Biological advisor: Geoffrey Wood [1], Pathobiology

Computational advisor: Dirk Steinke [2], Integrative Biology

The Bowhead whale is a large baleen whale that has a very long lifespan (over 150 years). Like most whales, bowheads are an example of a concept called Peto’s paradox. Despite having large bodies, and therefore a large number of cells at risk of transforming into cancer, whales have a much lower cancer rate than humans. Bowheads are known to have an extra copy of the gene PCNA which is involved in DNA repair. We have recently discovered that beluga, narwhals, and humpback whales also all have 2 full copies of PCNA, along with variable numbers of PCNA pseudogenes. Because the genomes of these species are not well annotated, we do not know the chromosomal location of the 2 PCNA copies. This MBinf project will use already obtained Pacific Biosciences (PacBio) long read DNA sequences from beluga and pilot whales to determine the chromosomal location of the full PCNA copies and potentially the pseudogenes. We will add Oxford Nanopore long read sequencing data to this and integrate these data with the available short read Illumina sequence data already publicly available. Knowing the location of the copies will help us to determine the manner in which they arose and the evolutionary timing of the gene duplication. We will compare these findings to our ongoing measurements of PCNA copy number in related species (even-toed ungulates) such as cows, deer, bison, and hippos.

This project is suitable for one or two semesters. The student is required to occasionally be on-site.

Knowledge/Skills

Experience with Python; some knowledge of genome assembly; experience working with long read DNA sequence data would be good.