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

doi:10.24272/j.issn.2095-8137.2020.377

Volume 42 Issue 3

May 2021

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Article Navigation > Zoological Research > 2021 > 42(3): 280-286

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

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

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

doi: 10.24272/j.issn.2095-8137.2020.377

Ming Zhang^{1, 2, 3, #},
Peng Cao^{1, 2, #},
Qing-Yan Dai^{1, 2, #},
Yong-Qiang Wang⁴,
Xiao-Tian Feng^{1, 2},
Hong-Ru Wang¹,
Hong Wu⁵,
Albert Min-Shan Ko¹,
Xiao-Wei Mao^{1, 2},
Yi-Chen Liu^{1, 2},
Li Yu⁵,
Christian Roos⁶,
Tilo Nadler⁷,
Wen Xiao⁸,
E. Andrew Bennett^{1, 2
,
,},
Qiao-Mei Fu^{1, 2, 3
,
,}

1.
Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
2.
CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
3.
University of Chinese Academy of Sciences, Beijing 100049, China
4.
Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi, Xinjiang 830011, China
5.
State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
6.
Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
7.
Wildlife Consultant, Cuc Phuong Commune, Nho Quan, Ninh Binh 430000, Vietnam
8.
Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan 671003, China

#Authors contributed equally to this work

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

Corresponding author: E-mail: eandrew@gmail.com; fuqiaomei@ivpp.ac.cn
Received Date: 2020-12-28
Accepted Date: 2021-03-19

Published Online: 2021-04-07

Publish Date: 2021-05-18

Abstract

Abstract

DNA studies of endangered or extinct species often rely on ancient or degraded remains. The majority of ancient DNA (aDNA) extraction protocols focus on skeletal elements, with skin and hair samples rarely explored. Similar to that found in bones and teeth, DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes. Thus, the development of effective DNA extraction methods is required for these materials. Here, we compared the performance of two DNA extraction protocols (commercial and custom laboratory aDNA methods) on hair and skin samples from decades-old museum specimens to Iron Age archaeological material. We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation, skin yielded more endogenous DNA than hair of the samples and protocols tested. While both methods recovered DNA from ancient soft tissue, the laboratory method performed better overall in terms of DNA yield and quality, which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.
- DNA extraction method,
- Ancient DNA,
- High-throughput sequencing,
- Historical and ancient skin materials

#Authors contributed equally to this work

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References(31)

