Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.
G3 (Bethesda). 2023 Jul 5;13(7). doi: 10.1093/g3journal/jkad106.
The leaf beetle Chrysomela aeneicollis has a broad geographic range across Western North America but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2,700-3,500 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here, we report a chromosome-scale genome assembly alongside a complete mitochondrial genome and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology with Tribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein-coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.
叶甲 Chrysomela aeneicollis 的分布范围很广，横跨北美西部，但仅限于西海岸高海拔的凉爽生境。加利福尼亚中部的种群仅出现在高海拔地区（2700-3500 米），那里氧气供应减少，与气候变化相关的近期干旱条件限制了它们的生存。在这里，我们报告了一个染色体水平的基因组组装，以及一个完整的线粒体基因组，并描述了在甲虫表现出显著的种群结构和对波动温度的适应的纬度梯度上，线粒体基因组之间的差异。我们组装的基因组由 21 个连锁群组成；其中一个我们根据雌性/雄性全基因组测序覆盖度和与 Tribolium castaneum 的同源性，确定为 X 染色体。我们在基因组中鉴定了重复序列，并发现它们广泛分布在所有连锁群中。使用参考转录组，我们总共注释了 12586 个蛋白质编码基因。我们还描述了线粒体 RNA 分子的假定二级结构的差异，这可能会产生对适应恶劣非生物条件很重要的功能差异。我们记录了线粒体 tRNA 分子的替换以及 16S rRNA 区域的替换和插入，这可能会影响与核基因组产物的分子间相互作用。这个第一个染色体水平的参考基因组将使在这个重要的模式生物中进行基因组研究成为可能，以了解气候变化对山地昆虫的生物学影响。
