The hyperdiverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome evolution of beetles, as well as genetic changes associated with specialization to high-elevation alpine habitats. In particular, this genome resource provides a foundation for expanding comparative molecular research into mechanisms of insect cold adaptation. Comparison to other beetles shows a strong signature of genome compaction, with N. riversi possessing a relatively small genome (~147 Mb) compared to other beetles, with associated reductions in repeat element content and intron length. Small genome size is not, however, associated with fewer protein-coding genes, and an analysis of gene family diversity shows significant expansions of genes associated with cellular membranes and membrane transport, as well as protein phosphorylation and muscle filament structure. Finally, our genomic analyses show that these high-elevation beetles have endosymbiotic Spiroplasma, with several metabolic pathways (e.g., propanoate biosynthesis) that might complement N. riversi, although its role as a beneficial symbiont or as a reproductive parasite remains equivocal.

中文翻译：

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高质量的carabid基因组组装提供了对甲虫基因组进化和冷适应的见解

高度多样化的鞘翅目包括地球上已知物种的约 25%。尽管最近在下一代测序方面取得了突破，但组装基因组中甲虫多样性的表现仍然有限。最值得注意的是，地面甲虫家族 Carabidae 包含超过 40,000 种描述的物种，尚未在比较基因组学框架中使用全基因组数据进行研究。在这里，我们为Nebria riversi生成了高质量的基因组组装，研究甲虫基因组进化的新颖性来源，以及与高海拔高山栖息地专业化相关的遗传变化。特别是，该基因组资源为将比较分子研究扩展到昆虫冷适应机制提供了基础。与其他甲虫的比较显示出基因组压实的强烈特征，与N. riversi与其他甲虫相比，它拥有相对较小的基因组（~147 Mb），并且相关的重复元件含量和内含子长度减少。然而，小的基因组大小与较少的蛋白质编码基因无关，对基因家族多样性的分析表明，与细胞膜和膜转运以及蛋白质磷酸化和肌丝结构相关的基因显着增加。最后，我们的基因组分析表明，这些高海拔甲虫具有内共生螺旋体，具有多种代谢途径（例如丙酸生物合成），可以补充N. riversi，尽管其作为有益共生体或生殖寄生虫的作用仍然模棱两可。