References

[1]	Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, et al. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences of the United States of America, 104(37): 14616−14621. doi: 10.1073/pnas.0704665104
[2]	Dabney J, Meyer M, Pääbo S. 2013. Ancient DNA damage. Cold Spring Harbor Perspectives in Biology, 5(7): a012567.
[3]	Daley T, Smith AD. 2013. Predicting the molecular complexity of sequencing libraries. Nature Methods, 10(4): 325−327. doi: 10.1038/nmeth.2375
[4]	Damgaard PB, Margaryan A, Schroeder H, Orlando L, Willerslev E, Allentoft ME. 2015. Improving access to endogenous DNA in ancient bones and teeth. Scientific Reports, 5: 11184. doi: 10.1038/srep11184
[5]	Ermini L, Der Sarkissian C, Willerslev E, Orlando L. 2015. Major transitions in human evolution revisited: a tribute to ancient DNA. Journal of Human Evolution, 79: 4−20. doi: 10.1016/j.jhevol.2014.06.015
[6]	Fulton TL, Wagner SM, Shapiro B. 2012. Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon. In: Shapiro B, Hofreiter M. Ancient DNA: Methods and Protocols. New York: Humana Press, 29–35.
[7]	Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, et al. 2016. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Molecular Ecology Resources, 16(2): 459−469. doi: 10.1111/1755-0998.12470
[8]	Gilbert MTP, Tomsho LP, Rendulic S, Packard M, Drautz DI, Sher A, et al. 2007. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science, 317(5846): 1927−1930. doi: 10.1126/science.1146971
[9]	Gilbert MTP, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, et al. 2004. Ancient mitochondrial DNA from hair. Current Biology, 14(12): R463−R464. doi: 10.1016/j.cub.2004.06.008
[10]	Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L. 2011. Mapdamage: testing for damage patterns in ancient DNA sequences. Bioinformatics, 27(15): 2153−2155. doi: 10.1093/bioinformatics/btr347
[11]	Glocke I, Meyer M. 2017. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Research, 27(7): 1230−1237. doi: 10.1101/gr.219675.116
[12]	Head SR, Komori HK, LaMere SA, Whisenant T, van Nieuwerburgh F, Salomon DR, et al. 2014. Library construction for next-generation sequencing: overviews and challenges. Biotechniques, 56(2): 61−77.
[13]	Hung CM, Lin RC, Chu JH, Yeh CF, Yao CJ, Li SH. 2013. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One, 8(2): e56301. doi: 10.1371/journal.pone.0056301
[14]	Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L. 2013. Mapdamage2.0: fast approximate bayesian estimates of ancient DNA damage parameters. Bioinformatics, 29(13): 1682−1684. doi: 10.1093/bioinformatics/btt193
[15]	Kircher M, Sawyer S, Meyer M. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the illumina platform. Nucleic Acids Research, 40(1): e3. doi: 10.1093/nar/gkr771
[16]	Ko AMS, Zhang YQ, Yang MA, Hu YB, Cao P, Feng XT, et al. 2018. Mitochondrial genome of a 22,000-year-old giant panda from southern China reveals a new panda lineage. Current Biology, 28(12): R693−R694. doi: 10.1016/j.cub.2018.05.008
[17]	Korlević P, Gerber T, Gansauge MT, Hajdinjak M, Nagel S, Aximu-Petri A, et al. 2015. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. BioTechniques, 59(2): 87−93.
[18]	Li H, Durbin R. 2010. Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics, 26(5): 589−595. doi: 10.1093/bioinformatics/btp698
[19]	Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. 2009. The sequence alignment/map format and samtools. Bioinformatics, 25(16): 2078−2079. doi: 10.1093/bioinformatics/btp352
[20]	Liedigk R, Yang MY, Jablonski NG, Momberg F, Geissmann T, Lwin N, et al. 2012. Evolutionary history of the odd-nosed monkeys and the phylogenetic position of the newly described Myanmar snub-nosed monkey Rhinopithecus strykeri. PLoS One, 7(5): e37418. doi: 10.1371/journal.pone.0037418
[21]	Meyer M, Fu QM, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature, 505(7483): 403−406. doi: 10.1038/nature12788
[22]	Meyer M, Kircher M. 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols, 6: 1−10.
[23]	Nieves-Colón MA, Ozga AT, Pestle WJ, Cucina A, Tiesler V, Stanton TW, et al. 2018. Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments. American Journal of Physical Anthropology, 166(4): 824−836. doi: 10.1002/ajpa.23472
[24]	Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, et al. 2011. True single-molecule DNA sequencing of a Pleistocene horse bone. Genome Research, 21(10): 1705−1719. doi: 10.1101/gr.122747.111
[25]	Overballe-Petersen S, Orlando L, Willerslev E. 2012. Next-generation sequencing offers new insights into DNA degradation. Trends in Biotechnology, 30(7): 364−368. doi: 10.1016/j.tibtech.2012.03.007
[26]	Pedersen MW, Overballe-Petersen S, Ermini L, Der Sarkissian C, Haile J, Hellstrom M, et al. 2015. Ancient and modern environmental DNA. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1660): 20130383. doi: 10.1098/rstb.2013.0383
[27]	Rasmussen M, Guo XS, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, et al. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science, 334(6052): 94−98. doi: 10.1126/science.1211177
[28]	Rasmussen M, Li YR, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature, 463(7282): 757−762. doi: 10.1038/nature08835
[29]	Renaud G, Stenzel U, Kelso J. 2014. Leehom: adaptor trimming and merging for illumina sequencing reads. Nucleic Acids Research, 42(18): e141. doi: 10.1093/nar/gku699
[30]	Rohland N, Glocke I, Aximu-Petri A, Meyer M. 2018. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nature Protocols, 13(11): 2447−2461. doi: 10.1038/s41596-018-0050-5
[31]	Yang MA, Fan XC, Sun B, Chen CY, Lang JF, Ko YC, et al. 2020. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science, 369(6501): 282−288. doi: 10.1126/science.aba0909