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

作者：Claire Mérot, Kristina Stenløkk, Clare J. Venney, Martin Laporte, Michel Moser, Éric Normandeau, Mariann Árnyasi, Matthew Kent, Clément Rougeux, Jullien M. Flynn, Sigbjørn Lien, Louis Bernatchez · 发表于：Molecular Ecology · 年份：2022 · DOI：10.1111/mec.16468 · 被引用次数：61 · 研究领域：Genetic diversity and population structure、Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations

Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the lake whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements and analysed the genomes in the light of related coregonid species. Next, we used a combination of long- and short-read sequencing to characterize SVs and genotype them at the population scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transpo...