CRISPR-linked DNA barcoding with Oxford Nanopore MinION

Research highlight: CRISPR-linked DNA barcode sequencing (Bethan Littleford-Coluhoun et al.)

Led by Bethan Littleford-Colquhoun, the Kartzinel Lab published a paper describes our efforts to repurpose CRISPR technology in ways that might help overcome persistent drawbacks to PCR and other targeted enrichment strategies in molecular ecology. This post provides a summary of the strategy we used and the lessons we learned in publishing A CRISPR-based strategy for targeted sequencing in biodiversity science at Molecular Ecology Resources. The article was originally posted as a BioRxiv preprint.

In this paper, we show that we can obtain highly accurate plant DNA barcodes and assemble entire chloroplast genomes. These advances could help with species identification, discovery, and the construction of DNA reference libraries for use in a variety of applications. Moreover, we show incredible accuracy when it comes to estimating the relative abundance of DNA from a mixture of species compared to typical PCR-based methods for DNA metabarcoding.

We hope the experimental methods will be of interest and that folks working in the field will see the great potential. Once scalable, these advantages could really transform the quality and completeness of many projects that we do in the lab -- and the kinds of project we know a lot of folks are out there trying to do around the world as well!

The approach was noted to be a potentially 'high risk / high reward' of the NSF CAREER award that supported our work, based in Yellowstone National Park. We'll update once it is peer-reviewed and published.