Squamate reptiles exhibit high variation in their phenotypic traits and geographical distribution and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46 Gbp genome assembly has a scaffold N50 of 11.52 Mbp with N50 contig size of 220.4 Kbp and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

中文翻译：

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普通蜥蜴（Zootoca vivipara）基因组的染色体水平组装。

有鳞爬行动物在其表型特征和地理分布方面表现出很大的变异，因此是进化和生态研究的迷人分类群。然而，这组物种的基因组资源非常有限，因此阻碍了研究工作。为了弥补这一差距，我们组装了普通蜥蜴Zootoca vivipara的高质量基因组（Lacertidae），使用高覆盖率的 Illumina（鸟枪和配偶对）和 PacBio 测序数据的组合，再加上 RNAseq 数据和遗传连锁图生成。1.46 Gbp 基因组组装的支架 N50 为 11.52 Mbp，N50 重叠群大小为 220.4 Kbp，只有 2.96% 的间隙。BUSCO 分析表明，97.7% 的单拷贝 Tetrapoda 直向同源物在组装中被回收。使用ab initio的组合将总共 19,829 个基因模型注释到基因组和基于同源性的方法。为了改进染色体水平的组装，我们从野生捕获的家庭中生成了一个高密度连锁图，并开发了一个新的分析管道来适应多个父系和未知的父亲基因型。我们成功地将几乎 90% 的基因组锚定和定位在 19 个连锁群上。这种带注释和定向的染色体水平参考基因组代表了促进有鳞爬行动物进化研究的宝贵资源。