With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the “Vertebrate Genomes Project (VGP)” pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32–36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.

中文翻译：

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加州海狮的 Hi-C 支架短读长和长读长基因组组装在 4500 万年的进化过程中的同线性推理中大体一致


随着染色质相互作用图谱的出现，染色体水平的基因组组装已成为多种生物体的现实。然而，脚手架的质量很难判断。为了探索这一差距，我们为一种新兴的致癌野生动物模型——加州海狮（ Zalophus californianus ）生成了多个染色体规模的基因组组装。短读长组装体采用两个独立的染色质相互作用图谱数据集（Hi-C 和 Chicago），长读长组装体采用三种数据类型（Hi-C、光学图谱和 10X 链接读长），遵循“脊椎动物基因组计划”（ VGP）”管道。在这两种方法中，18 个主要支架恢复了核型 (2 n = 36)，支架 N50 分别为 138 和 147 Mb。染色体水平上与其他鳍足类基因组 (2 n = 32–36)、雪貂 (2 n = 34)、小熊猫 (2 n = 36) 和家犬 (2 n = 78) 的同线性关系在不同方法中是一致的并恢复已知的裂变和聚变。使用一组 264 个基因组整合的单基因座犬细菌人工染色体探针进行比较染色体涂色和多色染色体平铺，提供了基因组组织的独立评估。在染色体内观察到这些方法之间的广泛差异，最常见的是以着丝粒和端粒为中心的易位，这些易位在 VGP 组装中得到了更好的解决。基因组学和细胞学方法一致认为 X 染色体具有近乎完美的同线性，并且结合起来可以对狗和海狮之间的常染色体重排进行详细研究。 这项研究展示了一种新兴癌症模型的高质量基因组，并强调即使是用 Hi-C 支架的高度碎片化的短读长组装体也可以产生适合比较基因组分析的可靠的染色体水平支架。