(External) Demonstrating the application of whole genome sequencing and assembly for marine conservation initiatives

Advisor: Nick Jeffery, Fisheries and Oceans Canada

Suggested co-advisors: Joey Bernhardt, Sally Adamowicz, Elizabeth Boulding, Ryan Gregory

Marine conservation planning initiatives are rapidly expanding across Canada, with the goal of protecting at least 30% of marine and coastal environments by 2030. To effectively monitor the large spatial coverage of these conservation areas in Canada's three ocean basins, new and advanced technologies, such as genomics, are needed. Genomics applications include population genomics, to investigate genetic diversity, population structure, and gene flow among different regions, and eDNA metabarcoding to monitor species assemblages and biodiversity. High throughput sequencing technologies have made whole genome sequencing and assembly far more accessible to scientists, who use these reference genomes in evolutionary studies, but the importance of high-quality genome assemblies is difficult to convey to science advisors and managers. In this project, the student will use and/or develop pipelines and existing software to visualize available reference genomes from the Canada Biogenomes Project, and conduct a phylogenetic/evolutionary study comparing related genomes in marine organisms, including fish and/or invertebrates. The goal of the project will be to make genome assemblies more accessible and digestible to non-experts, showcasing the power of DNA sequencing and applications of genome assemblies for downstream scientific research and science advice. 

This project is suitable for one or two semesters.

Knowledge/Skills

Knowledge of current sequencing technologies, software used for genome assembly (e.g., Abyss, Spades, etc), software for visualizing genomic data and synteny plots (e.g., IGV and circos), knowledge of coding in at least one of R, Python, C++, or shell scripting, marine biology background may be helpful but not necessary. Willingness to learn new software and coding is the main skill required, as well as working with large data files.