Environmental Barcoding through Massively Parallelized Sequencing
Summary
DNA barcoding represents a novel genomics exercise: collection of sequence information from a standard gene region – which acts as a barcode to identify the species – across eukaryotic life. Specifically, scientists have now identified a 648-base pair segment of the mitochondrial gene cytochrome c oxidase 1 (CO1) as the core barcode region for eukaryotes. The horizontal survey of sequence diversity in this gene region is valuable in many contexts: it enables identification and discovery of species, reveals factors influencing rates of molecular evolution and species age, and allows detailed study of evolutionary pathways in the CO1 protein.
It is now clear that DNA barcoding can transform species identifications. It will use two technology streams to do so: point-of-contact analysis of single specimens and massive barcode screens, which are the focus of this project. Point-of-contact devices will be critical in contexts such as port inspections and pest control. By contrast, massive barcode screens will permit analysis of mixed biotic samples.
Many eukaryotes are too small, too numerous, or too conjoined for analysis using conventional barcode protocols. This project will develop protocols for analysing any collection of eukaryotes. ‘Environmental barcoding’ requires coupling of massively parallelized sequencing technologies with new informatics tools. Such analysis will certainly advance monitoring of biodiversity. Imagine the new capacity to monitor environmental quality if we could rapidly determine the species composition of any environmental sample. However, the implications are broader - environmental barcoding represents the metagenomics tool for eukaryotic life.
Over two years, this project will develop environmental barcoding as a technology stream for sequencing platforms. The work will make use of new parallelized sequencers, but considerable technological innovation will be necessary if they are to support environmental barcoding. New informatics tools are necessary for analysis of sequence data, and new protocols for barcode recovery from large, admixed samples of life.
The project team also plans to show how environmental barcoding can support a real-world need: bio-monitoring of Canada’s inland waters. The team will carry out this work in close collaboration with researchers at Environment Canada, who are not only experts in environmental sampling but will be major end users of this technology, and with researchers at the Stanford Genome Technology Centre (California) - world leaders in massively parallelized sequencing technologies. The resulting environmental barcoding technology will reinforce Canada’s leadership in DNA barcoding by introducing the first application of this approach to biodiversity monitoring of eukaryote communities.
