Datasets associated with paper titled "Swabbing as a Non-lethal DNA Collection Method for Earthworm Barcoding: Performance and Citizen Science Perspectives"

Lethal sampling followed by destructive tissue subsampling is employed routinely in earthworm DNA barcoding studies. However, this approach may be ecologically disadvantageous and risks public disengagement with biodiversity and barcoding research due to negative emotional associations, particularly in Citizen Science (CS) projects. The study describes the performance of swab sampling as a non-lethal and emotionally-adaptive alternative to tissue sampling in earthworm barcoding. Three DNA collection methods, namely swab sampling with silica-based DNA extraction (Swab-QIAGEN), tissue sampling with silica-based DNA extraction (Tissue-QIAGEN), and tissue sampling with resin-based DNA extraction (Tissue-Chelex) were compared for generating cytochrome c oxidase I (COI) barcodes from 40 adult earthworms. All methods showed comparably high PCR amplification success rates (Tissue-Chelex=100%; Tissue-QIAGEN=100%; Swab-QIAGEN=97.5%), expect for one recalcitrant Swab-QIAGEN sample. Considering the pool of successfully amplified samples, the sequencing success rate for the Tissue-Chelex, Tissue-QIAGEN, and Swab-QIAGEN methods was 82.5% (33/40), 87.50% (35/40), and 66.7% (26/39), respectively—with 25 of 119 barcodes flagged as methodological failures due to unusable contigs, stop codons/indels, or contamination. Although swabs showed lower success rates overall, they produced the greatest proportion of reference-quality barcodes among functional sequences (80.8%; 21/26), indicating their strong potential for DNA collection compared to Tissue-Chelex (75.8%; 25/33) and Tissue-QIAGEN (68.6%; 24/35). All intra-specimen barcodes, excluding contaminations, received consistent homology-based taxonomic assignments with average similarity percentage above 99%, corresponding to a 90.4% morphospecies-genetic data concordance rate. The average intra-specimen pairwise sequence percentage identity was above 99% (<0.1% average sequencing error) across all methods, and no method-specific clustering was observed in the phylogenetic tree. Overall, the results indicated a high degree of interoperability and agreement between swab and tissue sampling methods for recovering the same or nearly-identical haplotypes with consistent taxonomic identities from each specimen. However, the swabbing methodology requires standardization before it can be confidently utilized in CS-based earthworm DNA barcoding projects.蚯蚓DNA条形码研究中，常规采用致死性采样后再进行破坏性组织分样的实验方案。然而该方法可能对生态环境造成不利影响，且由于会引发负面情绪联想，存在导致公众对生物多样性及条形码研究产生疏离的风险，这一点在公民科学（Citizen Science, CS）项目中尤为突出。本研究旨在评估拭子采样作为蚯蚓条形码研究中组织采样的非致死且情绪友好型替代方案的应用效果。本研究选取3种DNA采集方法进行对比，分别为：基于硅胶柱DNA提取的拭子采样法（Swab-QIAGEN）、基于硅胶柱DNA提取的组织采样法（Tissue-QIAGEN）以及基于树脂基DNA提取的组织采样法（Tissue-Chelex），以从40条成年蚯蚓中获取细胞色素c氧化酶I（cytochrome c oxidase I, COI）条形码序列。除1株难以扩增的Swab-QIAGEN样本外，所有方法的PCR扩增成功率均处于较高水平（Tissue-Chelex为100%；Tissue-QIAGEN为100%；Swab-QIAGEN为97.5%）。在成功完成扩增的样本池中，Tissue-Chelex、Tissue-QIAGEN和Swab-QIAGEN三种方法的测序成功率分别为82.5%（33/40）、87.50%（35/40）和66.7%（26/39）；119条条形码序列因存在不可用重叠群、终止密码子/插入缺失片段或污染问题被判定为方法学失败样本。尽管拭子采样法的整体成功率偏低，但在有效序列中，其产出的符合参考标准的条形码序列占比最高（80.8%；21/26），相较于Tissue-Chelex（75.8%；25/33）与Tissue-QIAGEN（68.6%；24/35），展现出更优异的DNA采集应用潜力。所有排除污染后的样本内条形码序列，均通过同源性分析获得了一致的分类学注释，平均相似性百分比高于99%，对应形态种与遗传数据的吻合率达90.4%。所有方法的样本内序列两两平均相似性百分比均高于99%（平均测序误差<0.1%），且系统发育树中未观察到按方法特异性形成的聚类簇。总体而言，研究结果表明，拭子采样与组织采样两种方法在从同一标本获取相同或近乎一致的单倍型、并获得一致分类学注释方面，具有高度的互操作性与一致性。但拭子采样法仍需进一步标准化，方可在基于公民科学的蚯蚓DNA条形码研究中放心应用。