Here, we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C) sequencing, and a previously published linkage map to produce a highly contiguous assembly composed of 7378 contigs (contig N50 = 1.8 Mb) assigned to 4120 scaffolds (scaffold N50 = 44.975 Mb). Long read sequencing data were generated using DNA from a female double haploid individual. 84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologues were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k-mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitochondrial genome assembly was also produced. Self-versus-self synteny analysis allowed us to identify homeologs resulting from the salmonid specific autotetraploid event (Ss4R) as well as regions exhibiting delayed rediploidization. Alignment with three other salmonid genomes and the Northern Pike (Esox lucius) genome also allowed us to identify homologous chromosomes in related taxa. We also generated multiple resources useful for future genomic research on Lake Trout, including a repeat library and a sex-averaged recombination map. A novel RNA sequencing data set for liver tissue was also generated in order to produce a publicly available set of annotations for 49,668 genes and pseudogenes. Potential applications of these resources to population genetics and the conservation of native populations are discussed.

中文翻译：

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湖鳟 (Salvelinus namaycush) 的染色体锚定基因组组装

在这里，我们展示了湖鳟（ Salvelinus namaycush）的带注释的染色体锚定基因组组装) - 一种高度多样化的鲑鱼物种，具有值得注意的保护问题，是适应和物种形成研究的优秀模型。我们利用 Pacific Biosciences 的长读长测序、双端 Illumina 测序、邻近连接 (Hi-C) 测序和先前发布的连锁图谱来生成由分配给 4120 的 7378 个重叠群（重叠群 N50 = 1.8 Mb）组成的高度连续组装支架（支架 N50 = 44.975 Mb）。使用来自女性双单倍体个体的 DNA 生成长读长测序数据。84.7% 的基因组被分配到 42 个染色体大小的支架上，并且回收了 93.2% 的基准通用单拷贝直系同源物，使该组装与目前可用的最佳鲑鱼基因组相提并论。基于 k-mer 频率分析的基因组大小估计与最终基因组的总大小高度相似，表明整个基因组已恢复。还产生了线粒体基因组组装。自我与自我同线性分析使我们能够识别由鲑鱼特异性同源四倍体事件 (Ss4R) 以及表现出延迟再二倍体化的区域产生的同源物。与其他三个鲑科动物基因组和北梭子鱼的比对（Esox lucius ) 基因组还使我们能够识别相关分类群中的同源染色体。我们还生成了多种资源，可用于未来对湖鳟的基因组研究，包括重复库和性别平均重组图。还生成了一个新的肝组织 RNA 测序数据集，以便为 49,668 个基因和假基因生成一组公开可用的注释。讨论了这些资源在种群遗传学和本地种群保护中的潜在应用。