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

Background: 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 subfamilyCoregoninae 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 the Salmonidaefamily, genomic resources for the subfamilyCoregoninae are lacking. Findings: PacBio sequencing from one wild caught Coregonussp. "Balchen" from Lake Thun was carried out 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 are of high quality based on standard metrics, and when comparing the assemblies to a previously published linkage map and when mapping additional short-read data (~30x Illumina data) to it. Conclusions: Here, we present the first de novo genome assembly for the Salmonid subfamilyCoregoninae. Our final wtdbg2 reference sequence was assembled into 40 chromosome-scale scaffolds with a total length of 2.2Gb, an N50 of 51.9Mb and was 93.3% complete for BUSCOs. It comprised of ~52% TEs and contained 46,397 genes.