Supporting data for "A chromosome-level genome assembly for the Eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology"

High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus <i>Sceloporus</i> have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources.<br> 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, <i>Sceloporus undulatus</i> . 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 provide improved reference-based genome assemblies for 34 additional <i>Sceloporus</i> species. 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 doubled the contig N50 but provided negligible gains in scaffold length.<br>These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

高质量基因组资源可为行为生态学、形态与生理适应性以及基因组结构演化的相关研究提供重要支撑。侧褶蜥属（*Sceloporus*）蜥蜴作为重要的生态、进化及生理研究模型已有悠久历史，因此其成为基因组资源开发的极具价值的研究对象。
本研究报道了东部围栏蜥蜴（*Sceloporus undulatus*）的高质量染色体水平参考基因组组装版本SceUnd1.0（采用10X Genomics Chromium、HiC及PacBio测序数据构建），同时还提供了其不同组织与发育阶段的转录组数据。我们通过与其他蛇类和蜥蜴的基因组组装进行同线性分析（synteny analysis），揭示了包括微染色体与宏染色体融合在内的广泛染色体演化模式。此外，我们利用该新组装基因组为另外34个侧褶蜥属（*Sceloporus*）物种构建了优化的参考基因组组装结果。
最后，我们利用RNAseq（RNA测序）和全基因组重测序数据，对三种组装策略进行了比较，这三种策略分别对应不同的测序成本与工作量：仅使用10X Genomics Chromium数据的Supernova组装、添加HiC数据的HiRise组装，以及添加PacBio测序数据的PBJelly组装。研究结果显示，Supernova组装可覆盖完整基因组，适用于RNAseq分析与单核苷酸多态性（SNP）检测，但添加HiC数据后得到的染色体水平支架则可支持同线性分析与全基因组关联定位分析。后续添加PacBio数据后，重叠群N50（contig N50）提升了一倍，但对支架长度的改善极为有限。
这些全新的基因组资源为这种已成为生理与进化生态学研究模型的生物的高级分子分析提供了极具价值的研究工具。