Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History

By

Santos, Bernardo F.
Miller, Meredith
Miklasevskaja, Margarita
Mckeown, Jaclyn
Redmond, Niamh
Coddington, Jonathan A.
Bird, Jessica
Miller, Scott E
Smith, Ashton
Brady, Seán G.
Buffington, Matthew L.
Chamorro, M. Lourdes
Dikow, Torsten, 1975-
Gates, Michael William 1969-
Goldstein, Paul Z.
Konstantinov, Alexander S, 1955-
Kula, Robert R
Silverson, Nicholas
Solis, M Alma
Dewaard, Stephanie
Naik, Suresh
Nikolova, Nadya
Pentinsaari, Mikko
Prosser, Sean
Sones, Jayme
Zakharov, Evgeny V.
deWaard, Jeremy

Type

Article

Date of Publication

2023-04-24

Original Publication

Biodiversity data journal

Volume

11

Pages

1--17

Subjects

Bins , CBG , Centre for Biodiversity Genomics , COI , cox1 , dark taxa , museum harvesting , National Museum of Natural History , Natural History collection , Otus , USNM

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia Pensoft Publishers [2013]-

Identifiers

DOI: https://doi.org/10.3897/BDJ.11.e100904
eLocator: e100904

 

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.