Data from: Trace DNA from insect skins: a comparison of five extraction protocols and direct PCR on chironomid pupal exuviae

Insect skins (exuviae) are of extracellular origin and shed during molting. The skins do not contain cells or DNA themselves, but epithelial cells and other cell-based structures might accidentally attach as they are shed. This source of trace DNA can be sufficient for PCR amplification and sequencing of target genes and aid in species identification through DNA barcoding or association of unknown life stages. Species identification is essential for biomonitoring programs, since species vary in sensitivities to environmental factors. However, it requires a DNA isolation protocol that optimizes the output of target DNA. Here we compare the relative effectiveness of five different DNA extraction protocols and direct PCR in isolation of DNA from chironomid pupal exuviae. Chironomidae (Diptera) is a species-rich group of aquatic macroinvertebrates widely distributed in freshwater environments and considered a valuable bioindicator of water quality. Genomic DNA was extracted from 61.2% of 570 sampled pupal exuviae. There were significant differences in the methods with regards to cost, handling time, DNA quantity, PCR success, sequence success, and the ability to sequence target taxa. The NucleoSpin® Tissue XS Kit, DNeasy® Blood and Tissue kit, and QuickExtract™ DNA Extraction Solution provided the best results in isolating DNA from single pupal exuviae. Direct PCR and DTAB/CTAB methods gave poor results. While the observed differences in DNA isolation methods on trace DNA will be relevant to research that focuses on aquatic macroinvertebrate ecology, taxonomy and systematics, they should also be of interest for studies using environmental barcoding and metabarcoding of aquatic environments.昆虫蜕皮（exuviae）属于细胞外结构，在昆虫蜕皮过程中脱落。其本身不含细胞或DNA，但在脱落过程中可能会意外附着上皮细胞及其他细胞类结构。这类痕量DNA来源足以实现靶基因的聚合酶链式反应（PCR）扩增与测序，可通过DNA条形码技术辅助物种鉴定，或用于关联未知的生命阶段。 物种鉴定对生物监测项目至关重要，因为不同物种对环境因子的敏感性存在差异。然而，该流程需要采用可优化靶DNA产出量的DNA提取方案。 本研究针对摇蚊科（Chironomidae，双翅目Diptera）蛹蜕皮的DNA提取，对比了5种不同DNA提取方案与直接PCR法的相对有效性。摇蚊科是一类物种丰富的水生大型无脊椎动物，广泛分布于淡水环境中，被视为极具价值的水质生物指示物。 本次研究共采集570份蛹蜕皮样本，其中61.2%的样本成功提取到基因组DNA。不同提取方法在成本、操作时长、DNA产量、PCR成功率、测序成功率以及靶类群测序能力方面均存在显著差异。 其中，NucleoSpin® Tissue XS试剂盒、DNeasy® Blood and Tissue试剂盒以及QuickExtract™ DNA提取溶液在单份蛹蜕皮样本的DNA提取中表现最优，而直接PCR法与DTAB/CTAB法的提取效果较差。 尽管本研究揭示的痕量DNA提取方法差异，与水生大型无脊椎动物的生态、分类及系统发育研究密切相关，但其研究结果同样可为水生环境的DNA条形码与元条形码（metabarcoding）相关研究提供参考。