The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.

中文翻译：

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超基因和其他选择信号的大西洋鲱鱼基因组的染色体级装配。

由于其庞大的种群规模和选择性中性位点的极低遗传分化，大西洋鲱鱼是探索生态适应遗传基础的典范物种。然而，由于高度片段化的基因组组装，迄今为止，此类研究受到阻碍。在这里，我们提供了一种基于杂交方法的染色体级基因组装配，该方法结合了从头开始的太平洋生物科学（PacBio）装配与Hi-C支持的支架。该组件包含26个常染色体，其大小在12.4至33.1 Mb的范围内，在染色体上的总大小为726 Mb，这已通过高分辨率连锁图得到了证实。鲱鱼基因组装配体与其他骨鱼的高质量装配体之间的比较表明，染色体间很少，但染色体内重排频繁。改进后的组件便于分析以前难以处理的大规模结构变异，例如，可以检测12号染色体在生态适应性上的7.8 Mb倒位。该超基因显示出种群之间的强遗传分化。基于染色体的装配还显着改善了先前检测到的选择信号的解释，使我们能够揭示数百个与生态适应相关的独立基因座。