Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

Abstract

Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions 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-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb 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.

Keywords: Lacertidae; linkage map; lizard genome; multiple paternity; reptile genomics; squamates.

Fig. 1.

The genome assembly and linkage map construction for the common lizard, Zootoca vivipara. (a) The genome assembly and linkage map generation pipelines used in the study. (b) The length of the male (M), female (F), and consensus linkage groups. (c) An example of Linkage Group 2 based on the male (orange) and female (green) genetic maps. Pearson correlation coefficients between the physical (X axis) and genetic (Y axis) distances are indicated. Gray and white bars represent scaffolds.

Fig. 2.

Zootoca vivipara genome assembly in the context of other Squamata genomes. (a) Maximum-likelihood tree based on the 269 single-copy orthologs from available Squamata genomes. (b) Synteny between Z. vivipara chromosome-level assembly and snake (Crotalus viridis) and closely related wall lizard genome (Podarcis muralis).