A de novo chromosome‐level genome assembly of Coregonus sp. “Balchen” : one representative of the Swiss Alpine whitefish radiation

De-Kayne, Rishi; Zoller, Stefan; Feulner, Philine G. D. (2020). A de novo chromosome‐level genome assembly of Coregonus sp. “Balchen” : one representative of the Swiss Alpine whitefish radiation. Molecular ecology resources, 20(4), pp. 1093-1109. Wiley 10.1111/1755-0998.13187

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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 ~90x 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% TEs and contained 44,525 genes.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)
08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE) > Aquatic Ecology

UniBE Contributor:

De-Kayne, Rishi and Feulner, Philine

Subjects:

500 Science > 570 Life sciences; biology

ISSN:

1755-098X

Publisher:

Wiley

Language:

English

Submitter:

Marcel Häsler

Date Deposited:

28 May 2020 11:51

Last Modified:

26 Jul 2020 01:32

Publisher DOI:

10.1111/1755-0998.13187

PubMed ID:

32395896

BORIS DOI:

10.7892/boris.144057

URI:

https://boris.unibe.ch/id/eprint/144057

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