0716-3581-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation