Next generation sequencing of ancient DNA: Requirements, strategies and perspectives

Genes

Volumn 1, Issue 2, 2010, Pages 227-243

  Knapp, Michael ^a   Hofreiter, Michael ^b  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Ancient DNA; Barcoding; Genome sequencing; Hybridization capture; Targeted sequencing

Indexed keywords

MITOCHONDRIAL DNA; SINGLE STRANDED DNA;

DNA BARCODING; DNA EXTRACTION; DNA FRAGMENTATION; DNA HYBRIDIZATION; DNA LIBRARY; DNA SEQUENCE; DNA TEMPLATE; HUMAN; METAGENOMICS; MITOCHONDRIAL GENOME; NONHUMAN; POLYMERASE CHAIN REACTION; PROCESS OPTIMIZATION; REVIEW;

EID: 79952098463     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes1020227     Document Type: Review

References (58)

1. Higuchi, R.; Bowman, B.; Freiberger, M.; Ryder, O.A.; Wilson, A.C. DNA-sequences from the quagga, an extinct member of the horse family. Nature 1984, 312, 282-284.
2. Saiki, R.K.; Scharf, S.; Faloona, F.; Mullis, K.B.; Horn, G.T.; Erlich, H.A.; Arnheim, N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle-cell anemia. Science 1985, 230, 1350-1354.
3. Mullis, K.B.; Faloona, F.A. Specific synthesis of DNA invitro via a polymerase-catalyzed chainreaction. Methods Enzymol. 1987, 155, 335-350.
4. Saiki, R.K.; Gelfand, D.H.; Stoffel, S.; Scharf, S.J.; Higuchi, R.; Horn, G.T.; Mullis, K.B.; Erlich, H.A. Primer-directed enzymatic amplification of DNA with a thermostable DNA-polymerase. Science 1988, 239, 487-491.
5. Margulies, M.; Egholm, M.; Altman, W.E.; Attiya, S.; Bader, J.S.; Bemben, L.A.; Berka, J.; Braverman, M.S.; Chen, Y.J.; Chen, Z.T., et al. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 2005, 437, 376-380.
6. Poinar, H.N.; Schwarz, C.; Qi, J.; Shapiro, B.; MacPhee, R.D.E.; Buigues, B.; Tikhonov, A.; Huson, D.H.; Tomsho, L.P.; Auch, A.; Rampp, M.; Miller, W.; Schuster, S.C. Metagenomics to paleogenomics: Large-scale sequencing of mammoth DNA. Science 2006, 311, 392-394.
7. Noonan, J.P.; Hofreiter, M.; Smith, D.; Priest, J.R.; Rohland, N.; Rabeder, G.; Krause, J.; Detter, J.C.; Pääbo, S.; Rubin, E.M. Genomic sequencing of Pleistocene cave bears. Science 2005, 309, 597-600.
8. Miller, W.; Drautz, D.I.; Ratan, A.; Pusey, B.; Qi, J.; Lesk, A.M.; Tomsho, L.P.; Packard, M.D.; Zhao, F.Q.; Sher, A.; Tikhonov, A.; Raney, B.; Patterson, N.; Lindblad-Toh, K.; Lander, E.S.; Knight, J.R.; Irzyk, G.P.; Fredrikson, K.M.; Harkins, T.T.; Sheridan, S.; Pringle, T.; Schuster, S.C. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 2008, 456, 387-U351.
9. Green, R.E.; Krause, J.; Briggs, A.W.; Maricic, T.; Stenzel, U.; Kircher, M.; Patterson, N.; Li, H.; Zhai, W.W.; Fritz, M.H.Y.; et al. A Draft Sequence of the Neandertal Genome. Science 2010, 328, 710-722.
10. Rasmussen, M.; Li, Y.R.; Lindgreen, S.; Pedersen, J.S.; Albrechtsen, A.; Moltke, I.; Metspalu, M.; Metspalu, E.; Kivisild, T.; Gupta, R.; et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 2010, 463, 757-762.
11. Ng, S.B.; Turner, E.H.; Robertson, P.D.; Flygare, S.D.; Bigham, A.W.; Lee, C.; Shaffer, T.; Wong, M.; Bhattacharjee, A.; Eichler, E.E.; Bamshad, M.; Nickerson, D.A.; Shendure, J. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009, 461, 272-U153.
12. Briggs, A.W.; Good, J.M.; Green, R.E.; Krause, J.; Maricic, T.; Stenzel, U.; Lalueza-Fox, C.; Rudan, P.; Brajkovic, D.; Kucan, Ž.; Gušic, I.; Schmitz, R.; Doronichev, V.B.; Golovanova, L.V.; de la Rasilla, M.; Fortea, J.; Rosas, A.; Pääbo, S. Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes. Science 2009, 325, 318-321.
