ArticleMolecular ecology resources2020
A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": One representative of the Swiss Alpine whitefish radiation.
Article in Molecular ecology resources, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 41 citations in OpenAlex.
- A Genomic Tool to Tackle Cryptic Diversity Demonstrates the Potential for Off-Target Use of GT-Seq Panels.Molecular ecology resources · 2026Article
- The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.Molecular ecology · 2025Review
- Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.).Molecular ecology · 2025Article
- Genetic Adaptation to Brackish Water and Spawning Season in European Cisco.Molecular ecology · 2025Article
- Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr.Molecular ecology · 2025Article
- Genomic and metabolomic insights into the biosynthesis of carotenoids and lipids in oleaginous red yeast Cystofilobasidium infirmominiatum HZR20 isolated from Mangrove plants in Southern China.Archives of microbiology · 2025Article
- The genome assembly of the farmed European whitefish Coregonus lavaretus L. from the Finnish selective breeding programme.BMC genomic data · 2025Article
- A chromosome-level genome assembly and evolutionary analysis of Coregonus ussuriensis Berg.Scientific data · 2024Article
- Epigenetic and Genetic Differentiation Between Coregonus Species Pairs.Genome biology and evolution · 2024Article
- Ecological disturbance reduces genomic diversity across an Alpine whitefish adaptive radiation.Evolutionary applications · 2024Article
- The late-evolving salmon and trout join the GnRH1 club.Histochemistry and cell biology · 2023Article
- Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.G3 (Bethesda, Md.) · 2023Article
- Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome.G3 (Bethesda, Md.) · 2023Article
- Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus.Journal of animal science · 2023Article
- Review
- High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Evolutionary applications · 2022Article
- Genomic architecture of adaptive radiation and hybridization in Alpine whitefish.Nature communications · 2022Article
- Genomic variation from an extinct species is retained in the extant radiation following speciation reversal.Nature ecology & evolution · 2022Article
- A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush).Molecular ecology resources · 2022Article
- Complex and divergent histories gave rise to genome-wide divergence patterns amongst European whitefish (Coregonus lavaretus).Journal of evolutionary biology · 2021Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well-curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught Coregonus sp. "Balchen" from Lake Thun to ~90× coverage. PacBio reads were assembled independently using three different assemblers, falcon, canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2-Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb and was 93.3% complete for BUSCOs. The assembly consisted of ~52% transposable elements and contained 44,525 genes.
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