Draft genome of a dung beetle, Phelotrupes auratus

Knowledge of population divergence history is key to understanding organism diversification mechanisms. The geotrupid dung beetle, Phelotrupes auratus, which inhabits montane forests and exhibits three color forms (red, green, and indigo), diverged into five local populations (west/red, south/green, south/indigo, south/red, and east/red) in the Kinki District of Honshu, Japan, based on the combined interpretation of genetic cluster and color-form data. Here, we estimated the demographic histories of these local populations using the newly assembled draft genome sequence of P. auratus and whole-genome resequencing data obtained from each local population. Using coalescent simulation analysis, we estimated P. auratus population divergences at ca. 3,800, 2,100, 600, and 200 years ago, with no substantial gene flow between diverged populations, implying the existence of persistent barriers to gene flow. Notably, the last two divergence events led to three local populations with different co..., We constructed this draft genome using ONT PromethION long reads and Illumina HiSeq X short reads from an adult individual of Phelotrupes auratus by de novo assembly using MaSuRCA 3.4.2 (Zimin et al., 2013). The constructed draft genome was polished with racon 1.4.13 (Vaser et al., 2017) and Pilon 1.23 (Walker et al., 2014), then curated using Purge Haplotigs 1.0.4 (Roach, Schmidt, & Borneman, 2018).,阐明生物的多样化机制，核心在于解析其种群分化历史。栖息于山地森林、兼具红、绿、靛蓝三种色型的蜣螂科（Geotrupidae）亮斑蜣螂*Phelotrupes auratus*，经遗传聚类与色型数据的综合分析，在日本本州岛近畿地区分化为5个本地种群：西部/红色型、南部/绿色型、南部/靛蓝色型、南部/红色型以及东部/红色型。 本研究利用全新组装的亮斑蜣螂*Phelotrupes auratus*草图基因组序列，以及各本地种群的全基因组重测序数据，对这些种群的动态历史展开推断。 通过溯祖模拟分析（coalescent simulation analysis），我们推断该蜣螂的种群分化事件分别发生于约3800年、2100年、600年及200年前；分化后的种群间未出现显著基因交流，提示存在持续存在的基因流障碍。值得注意的是，后两次分化事件形成了3个具有不同……的本地种群。 本研究从一头成年亮斑蜣螂*Phelotrupes auratus*个体中获取ONT PromethION长读长序列与Illumina HiSeq X短读长序列，通过MaSuRCA 3.4.2（Zimin等，2013）进行从头组装，构建了该物种的草图基因组。 所构建的草图基因组经racon 1.4.13（Vaser等，2017）与Pilon 1.23（Walker等，2014）进行抛光校正后，再通过Purge Haplotigs 1.0.4（Roach、Schmidt & Borneman，2018）完成单倍体分型校正。