13. Krause, J.; Briggs, A.W.; Kircher, M.; Maricic, T.; Zwyns, N.; Derevianko, A.; Pääbo, S. A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia. Curr. Biol. 2010, 20, 231-236.
14. Krause, J.; Fu, Q.M.; Good, J.M.; Viola, B.; Shunkov, M.V.; Derevianko, A.P.; Pääbo, S. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 2010, 464, 894-897.
15. Burbano, H.A.; Hodges, E.; Green, R.E.; Briggs, A.W.; Krause, J.; Meyer, M.; Good, J.M.; Maricic, T.; Johnson, P.L.F.; Xuan, Z.Y.; Rooks, M.; Bhattacharjee, A.; Brizuela, L.; Albert, F.W.; de la Rasilla, M.; Fortea, J.; Rosas, A.; Lachmann, M.; Hannon, G.J.; Pääbo, S. Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture. Science 2010, 328, 723-725.
16. Millar, C.D.; Huynen, L.; Subramanian, S.; Mohandesan, E.; Lambert, D.M. New developments in ancient genomics. Trends Ecol. Evol. 2008, 23, 386-393.
17. Poinar, H.; Kuch, M.; McDonald, G.; Martin, P.; Pääbo, S. Nuclear gene sequences from a late Pleistocene sloth coprolite. Curr. Biol. 2003, 13, 1150-1152.
18. Lambert, D.M.; Ritchie, P.A.; Millar, C.D.; Holland, B.; Drummond, A.J.; Baroni, C. Rates of evolution in ancient DNA from Adelie penguins. Science 2002, 295, 2270-2273.
19. Shapiro, B.; Drummond, A.J.; Rambaut, A.; Wilson, M.C.; Matheus, P.E.; Sher, A.V.; Pybus, O.G.; Gilbert, M.T.P.; Barnes, I.; Binladen, J.; Willerslev, E.; Hansen, A.J.; Baryshnikov, G.F.; Burns, J.A.; Davydov, S.; Driver, J.C.; Froese, D.G.; Harington, C.R.; Keddie, G.; Kosintsev, P.; Kunz, M.L.; Martin, L.D.; Stephenson, R.O.; Storer, J.; Tedford, R.; Zimov, S.; Cooper, A. Rise and fall of the Beringian steppe bison. Science 2004, 306, 1561-1565.
20. Krause, J.; Dear, P.H.; Pollack, J.L.; Slatkin, M.; Spriggs, H.; Barnes, I.; Lister, A.M.; Ebersberger, I.; Pääbo, S.; Hofreiter, M. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 2006, 439, 724-727.
21. Debruyne, R.; Schwarz, C.; Poinar, H. Comment on Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science 2008, 322, 857b.
22. Maricic, T.; Pääbo, S. Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands. Biotechniques 2009, 46, 51-57.
23. Meyer, M.; Kircher, M. Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing. Cold Spring Harb. Protoc. 2010, doi:10.1101/pdb.prot5448.
24. Green, R.E.; Krause, J.; Ptak, S.E.; Briggs, A.W.; Ronan, M.T.; Simons, J.F.; Du, L.; Egholm, M.; Rothberg, J.M.; Paunovic, M.; Pääbo, S. Analysis of one million base pairs of Neanderthal DNA. Nature 2006, 444, 330-336.
25. Gilbert, M.T.P.; Tomsho, L.P.; Rendulic, S.; Packard, M.; Drautz, D.I.; Sher, A.; Tikhonov, A.; Dalén, L.; Kuznetsova, T.; Kosintsev, P.; Campos, P.F.; Higham, T.; Collins, M.J.; Wilson, A.S.; Shidlovskiy, F.; Buigues, B.; Ericson, P.G.P.; Germonpré, M.; Götherström, A.; Iacumin, P.; Nikolaev, V.; Nowak-Kemp, M.; Willerslev, E.; Knight, J.R.; Irzyk, G.P.; Perbost, C.S.; Fredrikson, K.M.; Harkins, T.T.; Sheridan, S.; Miller, W.; Schuster, S.C. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science 2007, 317, 1927-1930.
26. Gilbert, M.T.P.; Drautz, D.I.; Lesk, A.M.; Ho, S.Y.W.; Qi, J.; Ratan, A.; Hsu, C.H.; Sher, A.; Dalén, L.; Götherström, A.; et al. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 8327-8332.
