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PhD project: Characterization & exploitation of copy number variation in Atlantic salmon
Xelect Ltd (St Andrews, Scotland)
My four year PhD is funded by a BBSRC industrial CASE PhD studentship, with additional support from our commercial partner Xelect Ltd (see http://xelect.co.uk/). I am looking into copy number variation (CNVs) in the Atlantic salmon (Salmo salar) genome. CNVs are deletions and duplications within the genome (ranging from thousands to hundreds of thousands of bases in size) that are a major source of population-level genomic variation and often overlap with genes. The extent of CNV is uncharacterized in salmonid fish and potentially represents a source of phenotypic variation. I am particularly interested in finding CNVs affecting traits of high commercial value in salmon aquaculture. I am also investigating how genome duplication has influenced the CNV landscape in collaboration with scientists at CIGENE (see https://cigene.no/). To find and characterize CNVs, I am employing whole genome re-sequencing and a range of state-of-the-art bioinformatics approaches.
Biography and previous work
After graduating with a first class BSc (Hons) degree from the University of Manchester, I worked in multiple fisheries projects with the Charles Darwin Foundation in the Galapagos Islands and the Smithsonian institute in Florida, USA. My main project investigated life-history traits and population connectivity of Paralabrax albomaculatus, an endemic, endangered fish of commercial importance (e.g. see publication below). Additionally, I have been, and still am involved in several genetic connectivity projects of multiple marine species undertaken by students at the University of San Francisco, de Quito, Ecuador.
Bertolotti, A. C., Griffiths, S. M., Truelove, N. K., Box, S. J., Preziosi, R. F., & Salinas de Leon, P. (2015). Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus). PeerJ, 3, e1253.
Left: pipeline being used to detect CNVs in Atlantic salmon. Right: example image from the Integrative Genome Viewer (IGV) demonstrating CNVs in different salmon individuals in a 300kb region on Chr 11.