Data files: Reference genome of European whitefish (<i>Coregonus lavaretus L.</i>) from Finland

<b>Datafile 2: Summary of the European whitefish assemblies.</b> The main assembly includes both PacBio and OmniC sequence data, while the alternative assembly was based on PacBio sequence data only. The main assembly is publicly available at the ENA under the accession PRJEB69218. The alternative assembly is available upon request from Antti Kause.<b>Datafile 3: Smudgeplot of European whitefish</b>. The k-mer based smudgeplot analysis was performed using PacBio Hi-Fi reads to assess the heterozygosity and ploidy of the European whitefish genome. The analysis indicated that 35% of the genome is fully diverged diploid, indicated by the “AB” pattern. Conversely, 63% of the genome is either tetraploid or highly similar diploid paralogs as evidenced by “AABB” pattern, suggesting that the diploid resolution in these regions is not complete. In the smudgeplot, the x-axis represents the coverage ratio, while the y-axis indicates the total coverage. “A” and “B” represent different alleles, 1n = haploid, 2n = diploid, 3n = triploid, 4n = tetraploid, and so on.