Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History
- PMID: 38327288
- PMCID: PMC10848724
- DOI: 10.3897/BDJ.11.e100904
Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History
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.
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
Similar articles
-
A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections.Biodivers Data J. 2023 May 10;11:e100677. doi: 10.3897/BDJ.11.e100677. eCollection 2023. Biodivers Data J. 2023. PMID: 38327333 Free PMC article.
-
Hydroids (Cnidaria, Hydrozoa) from Mauritanian Coral Mounds.Zootaxa. 2020 Nov 16;4878(3):zootaxa.4878.3.2. doi: 10.11646/zootaxa.4878.3.2. Zootaxa. 2020. PMID: 33311142
-
Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing.PeerJ. 2022 Aug 5;10:e13790. doi: 10.7717/peerj.13790. eCollection 2022. PeerJ. 2022. PMID: 35959477 Free PMC article.
-
DNA barcoding, an effective tool for species identification: a review.Mol Biol Rep. 2023 Jan;50(1):761-775. doi: 10.1007/s11033-022-08015-7. Epub 2022 Oct 29. Mol Biol Rep. 2023. PMID: 36308581 Review.
-
DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work.Sci Total Environ. 2019 Aug 15;678:499-524. doi: 10.1016/j.scitotenv.2019.04.247. Epub 2019 Apr 27. Sci Total Environ. 2019. PMID: 31077928 Review.
Cited by
-
Taxonomy and Biological Control: New Challenges in an Old Relationship.Neotrop Entomol. 2023 Jun;52(3):351-372. doi: 10.1007/s13744-023-01025-5. Epub 2023 Jan 19. Neotrop Entomol. 2023. PMID: 36656493 Free PMC article.
-
A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections.Biodivers Data J. 2023 May 10;11:e100677. doi: 10.3897/BDJ.11.e100677. eCollection 2023. Biodivers Data J. 2023. PMID: 38327333 Free PMC article.
-
Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.Biodivers Data J. 2023 Oct 27;11:e102317. doi: 10.3897/BDJ.11.e102317. eCollection 2023. Biodivers Data J. 2023. PMID: 38327316 Free PMC article.
References
LinkOut - more resources
Full Text Sources
Research Materials
Miscellaneous