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.

中文翻译：

---

从头染色体水平的基因组装配的Coregonus sp。“ Balchen”：瑞士高山白鲑辐射的一位代表。

由于鲑鱼的生活史策略令人难以置信的多样性以及许多鲑鱼种类的多样化速度，因此鲑鱼特别受进化生物学家的关注。仅在瑞士，自上次冰川最大期以来，已经有超过30种来自美洲锥gon科的高山白鲑进化了出来，这些物种表现出各种各样的形态和行为表型。这与在所有鲑科鱼类的祖先中发生的全基因组重复相结合，使高山白鱼辐射成为一个特别有趣的系统，在该系统中研究适应性和物种形成的遗传基础以及倍性变化和随后的重倍化对基因组进化的影响。尽管鲑科中许多物种都有精心策划的基因组组装，Coregoninae亚科的基因组资源不足。为了组装白鱼参考基因组，我们从一个野生捕获物中进行了PacBio测序Coregonus sp。从图恩湖到大约90倍覆盖范围的“ Balchen ”。PacBio读段独立地使用三种不同的装配，装配隼，CANU和wtdbg2并随后用另外的HI-C数据脚手架。这三个程序集都是高度连续的，与以前发布的Coregonus连锁图具有很强的共性，并且当将其他短读数据映射到每个程序集时，在大多数染色体规模的支架上的覆盖率甚至都很高。在这里，我们介绍鲑鱼亚科Coregoninae的第一个从头基因组组装。最终的2.2 Gb wtdbg2组装包括40个脚手架，N50为51.9 Mb，对于BUSCO，完成率为93.3％。该装配体由约52％的转座元件组成，并包含44,525个基因。