Received date: 2020-07-30
Revised date: 2020-09-27
Online published: 2020-11-10
There are many methods to extract ancient DNA from ancient raw materials. Generally, the research of ancient DNA is subject to factors such as serious degradation, while the low content of endogenous ancient DNA, the high content of microbial and modern human DNA. Whether we can successfully obtain reliable and sufficient endogenous ancient DNA has always been a practical difficulty and challenge in the field of ancient DNA research. The most direct and convenient strategy to eliminate the pollution effectively is in the procedure of ancient DNA extraction. This paper summarized the common methods of ancient DNA extraction to remove exogenous pollutants. We compared and analyzed the advantages and disadvantages of each method. This paper also introduced the time commonly used in the bone lysis step and suggested the best incubation time was 4 days at room temperature by exploring the effect of different lysis time on the recovery efficiency of ancient DNA. At the same time, we surveyed the representative methods of ancient DNA purification and the performance in the application. Our summary and experience could provide reference information for researchers in the field of ancient DNA research.
Jing ZHAO , Chuanchao WANG . Comparison and summary of ancient DNA extraction technology[J]. Acta Anthropologica Sinica, 2020 , 39(04) : 706 -716 . DOI: 10.16359/j.cnki.cn11-1963/q.2020.0062
| [1] | Campos PF, Willerslev E, Sher A, et al. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010,107(12):5675-5680 |
| [2] | Leonard JA, Wayne RK, Cooper A. Population genetics of ice age brown bears[J]. Proceedings of the National Academy of Sciences of the United States of America, 2000,97(4):1651-1654 |
| [3] | Pinsky ML, Newsome SD, Dickerson BR, et al. Dispersal provided resilience to range collapse in a marine mammal: insights from the past to inform conservation biology[J]. Mol Ecol, 2010,19(12):2418-2429 |
| [4] | Shapiro B, Drummond AJ, Rambaut A, et al. Rise and fall of the Beringian steppe bison[J]. Science, 2004,306(5701):1561-1565 |
| [5] | Stiller M, Baryshnikov G, Bocherens H, et al. Withering away--25,000 years of genetic decline preceded cave bear extinction[J]. Mol Biol Evol, 2010,27(5):975-978 |
| [6] | Ning C, Li TJ, Wang K, et al. Ancient genomes from northern China suggest links between subsistence changes and human migration[J]. Nature communications, 2020,11(1):2700 |
| [7] | Wang K, Goldstein S, Bleasdale M, et al. Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa[J]. Science Advance, 2020, 6 eaaz0183 |
| [8] | Narasimhan VM, Patterson N, Moorjani P, et al. The Genomic Formation of South and Central Asia[J]. bioRxiv, 2018 |
| [9] | Green RE, Krause J, Briggs AW, et al. A draft sequence of the Neandertal genome[J]. Science, 2010,328(5979):710-722 |
| [10] | Shapiro B, Sibthorpe D, Rambaut A, et al. Flight of the Dodo[J]. Science, 2002,2951683 |
| [11] | Krause J, Unger T, Nocon A, et al. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary[J]. BMC Evol Biol, 2008,8220 |
| [12] | Orlando L, Metcalf J, Alberdi M, et al. Revising the recent evolutionary history of equids using ancient DNA[J]. Proc Natl Acad Sci USA, 2009, 10621754-21759 |
| [13] | Barquera R, Krause J. An ancient view on host-pathogen interaction across time and space[J]. Current opinion in immunology, 2020, 6565-69. |
| [14] | 吴苡婷. 古DNA检测技术在抗击新冠中的特殊作用[N]. 上海科技报, 2020. |
| [15] | Collins MJ, Nielsen-Marsh CM, Hiller J, et al. The survival of organic matter in bone: a review[J]. Archaeometry, 2002,44(3):383-394 |
| [16] | Hofreiter M, Paijmans JL, Goodchild H, et al. The future of ancient DNA: Technical advances and conceptual shifts[J]. Bioessays, 2015,37(3):284-293 |
| [17] | Campos PF, Craig OE, Turner-Walker G, et al. DNA in ancient bone - where is it located and how should we extract it?[J]. Ann Anat, 2012,194(1):7-16 |
