Genomic differences between dwarf and normal American lake whitefish

Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads


Understanding the processes underlying the evolution of species and how genomes diverge during speciation is a fundamental goal of evolutionary genomics. American lake whitefish (Coregonus clupeaformis) is a salmonid fish well suited for studying speciation, as it exists in two distinct forms: Dwarf and Normal. As indicated by their names, the Dwarf whitefish is smaller than the Normal whitefish, but in addition to physical differences, they also take up different habitats, often in the same lakes. Normal whitefish thrives as the bottom of lakes (the benthic zone), while the Dwarf whitefish lives is the top layer (limnetic zone). The types are still considered one species, but hybrids are rare and tend to have a lower chance of survival, suggesting they are in the process of becoming two distinct species. To better understand the genomics driving the separation of these sympatric types of whitefish was the main goal of a recent collaboration between scientists from Université Laval in Québec, Canada, and CIGENE.


The American Lake Whitefish exists as two types: Dwarf and Normal, occupying different habitats.

By using a combination of long- and short-read sequencing of whitefish from two different lakes, we were able to find 13 million single nucleotide polymorphisms (SNPs) between Dwarf and Normal whitefish, and more than 100,000 larger structural variants (SVs). Though the SVs are fewer in number, they cover more than five times the number of base pairs compared to SNPs. A large proportion of the SVs were found to be active transposable elements, which are genes that can “jump” or move around in the genome. We found that the structural variants, and particularly those caused by transposable elements, played an important role in American lake whitefish speciation.

Claire Mérot, Kristina S R Stenløkk, Clare Venney, Martin Laporte, Michel Moser, Eric Normandeau, Mariann Árnyasi, Matthew Kent, Clément Rougeux, Jullien M Flynn, Sigbjørn Lien, Louis Bernatchez

Mol Ecol. 2022 Apr 13. doi: 10.1111/mec.16468. Online ahead of print.

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