This has lead researchers to propose an alternate method that uses low-pass sequencing to generate genome skims, and subsequently identifies chloroplast or mitochondrial marker genes or assembles the organelle genome. While low costs have kept PCR-based pipelines attractive, decreasing costs of shotgun sequencing have now made it possible to shotgun sequence 1–2 Gb of total DNA per reference specimen sample for as low as $80, even after including sample preparation and labor costs.

For example, in a recent study, 896 out of 4,174 wasp species could not be distinguished from each other using COI barcodes.

Moreover, since barcode markers are relatively short regions, their phylogenetic signal and identification resolution can be limited. PCR for marker gene amplification requires relatively high-quality DNA and thus cannot be applied to samples in which the DNA is heavily fragmented. However, the traditional approach to (meta)barcoding, despite its success, has some drawbacks. Computational methods for finding the closest match in a reference dataset (e.g., TaxI ), and for placement of a query into existing marker trees have been developed. To increase coverage, reference databases with millions of barcodes have been generated (e.g., Barcode of Life Data System, BOLD, for COI ). The accuracy of (meta)barcoding depends on the coverage of the reference database and the method used to search queries against it. Beyond the barcoding application, the barcoding marker genes have also been used to delimitate species and to infer phylogenies. In the case of metabarcoding, the goal is to deconstruct the taxonomic composition of a mixed sample consisting of multiple species. Barcoding is used for taxonomic identification of single-species samples. Traditional (meta)barcoding is based on DNA sequencing of taxonomically informative and group-specific marker genes (e.g., mitochondrial COI and 12S/16S for animals, chloroplast genes like matK for plants, and ITS for fungi) that are variable enough for taxonomic identification, but have flanking regions that are sufficiently conserved to allow for PCR amplification using universal primers. The current molecular technique of choice is (meta)barcoding.

The ability to quickly and inexpensively study the taxonomic diversity in an environment is critical in this era of rapid climate and biodiversity changes.

Free barcode samples