Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA.
Department of Biology, California State University Fresno, Fresno, CA 93740, USA.
Gigascience. 2021 Oct 1;10(10). doi: 10.1093/gigascience/giab066.
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.
We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences 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 provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 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 Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism 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.
These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.
高质量的基因组资源有助于研究行为生态学、形态和生理适应以及基因组结构的演化。Sceloporus 属的蜥蜴作为重要的生态、进化和生理模型具有悠久的历史，因此成为开发基因组资源的有价值目标。
我们提供了高质量的染色体水平参考基因组组装 SceUnd1.0（使用 10X Genomics Chromium、HiC 和 Pacific Biosciences 数据），以及东部围栏蜥蜴 Sceloporus undulatus 的组织/发育阶段转录组。我们与其他蛇和蜥蜴组装进行了同线性分析，以鉴定染色体进化的广泛模式，包括微染色体和宏染色体的融合。我们还使用这个新的组装为 34 种其他 Sceloporus 物种提供了改进的基于参考的基因组组装。最后，我们使用 RNAseq 和全基因组重测序数据比较了 3 个组装，每个组装都代表了成本和努力的增加水平：使用 10X Genomics Chromium 数据的 Supernova 组装、添加了 HiC 数据的 HiRise 组装和添加了 Pacific Biosciences 测序数据的 PBJelly 组装。我们发现 Supernova 组装包含完整的基因组，是 RNAseq 和单核苷酸多态性调用的合适参考，但添加 HiC 数据提供的染色体水平支架允许同线性和全基因组关联作图分析。随后添加 PacBio 数据将 contig N50 增加了一倍，但支架长度几乎没有增加。
这些新的基因组资源为已经成为生理学和进化生态学模型的生物体的高级分子分析提供了有价值的工具。