27. Gilbert, M.T.P.; Kivisild, T.; Grønnow, B.; Andersen, P.K.; Metspalu, E.; Reidla, M.; Tamm, E.; Axelsson, E.; Götherström, A.; Campos, P.F.; Rasmussen, M.; Metspalu, M.; Higham, T.F.G.; Schwenninger, J.L.; Nathan, R.; De Hoog, C.J.; Koch, A.; Møller, L.N.; Andreasen, C.; Meldgaard, M.; Villems, R.; Bendixen, C.; Willerslev, E. Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 2008, 320, 1787-1789.
28. Green, R.E.; Malaspinas, A.S.; Krause, J.; Briggs, A.W.; Johnson, P.L.F.; Uhler, C.; Meyer, M.; Good, J.M.; Maricic, T.; Stenzel, U.; Prüfer, K.; Siebauer, M.; Burbano, H.A.; Ronan, M.; Rothberg, J.M.; Egholm, M.; Rudan, P.; Brajković, D.; Kucan, Ž.; Gušić, I.; Wikström, M.; Laakkonen, L.; Kelso, J.; Slatkin, M.; Pääbo, S. A complete neandertal mitochondrial genome sequence determined by high-throughput Sequencing. Cell 2008, 134, 416-426.
29. Miller, W.; Drautz, D.I.; Janecka, J.E.; Lesk, A.M.; Ratan, A.; Tomsho, L.P.; Packard, M.; Zhang, Y.; McClellan, L.R.; Qi, J.; Zhao, F.; Gilbert, M.T.P.; Dalén, L.; Arsuaga, J.L.; Ericson, P.G.P.; Huson, D.H.; Helgen, K.M.; Murphy, W.J.; Götherström, A.; Schuster, S.C. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res. 2009, 19, 213-220.
30. Allentoft, M.E.; Schuster, S.C.; Holdaway, R.N.; Hale, M.L.; McLay, E.; Oskam, C.; Gilbert, M.T.P.; Spencer, P.; Willerslev, E.; Bunce, M. Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. Biotechniques 2009, 46, 195-200.
31. Ramírez, O.; Gigli, E.; Bover, P.; Alcover, J.A.; Bertranpetit, J.; Castresana, J.; Lalueza-Fox, C. Paleogenomics in a Temperate Environment: Shotgun Sequencing from an Extinct Mediterranean Caprine. Plos One 2009, 4, e5670, doi:5610.1371/journal.pone.0005670.
32. Willerslev, E.; Gilbert, M.T.P.; Binladen, J.; Ho, S.Y.W.; Campos, P.F.; Ratan, A.; Tomsho, L.P.; da Fonseca, R.R.; Sher, A.; Kuznetsova, T.V.; Nowak-Kemp, M.; Roth, T.L.; Miller, W.; Schuster, S.C. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol. Biol. 2009, 9, 95, doi:10.1186/1471-2148-1189-1195.
33. Zhao, F.Q.; Qi, J.; Schuster, S.C. Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius. Genome Res. 2009, 19, 1384-1392.
34. Stiller, M.; Knapp, M.; Stenzel, U.; Hofreiter, M.; Meyer, M. Direct multiplex sequencing (DMPS)-a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res. 2009, 19, 1843-1848.
35. Edwards, C.J.; Magee, D.A.; Park, S.D.E.; McGettigan, P.A.; Lohan, A.J.; Murphy, A.; Finlay, E.K.; Shapiro, B.; Chamberlain, A.T.; Richards, M.B.; Bradley, D.G.; Loftus, B.J.; MacHugh, D.E. A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius). Plos One 2010, 5, e9255, doi:9210.1371/journal.pone.0009255.
36. Lindqvist, C.; Schuster, S.C.; Sun, Y.Z.; Talbot, S.L.; Qi, J.; Ratan, A.; Tomsho, L.P.; Kasson, L.; Zeyl, E.; Aars, J.; Miller, W.; Ingólfsson, Ó.; Bachmann, L.; Wiig, Ø. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 5053-5057.
37. Ho, S.Y.W.; Gilbert, M.T.P. Ancient mitogenomics. Mitochondrion (Kidlington) 2010, 10, 1-11.
38. Sanger, F.; Nicklen, S.; Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U. S. A. 1977, 74, 5463-5467.
39. Meyer, M.; Stenzel, U.; Myles, S.; Prüfer, K.; Hofreiter, M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 2007, 35, No. 15 e97.
40. Römpler, H.; Dear, P.H.; Krause, J.; Meyer, M.; Rohland, N.; Schöneberg, T.; Spriggs, H.; Stiller, M.; Hofreiter, M. Multiplex amplification of ancient DNA. Nat. Protoc. 2006, 1, 720-728.