| [18] | Korlevic P, Gerber T, Gansauge MT, et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth[J]. BioTechniques, 2015,59(2):87-93 |
| [19] | Lindahl T. Instability and decay of the primary structure of DNA[J]. Nature, 1993, 362709-715 |
| [20] | Brundin M, Figdor D, Sundqvist G, et al. DNA binding to hydroxyapatite: a potential mechanism for preservation of microbial DNA[J]. J Endod, 2013,39(2):211-216 |
| [21] | Svintradze DV, Mrevlishvili GM, Metreveli N, et al. Collagen-DNA Complex[J]. Biomacromolecules, 2008, 921-28 |
| [22] | Reich D, Green RE, Kircher M, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia[J]. Nature, 2010,468(7327):1053-1060 |
| [23] | Prufer K, Racimo F, Patterson N, et al. The complete genome sequence of a Neanderthal from the Altai Mountains[J]. Nature, 2014,505(7481):43-49 |
| [24] | Gamba C, Jones ER, Teasdale MD, et al. Genome flux and stasis in a five-millennium transect of European prehistory[J]. Nature, communications, 2014,55257 |
| [25] | Burbano HA, Hodges E, Green RE, et al. Targeted Investigation of the Neandertal Genome by Array-Based Sequence[J]. Science, 2010, 328723-725 |
| [26] | Avila-Arcos MC, Cappellini E, Romero-Navarro JA, et al. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA[J]. Sci Rep, 2011,174 |
| [27] | Fu QM, Meyer M, Gao X, et al. DNA analysis of an early modern human from Tianyuan Cave, China[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013,110(6):2223-2227 |
| [28] | Carpenter ML, Buenrostro JD, Valdiosera C, et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries[J]. Am J Hum Genet, 2013,93(5):852-864 |
| [29] | Castellano S, Parra G, Sanchez-Quinto FA, et al. Patterns of coding variation in the complete exomes of three Neandertals[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014,111(18):6666-6671 |
| [30] | Meynert AM, Ansari M, FitzPatrick DR, et al. Variant detection sensitivity and biases in whole genome and exome sequencing[J]. BMC Bioinformatics, 2014,15247 |
| [31] | Briggs AW, Stenzel U, Johnson PLF, et al. Patterns of damage in genomic DNA sequences from a Neandertal[J]. Proc. Natl. Acad. Sci, 2007, 10414616-14621 |
| [32] | Gansauge MT, Meyer M. Selective enrichment of damaged DNA molecules for ancient genome sequencing[J]. Genome Res, 2014,24(9):1543-1549 |
| [33] | Geigl E. On the circumstances surrounding the preservation and analysis of very old DNA[J]. Archaeometry, 2002, 44337-342 |
| [34] | H?ss M, Dilling A, Currant A, et al. Molecular phylogeny of the extinct ground sloth mylodon darwinii[J]. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93181-185 |
| [35] | Hansen AJ, Mitchell DL, Wiuf C, et al. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments[J]. Genetics, 2006, 1731175-1179 |
| [36] | Hofreiter M, Jaenicke V, Serre D, et al. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient dna[J]. Nucleic Acids Research, 2001, 294793-4799 |
| [37] | Rohland N, Hofreiter M. Comparison and optimization of ancient DNA extraction[J]. BioTechniques, 2007, 42343-352 |
| [38] | Tebbe CC, Vahjen W. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast[J]. Appl Environ Microbiol, 1993, 592657-2665 |
| [39] | Tuross N. The biochemistry of ancient DNA in bone[J]. Experientia, 1994, 50530-535 |
| [40] | Li R, Liriano L. A bone sample cleaning method using trypsin for the isolation of DNA[J]. Leg Med (Tokyo), 2011,13(6):304-308 |
| [41] | Kemp BM, Smith DG. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth[J]. Forensic Sci Int, 2005,154(1):53-61 |
| [42] | Barta JL, Monroe C, Kemp BM. Further evaluation of the efficacy of contamination removal from bone surfaces[J]. Forensic Sci Int, 2013,231(1-3):340-348 |
| [43] | Salamon M, Tuross N, Arensburg B, et al. Relatively well preserved DNA is present in the crystal aggregates of fossil bones[J]. PNAS, 2005,102(39):13783-13788 |
| [44] | Malmstrom H, Svensson EM, Gilbert MT, et al. More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA[J]. Mol Biol Evol, 2007,24(4):998-1004 |
