Mapping the genome of lake trout to ensure its survival


Published: 24Sep2021

Lake trout, once the top predator fish across the Great Lakes, reached near extinction between the 1940s and 1960s due to pollution, overfishing, and predation by the invasive lamprey eel. Once showing striking levels of diversity in terms of size, appearance, and ability to adapt to varied environments, now the only lake trout populations to have survived are to be found in Lake Superior and Lake Huron. An international team of researchers from the U.S. and Canada, including researchers from McGill University, have now managed to create a reference genome for lake trout to support U.S. state and federal agencies with reintroduction and conservation efforts.

Genomes of salmonids, a family that includes lake trout, are harder to compile than those of many other animals, the research team said. “Between 80-100 million years ago, the ancestor of all salmonid species that lake trout belong to went through a whole genome duplication event. As a result, salmonid genomes are difficult to assemble due to their highly repetitive nature and an abundance of duplicated genomic regions with similar sequences,” explains Ioannis Ragousis, co-author of the study and head of Genome Sciences at the McGill Genome Centre, where the sequencing took place. “The assembly methodology we applied at the McGill Genome Centre generated the sequence of whole chromosomes and allowed the construction of a map describing patterns of recombination across the genome. I am very excited by the wide range of possible applications for this novel genetic resource”

The newly released genome assembly will allow researchers to better understand the genetic basis for traits that allowed lake trout to exploit a diversity of niches and habitats across their range. It will also help identify the genes and biological processes associated with variation in survival and reproductive success among the various hatchery populations that have been used to reintroduce lake trout to the Great Lakes.

The study: “A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush)” by Seth R. Smith was recently published in Molecular Ecology Resources


The research was funded by the CanSeq150 - a platform for genome sequencing and analysis initiated by Canada’s Genomics Enterprise (CGEn). The McGill Genome Centre is one of the three CGEn nodes.

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