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

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.

Keywords: Alpine whitefish; Coregonus; Salmonidae; genome assembly; whitefish.

Figure 1

Workflow outlining the different steps and tools used to assemble the whitefish genome (coloured in blue). New input produced for this study is coloured in purple and previously published resources used for repeat masking and annotation in orange. Final outputs are shown in green [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 2

genomescope profile established based on short read data, which estimates the genome size of Coregonus sp. “Balchen” to be 2.6 Mb [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 3

Coregonus sp. “Balchen” contig contact map from Hi‐C scaffolding of the wtdbg2 assembly. The intensity of red represents the relative contact density between contigs. The highest contact density is found within whitefish scaffolds (WFSs), which are outlined in blue [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 4

For each of the whitefish scaffolds (WFSs) coverage of Illumina data mapped to the wtdbg2 assembly is plotted in 30‐kb windows. Most windows show an average coverage of around 17× (black points). Windows with coverage > 20× and < 10× are coloured in red and blue, respectively. Putative collapsed duplicate regions are highlighted in grey [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 5

Circos plot comparing the structure of the C. sp. “Albock” linkage map (right; De‐Kayne & Feulner, 2018) and the 40 whitefish scaffolds (WFSs) of the wtdbg2 c. sp. “Balchen” assembly (left). Lines indicate mapping locations of RAD loci from the linkage map in the genome assembly. Most mappings suggest a good match between linkage map and genome assembly (high synteny between linkage groups and WFSs) and only few lines map discordantly. Genome assembly regions which represent collapsed duplicate regions are identified in grey around the left perimeter [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 6

Coregonus sp. “Balchen” transposable element divergence landscape. Transposable elements within the whitefish genome have been characterized (different classes represented by distinct colours). The plot shows the relative abundance of each class and their relative age (molecular clock estimate). Note the ongoing DNA element diversification within the whitefish genome, particularly in DNA elements and LINEs [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 7

Homeologous whitefish scaffolds (WFSs) within the whitefish genome identified using symap. Links between homeologues are coloured according to their mean sequence similarity based on lastz alignments for each syntenic link in both directions. Genome assembly regions which are thought to be collapsed are identified in grey on the outermost track [Colour figure can be viewed at wileyonlinelibrary.com]