Data from: Lessons from genome skimming of arthropod-preserving ethanol

Field-collected specimens of invertebrates are regularly killed and preserved in ethanol, prior to DNA extraction from the specimens, while the ethanol fraction is usually discarded. However, DNA may be released from the specimens into the ethanol, which can potentially be exploited to study species diversity in the sample without the need for DNA extraction from tissue. We used shallow shotgun sequencing of the total DNA to characterize the preservative ethanol from two pools of insects (from a freshwater habitat and terrestrial habitat) to evaluate the efficiency of DNA transfer from the specimens to the ethanol. In parallel, the specimens themselves were subjected to bulk DNA extraction and shotgun sequencing, followed by assembly of mitochondrial genomes for 39 of 40 species in the two pools. Shotgun sequencing from the ethanol fraction and read-matching to the mitogenomes detected ~40% of the arthropod species in the ethanol, confirming the transfer of DNA whose quantity was correlated to the biomass of specimens. The comparison of diversity profiles of microbiota in specimen and ethanol samples showed that ‘closed association’ (internal tissue) bacterial species tend to be more abundant in DNA extracted from the specimens, while ‘open association’ symbionts were enriched in the preservative fluid. The vomiting reflex of many insects also ensures that gut content is released into the ethanol, which provides easy access to DNA from prey items. Shotgun sequencing of DNA from preservative ethanol provides novel opportunities for characterizing the functional or ecological components of an ecosystem and their trophic interactions.野外采集的无脊椎动物标本通常先经处死并以乙醇固定保存，后续再从标本中提取DNA，而留存的乙醇保存液通常会被直接丢弃。然而，标本中的DNA可能会释放至乙醇保存液中，这一特性有望无需从动物组织中提取DNA，即可用于样本内物种多样性的研究。本研究针对两组分别采自淡水生境与陆生生境的昆虫混合样本的乙醇保存液，通过总DNA浅层鸟枪测序（shallow shotgun sequencing）对其进行表征，以评估标本DNA向乙醇保存液的转移效率。与此同时，我们对两组混合样本中的昆虫标本分别进行批量DNA提取与鸟枪测序，并完成了40个物种中39个物种的线粒体基因组（mitochondrial genomes）组装。对乙醇保存液的鸟枪测序结果与线粒体基因组进行序列比对后，检测到样本中约40%的节肢动物物种存在于乙醇保存液内，证实了DNA的转移现象，且DNA含量与标本生物量呈正相关。对比标本与乙醇保存液样本的微生物组（microbiota）多样性特征发现，‘封闭关联’（即宿主体内组织）的细菌类群在标本提取的DNA中丰度更高，而‘开放关联’的共生菌则在乙醇保存液中更为富集。多数昆虫的呕吐反射机制会使其肠道内容物释放至乙醇保存液中，这也为获取猎物的DNA提供了便捷途径。对乙醇保存液中的DNA进行鸟枪测序，为解析生态系统的功能与生态组成及其营养级互作关系提供了全新的研究思路。