| [45] | Dabney J, Knapp M, Glocke I, et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013,110(39):15758-15763 |
| [46] | Hajdinjak M, Fu QM, Hubner A, et al. Reconstructing the genetic history of late Neanderthals[J]. Nature, 2018 |
| [47] | Ginolhac A, Vilstrup J, Stenderup J, et al. Improving the performance of true single molecule sequencing for ancient DNA[J]. BMC Genomics, 2012,13177 |
| [48] | Peter B. Damgaard AM, Hannes Schroeder, Ludovic Orlando,, Eske Willerslev MEA. Improving access to endogenous DNA in ancient bones and teeth[J]. Scientific Reports, 2015,511184 |
| [49] | Sikora M, Pitulko VV, Sousa VC, et al. The population history of northeastern Siberia since the Pleistocene[J]. Nature, 2019,570(7760):182-188 |
| [50] | Bernardi G. Chromatography of Nucleic Acids on Hydroxyapatite[J]. Nature, 1965, 206779-783 |
| [51] | Grunenwald A, Keyser C, Sautereau AM, et al. Adsorption of DNA on biomimetic apatites: Toward the understanding of the role of bone and tooth mineral on the preservation of ancient DNA[J]. Appl Surf Sci, 2014, 292867-875 |
| [52] | Persson P. A method to recover DNA from ancient bones[J]. Ancient DNA Newsl, 1992, 125-27 |
| [53] | G?therstr?m A, Lidén K. A modified DNA extraction method for bone and teeth[J]. Laborativ Arkeologi, 1996, 953-56 |
| [54] | Bajorath J, Saenger W, Pal GP. Autolysis and inhibition of proteinase K, a subtilisin-related serine proteinase isolated from the fungus Tritirachium album Limber[J]. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, 1988,954:176-182 |
| [55] | 刘杨柳, 武小芳, 胡树样, 等. 蛋白酶K的性质及其在核酸提取中的应用[J]. 食品研究与开发, 2017,38(10):196-199 |
| [56] | Hofreiter M, Rabeder G, Jaenicke-Despres V, et al. Evidence for reproductive isolation between cave bear populations[J]. Curr Biol, 2004,14(1):40-43 |
| [57] | Rohland N, Hofreiter M. Ancient DNA extraction from bones and teeth[J]. Nature protocols, 2007,2(7):1756-1762 |
| [58] | Yang DY, Eng B, Waye JS, et al. Improved DNA extraction from Ancient Bones Using Silica-Based Spin Columns[J]. American Journal of Physical Anthropology, 1998,105(4):539-543 |
| [59] | Juras A, Makarowicz P, Chylenski M, et al. Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations[J]. Am J Phys Anthropol, 2020,172(2):176-188 |
| [60] | Rohland N, Siedel H, Hofreiter M. A rapid column-based ancient DNA extraction method for increased sample throughput[J]. Molecular ecology resources, 2010,10(4):677-683 |
| [61] | Sullivan NO, Posth C, Coia V, et al. Ancient genome-wide analyses infer kinship structure[J]. Science Advance, 2018, 4 eaao1262 |
| [62] | Gaudio D, Fernandes DM, Schmidt R, et al. Genome-Wide DNA from Degraded Petrous Bones and the Assessment of Sex and Probable Geographic Origins of Forensic Cases[J]. Sci Rep, 2019,9(1):8226 |
| [63] | 杨百全, 王利君, 遇长青, 等. 磁珠法回收纯化 DNA样本[J]. 中国法医学杂志, 2006,21:10-11 |
| [64] | Zhao J, Liu FE, Lin S, et al. Investigation on maternal lineage of a Neolithic group from northern Shaanxi based on ancient DNA[J]. Mitochondrial DNA A DNA Mapp Seq Anal, 2017,28(5):732-739 |
| [65] | Kalmár T, Bachrati CZ, Marcsik A, et al. A simple and efficient method for PCR amplifiable DNA extraction from ancient bones[J]. Nucleic Acids Research, 2000,28(12):E67 |
| [66] | Orlando L, Ginolhac A, Raghavan M, et al. True single-molecule DNA sequencing of a pleistocene horse bone[J]. Genome Res, 2011,21(10):1705-1719 |
| [67] | Rohland N, Siedel H, Hofreiter M. Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens[J]. BioTechniques, 2004, 36814-821 |
| [68] | Hervella M, Iniguez MG, Izagirre N, et al. Nondestructive methods for recovery of biological material from human teeth for DNA extraction[J]. J Forensic Sci, 2015,60(1):136-141 |
| [69] | Gomes C, Palomo-Díez S, Roig J, et al. Nondestructive extraction DNA method from bones or teeth, true or false?[J]. Forensic Science International: Genetics Supplement Series, 2015, 5e279-e282 |
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