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Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples

Ming Zhang Peng Cao Qing-Yan Dai Yong-Qiang Wang Xiao-Tian Feng Hong-Ru Wang Hong Wu Albert Min-Shan Ko Xiao-Wei Mao Yi-Chen Liu Li Yu Christian Roos Tilo Nadler Wen Xiao E. Andrew Bennett Qiao-Mei Fu

Ming Zhang, Peng Cao, Qing-Yan Dai, Yong-Qiang Wang, Xiao-Tian Feng, Hong-Ru Wang, Hong Wu, Albert Min-Shan Ko, Xiao-Wei Mao, Yi-Chen Liu, Li Yu, Christian Roos, Tilo Nadler, Wen Xiao, E. Andrew Bennett, Qiao-Mei Fu. Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples. Zoological Research, 2021, 42(3): 280-286. doi: 10.24272/j.issn.2095-8137.2020.377
Citation: Ming Zhang, Peng Cao, Qing-Yan Dai, Yong-Qiang Wang, Xiao-Tian Feng, Hong-Ru Wang, Hong Wu, Albert Min-Shan Ko, Xiao-Wei Mao, Yi-Chen Liu, Li Yu, Christian Roos, Tilo Nadler, Wen Xiao, E. Andrew Bennett, Qiao-Mei Fu. Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples. Zoological Research, 2021, 42(3): 280-286. doi: 10.24272/j.issn.2095-8137.2020.377

陈旧动物皮张的古DNA提取方法比较研究

doi: 10.24272/j.issn.2095-8137.2020.377

Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples

Funds: This work was supported by the Chinese Academy of Sciences (CAS, XDB26000000), National Natural Science Foundation of China (41925009, 41630102, 41672021), CAS (XDA1905010, QYZDB-SSW-DQC003), “Research on the Roots of Chinese Civilization” of Zhengzhou University (XKZDJC202006), Tencent Foundation through the XPLORER PRIZE, and Howard Hughes Medical Institute (55008731)
More Information
  • 摘要: 濒危或已灭绝动物的DNA研究通常依据古代或已严重降解的标本遗存。比较成熟的古DNA(ancient DNA,aDNA)提取方法主要针对于骨骼样本,对于皮张和毛发的研究较为少见。与古代的骨骼和牙齿情况相似,陈旧皮张样品中的DNA也由于自然降解等情况的存在,使得获取到的DNA片段长度极短、内源DNA含量极低。因此,针对这些样品,需要开发有效的DNA提取方法。本研究以几十年前到铁器时代的动物皮张和毛发样品为材料,比较2种提取方法(试剂盒法和古DNA实验室法)及相互组合的2种方法的DNA提取效果。研究发现除样品本身的差别(如年代等),皮张样品比毛发样品保留更多的内源DNA。所有方法都能够从陈旧的皮张样品中获取内源DNA,但是实验室的方法在DNA产量和质量上整体优于其它方法,实验室方法在纯化上的表现优于试剂盒方法。
    #Authors contributed equally to this work
  • Figure  1.  Experimental design, DNA yield of each sample, and sequence content of library bar plots of this study

    A: Experimental design showing different combinations of applied extraction and binding buffers (from kit (K) or laboratory (L)). KK: Both buffers from kit; KL: Lysis buffer from kit, laboratory-made binding buffer; LK: Laboratory-made lysis buffer, binding buffer from kit; LL: Both buffers made in laboratory. B: DNA yield of each sample. (a) Normalized amount of DNA for historical skin samples of monkeys, y-axis shows results of normalized molecule number. (b) Normalized amount of DNA for historical hair samples of monkeys. (c) Normalized amount of DNA for ancient samples of dogs. C: Sequence content of library bar plots (a) DNA yield. (b) Number of uniquely mapped reads. (c) Clonality. Percentage shown as a fraction of highest value among different methods for same samples. Dotted horizontal bar represents average values of each method.

    Table  1.   Samples used in this study

    SampleRegion, countrySample age (years before present)Species
    Skin-1Yunnan Province, China~30Rhinopithecus strykeri
    Hair-1Yunnan Province, China~30Rhinopithecus strykeri
    Skin-2Yunnan Province, China~50Rhinopithecus strykeri
    Hair-2Yunnan Province, China~50Rhinopithecus strykeri
    Skin-3Na Hang, VietnamSeveral decadesRhinopithecus avunculus
    Skin-4Xinjiang Uyghur Autonomous Region, China~2 400–3 100Canis lupus familiaris
    Skin-5Xinjiang Uyghur Autonomous Region, China~2 400–3 100Canis lupus familiaris
    Skin-6Xinjiang Uyghur Autonomous Region, China~2 400–3 100Canis lupus familiaris
    下载: 导出CSV
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出版历程
  • 收稿日期:  2020-12-28
  • 录用日期:  2021-03-19
  • 网络出版日期:  2021-04-07
  • 刊出日期:  2021-05-18

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