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

Abstract

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Epigenetic and genetic differentiation betweenCoregonusspecies pairs

“…We observed genetic differentiation between species in all four lakes, consistent with previous studies showing genetic differences between whitefish benthic-limnetic species Østbye et al 2006;Rogers and Bernatchez 2007;Bernatchez et al 2010;Siwertsson et al 2013;Dion-Côté et al 2017;Rougeux et al 2017;Feulner and Seehausen 2019;Rougeux, Gagnaire, Praebel, et al 2019;De-Kayne et al 2022;Mérot et al 2022). There was relatively high genetic differentiation between species and lakes in North America, though differentiation between lakes was greater in Europe than in North America.…”

“…There was relatively high genetic differentiation between species and lakes in North America, though differentiation between lakes was greater in Europe than in North America. There was greater differentiation between species in Cliff Lake than Indian Lake, as previously reported in our sister study (Mérot et al 2022). Genetic differentiation between lakes was greater than between species in Europe (Table 1B), likely due to the Zurich Lake and Langfjordvatn Lake populations having occupied two different glacial refugia during the last glaciation period .…”

“…The extent of genetic differentiation between the benthic and the limnetic species varied among lakes. FST estimates for Cliff Lake and Indian Lake in North America were previously published in Mérot et al (2022). In North America, moderate to high divergence between lakes both within and between species was observed (FST between lakes: 0.084 between Cliff Lake and Indian Lake limnetic species to 0.182 between Cliff Lake and Indian Lake benthic species), with greater FST between species in Cliff Lake than Indian Lake (0.098 for Indian Lake and 0.175 for Cliff Lake; Table 1A).…”

“…WGS was performed using paired end 150 bp sequencing on an Illumina HiSeq4000 with estimated 5X coverage. The North American samples were previously used and sequenced in Mérot et al (2022). WGBS was performed using paired end 150 bp sequencing on the Illumina HiSeqXwith samples randomly distributed across 16 lanes (four individuals pooled per lane) with estimated 10X coverage.…”

High‐density genomic data reveal fine‐scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

“…It is important to note that our results only suggest a putative inversion. Future studies could take advantage of the recently released long‐read genome assemblies of lake whitefish (Mérot et al, 2022 ) to verify the existence of this putative chromosomal inversion.…”