Department of Biology, La Sierra University, Riverside, CA, United States.
Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.
J Hered. 2022 Nov 30;113(6):641-648. doi: 10.1093/jhered/esac048.
The rubber boa, Charina bottae is a semi-fossorial, cold-temperature adapted snake that ranges across the wetter and cooler ecoregions of the California Floristic Province. The rubber boa is 1 of 2 species in the family Boidae native to California and currently has 2 recognized subspecies, the Northern rubber boa C. bottae bottae and the Southern rubber boa C. bottae umbratica. Recent genomic work on C. bottae indicates that these 2 subspecies are collectively composed of 4 divergent lineages that separated during the late Miocene. Analysis of habitat suitability indicates that C. bottae umbratica montane sky-island populations from southern California will lose the majority of their habit over the next 70 yr, and is listed as Threatened under the California Endangered Species Act. Here, we report a new, chromosome-level assembly of C. bottae bottae as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome 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 289 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.3 Mb, a scaffold N50 of 97 Mb, and BUSCO completeness score of 96.3%, and represents the first reference genome for the Boidae snake family. This genome will enable studies of genetic differentiation and connectivity among C. bottae bottae and C. bottae umbratica populations across California and help manage locally endemic lineages as they confront challenges from human-induced climate warming, droughts, and wildfires across California.
橡胶蟒，Charina bottae 是一种半穴居的、适应低温的蛇，分布于加利福尼亚植物区潮湿和凉爽的生态区。橡胶蟒是加利福尼亚本土的蚺科 2 种蛇之一，目前有 2 个公认的亚种，北方橡胶蟒 C. bottae bottae 和南方橡胶蟒 C. bottae umbratica。最近对 C. bottae 的基因组研究表明，这 2 个亚种共同由 4 个在中新世晚期分离的分化谱系组成。栖息地适宜性分析表明，来自加利福尼亚南部的 C. bottae umbratica 山地岛屿种群在未来 70 年内将失去其大部分栖息地，根据加利福尼亚濒危物种法案，被列为受威胁物种。在这里，我们报告了 C. bottae bottae 的一个新的染色体水平基因组组装，作为加利福尼亚保护基因组学项目（CCGP）的一部分。与 CCGP 的参考基因组策略一致，我们使用太平洋生物科学的 HiFi 长读长和 Hi-C 染色质邻近测序技术生成了一个从头组装的基因组。该组装包含 289 个支架，覆盖了 1804944895bp，具有 37.3Mb 的 contig N50、97Mb 的 scaffold N50 和 96.3%的 BUSCO 完整性得分，是蚺科蛇家族的第一个参考基因组。这个基因组将使研究 C. bottae bottae 和 C. bottae umbratica 种群在加利福尼亚的遗传分化和连通性成为可能，并帮助管理当地特有的谱系，因为它们面临着人类引起的气候变暖、干旱和野火在加利福尼亚的挑战。
