Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States.
Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States.
J Hered. 2023 Aug 23;114(5):521-528. doi: 10.1093/jhered/esad037.
Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.
刺蜥蜴（Sceloporus 属）长期以来一直是行为学、热生理学、饮食生态学、媒介生物学、物种形成和生物地理学研究的重要系统。西部栅栏蜥蜴（Sceloporus occidentalis）分布于美国西部和墨西哥北下加利福尼亚州的大部分主要生物地理区域，栖息于从草原到灌木到开阔林地等广泛的生境中。作为小型变温动物，刺蜥蜴特别容易受到气候变化的影响，而 S. occidentalis 也已成为研究土地利用变化和城市化对小型脊椎动物影响的重要系统。在这里，我们报告了 S. occidentalis 的一个新的参考基因组组装，这是加利福尼亚保护基因组学项目（CCGP）的一部分。与 CCGP 的参考基因组学策略一致，我们使用了太平洋生物科学的 HiFi 长读和 Hi-C 染色质邻近测序技术来生成从头组装的基因组。该组装总共包含 608 个支架，跨度为 2856Mb，具有 18.9Mb 的 contig N50、98.4Mb 的 scaffold N50 和基于四足动物基因集的 98.1%的 BUSCO 完整性得分。这个参考基因组将有助于理解 S. occidentalis 的生态和进化动态、加利福尼亚特有岛屿栅栏蜥蜴（S. beckii）的物种状况以及 Sceloporus 蜥蜴的壮观辐射。
