Unlocking inaccessible historical genomes preserved in formalin
Unlocking inaccessible historical genomes preserved in formalin
复制标题
解锁福尔马林中保存的难以获取的历史基因组
DOI：
10.1101/2021.04.18.440380
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
C. Holleley
中科院分区：
文献类型：
--
作者：
Erin E. Hahn;Marina Alexander;Alicia Grealy;J. Stiller;D. Gardiner;C. Holleley
博物馆标本代表了历史基因组数据的无与伦比的记录。然而，广泛使用的福尔马林保存方法阻碍了大部分标本的基因组分析。福尔马林保存标本的有限DNA测序产生了低基因组覆盖率，取得了不可预测的成功。我们着手改进样品处理方法，并确定预测测序成功的标本特征。利用1936年至2015年收集的一组分类学上不同的标本，并在保存质量方面有所不同，我们比较了几种端到端全基因组测序工作流程以及基于k聚体的无修剪读段比对方法的有效性，以最大限度地映射内源性序列。结果我们从福尔马林固定的组织中恢复了完整的线粒体基因组和高达3倍的核基因组覆盖率。热碱裂解结合酚-氯仿抽提法在回收DNA方面优于蛋白酶K消化法，而文库制备方法对测序成功率影响不大。DNA产量的最强预测因子是整体样本条件，其与保存条件相互作用加速DNA降解。结论：我们证明了一个显着的进步，在能力超越有限的恢复少数位点通过PCR或靶捕获测序。为了便于战略选择合适的标本进行基因组测序，我们提出了一个决策框架，利用独立的和非破坏性的评估标准。福尔马林固定标本的测序将有助于更好地了解遗传适应的时间趋势，包括与气候变化有关的趋势。我们的工作通过解锁被视为有效分子资源的标本基因组，提高了世界各地博物馆藏品的价值。
Background Museum specimens represent an unparalleled record of historical genomic data. However, the wide-spread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1936 and 2015 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. Results We recovered complete mitochondrial genomes and up to 3X nuclear genome coverage from formalin-fixed tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out- performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Conclusions We demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and non-destructive assessment criteria. Sequencing of formalin-fixed specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.
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影响因子：
3.2
作者：
Burrell, Andrew S.;Disotell, Todd R.;Bergey, Christina M.
通讯作者：
Bergey, Christina M.
影响因子：
2.6
作者：
Linck EB;Hanna ZR;Sellas A;Dumbacher JP
通讯作者：
Dumbacher JP
基于古基因组荟萃分析的古代DNA衰变新模型
DOI：
10.1101/109140
发表时间：
2017
期刊：
--
影响因子：
--
作者：
Kistler L
通讯作者：
Kistler L
影响因子：
16.8
作者：
Feigin, Charles Y.;Newton, Axel H.;Pask, Andrew J.
通讯作者：
Pask, Andrew J.
影响因子：
7.7
作者：
Tsai, Whitney L. E.;Schedl, Margaret E.;McCormack, John E.
通讯作者：
McCormack, John E.