Data for A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology

Abstract

Background: High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings: We present a high-quality chromosome-level reference genome assembly, SceUnd1.0, (utilizing 10X Genomics Chromium, HiC, and PacBio data) and tissue/developmental stage transcriptomes for the Eastern Fence Lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to improve genome assemblies for 34 additional Sceloporus species, improving these assemblies from 1% coverage to 43% coverage on average. Finally, we used RNAseq and whole-genome resequencing data to compare three assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium; HiRise Assembly that added data from HiC; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and SNP calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole genome association mapping analyses. The subsequent addition of PacBio data provided negligible gains. Conclusions: These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.