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

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 Coregonuslinkage 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 novogenome 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.