Data from: Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA

Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3–6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58–159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1–10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers, and library amplification. We present these guidelines to facilitate more economical use of valuable DNA, and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens.

尽管现有技术已实现老旧博物馆标本的DNA测序，但针对体型微小的历史标本开展测序仍颇具挑战性且结果可靠性不足，因多数此类标本仅携带微量碎片化DNA。若此类标本为独有的馆藏珍品，可靠的测序方法便显得尤为关键。本研究针对已干燥保存于博物馆58至159年、几乎无合适替代标本的甲虫类历史标本（含模式标本（nomenclatural types），体型仅3至6毫米）开展测序尝试。为明确最优样本制备方案并形成标准化制备指南，我们以1至10纳克的低起始输入DNA量为基准，对比了多种不同的文库制备方案。此外，我们还探索了一系列低成本优化手段，旨在提升低DNA含量历史标本的文库制备效率与测序成功率，例如DNA酶促修复技术。尽管采用低起始DNA量的实验方案，我们仍成功完成了所有历史标本的样本制备与测序工作。我们整理了涵盖DNA修复、磁珠操作、减少接头二聚体及文库扩增等环节的操作指南。本研究提出的上述指南，可助力珍贵DNA样本的更经济化使用，并为针对难以测序、不可替代的历史标本的研究项目提供更稳定的实验结果保障。