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Skimming for Barcodes: Rapid Production of Mitochondrial Genome and Nuclear Ribosomal Repeat Reference Markers Through Shallow Shotgun Sequencing

August 05, 2022

We evaluate the feasibility of genome skimming to generate barcode references databases by testing across a diverse selection of 12 marine fish species.


DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments.

The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions.

Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.

Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. 2022. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 10:e13790.  https://doi.org/10.7717/peerj.13790.

Last updated by Pacific Islands Fisheries Science Center on 08/12/2022