K. M. Sumby, J. R. Stephen, J. J. Austin, R. K. Schilling, T. R. Cavagnaro
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评估冷冻档案 DNA 样品完整性的新方法：短线程和长线程 16S rRNA 基因序列的阿尔法多样性比率
几十年来，在大学、政府机构和商业服务提供商的实验室中积累了为一系列研究和应用问题收集和分析的 DNA 档案样本。这些 DNA 档案是宝贵的基因组信息库，但在很大程度上尚未得到开发利用。随着高通量测序成本的降低和获取途径的增加，我们预测回溯性研究将会增加，以探索这些档案样本中蕴藏的丰富信息。然而，要做到这一点，我们需要对 DNA 样本的完整性有信心，因为这些样本通常是在不理想的条件下保存的，而且它们也不适合用于下游基因组分析。在此，我们借鉴古 DNA 中一个成熟的概念来评估样本的完整性，即冷冻 DNA 样本中恢复的扩增子信息含量的损失，并基于短线程和长线程 16S rRNA 基因序列的⍺-多样性比率。使用 PacBio 全长读数（V1-V9，1.5 kbp）和 Illumina 短读数（V3-V4，200-450 bp）对 2001 年至 2021 年期间从澳大利亚西部和南部农业区采集的 87 个从土壤中提取的储存 DNA 样本的 16S rRNA 可变区进行测序。当计算长读码和短读码的多样性比值以评估DNA降解情况时，年龄较大的样本与年龄较小的样本相比，多样性比值并没有降低。我们建议将此作为一种新方法，在利用档案 DNA 开展大规模多样性分析项目之前确认 DNA 的完整性。
期刊介绍：
A British Ecological Society journal, Methods in Ecology and Evolution (MEE) promotes the development of new methods in ecology and evolution, and facilitates their dissemination and uptake by the research community. MEE brings together papers from previously disparate sub-disciplines to provide a single forum for tracking methodological developments in all areas.
MEE publishes methodological papers in any area of ecology and evolution, including:
-Phylogenetic analysis
-Statistical methods
-Conservation & management
-Theoretical methods
-Practical methods, including lab and field
-This list is not exhaustive, and we welcome enquiries about possible submissions. Methods are defined in the widest terms and may be analytical, practical or conceptual.
A primary aim of the journal is to maximise the uptake of techniques by the community. We recognise that a major stumbling block in the uptake and application of new methods is the accessibility of methods. For example, users may need computer code, example applications or demonstrations of methods.
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