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. 2023 Apr 24:11:e100904.
doi: 10.3897/BDJ.11.e100904. eCollection 2023.

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

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

Bernardo F Santos et al. Biodivers Data J. .

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.

Keywords: BINs; CBG; COI; Centre for Biodiversity Genomics; National Museum of Natural History; OTUs; USNM; cox1; dark taxa; museum harvesting; natural history collection.

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Conflict of interest statement

No conflict of interest to declare Disclaimer: This article is (co-)authored by any of the Editors-in-Chief, Managing Editors or their deputies in this journal.

Figures

Figure 1.
Figure 1.
Sanger and NGS Sequencing Flowchart for 8,549 USNM specimens.
Figure 2.
Figure 2.
Success length for COI sequencing by specimen collection date (given in percentage values at each bar) for the 8,549 USNM specimens selected in 2018 and 2019. The green bar represents the percentage of specimens collected per decade with recovered sequences (> 300 bp) and orange represents specimens with failed sequences (0 - 299 bp) or flagged sequences.
Figure 3.
Figure 3.
Sequencing results by taxonomic group for 4,508 USNM genera. Inner pie chart shows the proportion of sampled taxa in each taxonomic group and the outer chart shows the distribution of sequencing success within each taxonomic group. Other Orders: Mecoptera, Megaloptera, Neuroptera, Odonata, Plecoptera, Raphidioptera and Trichoptera.

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