41. Römpler, H.; Rohland, N.; Lalueza-Fox, C.; Willerslev, E.; Kuznetsova, T.; Rabeder, G.; Bertranpetit, J.; Schöneberg, T.; Hofreiter, M. Nuclear gene indicates coat-color polymorphism in mammoths. Science 2006, 313, 62-62.
42. Rohland, N.; Malaspinas, A.S.; Pollack, J.L.; Slatkin, M.; Matheus, P.; Hofreiter, M. Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol. 2007, 5, 1663-1671.
43. Krause, J.; Unger, T.; Noçon, A.; Malaspinas, A.S.; Kolokotronis, S.O.; Stiller, M.; Soibelzon, L.; Spriggs, H.; Dear, P.H.; Briggs, A.W.; Bray, S.C.E.; O'Brien, S.J.; Rabeder, G.; Matheus, P.; Cooper, A.; Slatkin, M.; Pääbo, S.; Hofreiter, M. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol. Biol. 2008, 8, 220, doi:210.1186/1471-2148-1188-1220.
44. Prüfer, K.; Stenzel, U.; Hofreiter, M.; Pääbo, S.; Kelso, J.; Green, R.E. Computational challenges in the analysis of ancient DNA. Genome Biology 2010, 11, R47.
45. Hofreiter, M.; Jaenicke, V.; Serre, D.; von Haeseler, A.; Pääbo, S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001, 29, 4793-4799.
46. Willerslev, E.; Hansen, A.J.; Binladen, J.; Brand, T.B.; Gilbert, M.T.P.; Shapiro, B.; Bunce, M.; Wiuf, C.; Gilichinsky, D.A.; Cooper, A. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 2003, 300, 791-795.
47. Hofreiter, M.; Mead, J.I.; Martin, P.; Poinar, H.N. Molecular caving. Curr. Biol. 2003, 13, R693-R695.
48. Willerslev, E.; Cappellini, E.; Boomsma, W.; Nielsen, R.; Hebsgaard, M.B.; Brand, T.B.; Hofreiter, M.; Bunce, M.; Poinar, H.N.; Dahl-Jensen, D.; Johnsen, S.; Steffensen, J.P.; Bennike, O.; Schwenninger, J.L.; Nathan, R.; Armitage, S.; de Hoog, C.J.; Alfimov, V.; Christl, M.; Beer, J.; Muscheler, R.; Barker, J.; Sharp, M.; Penkman, K.E.H.; Haile, J.; Taberlet, P.; Gilbert, M.T.P.; Casoli, A.; Campani, E.; Collins, M.J. Ancient biomolecules from deep ice cores reveal a forested Southern Greenland. Science 2007, 317, 111-114.
49. Albert, T.J.; Molla, M.N.; Muzny, D.M.; Nazareth, L.; Wheeler, D.; Song, X.Z.; Richmond, T.A.; Middle, C.M.; Rodesch, M.J.; Packard, C.J.; Weinstock, G.M.; Gibbs, R.A. Direct selection of human genomic loci by microarray hybridization. Nat. Meth. 2007, 4, 903-905.
50. Hodges, E.; Xuan, Z.; Balija, V.; Kramer, M.; Molla, M.N.; Smith, S.W.; Middle, C.M.; Rodesch, M.J.; Albert, T.J.; Hannon, G.J.; McCombie, W.R. Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 2007, 39, 1522-1527.
51. Gnirke, A.; Melnikov, A.; Maguire, J.; Rogov, P.; LeProust, E.M.; Brockman, W.; Fennell, T.; Giannoukos, G.; Fisher, S.; Russ, C.; Gabriel, S.; Jaffe, D.B.; Lander, E.S.; Nusbaum, C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 2009, 27, 182-189.
52. Hodges, E.; Rooks, M.; Xuan, Z.Y.; Bhattacharjee, A.; Gordon, D.B.; Brizuela, L.; McCombie, W.R.; Hannon, G.J. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat. Protoc. 2009, 4, 960-974.
53. Mamanova, L.; Coffey, A.J.; Scott, C.E.; Kozarewa, I.; Turner, E.H.; Kumar, A.; Howard, E.; Shendure, J.; Turner, D.J. Target-enrichment strategies for next-generation sequencing. Nat. Meth. 2010, 7, 111-118.
54. Noonan, J.P.; Coop, G.; Kudaravalli, S.; Smith, D.; Krause, J.; Alessi, J.; Platt, D.; Pääbo, S.; Pritchard, J.K.; Rubin, E.M. Sequencing and analysis of Neanderthal genomic DNA. Science 2006, 314, 1113-1118.
55. Anderung, C.; Persson, P.; Bouwman, A.; Elburg, R.; Götherström, A. Fishing for ancient DNA. Forensic Sci. Int.: Genetics 2008, 2, 104-107.
56. Briggs, A.W.; Good, J.M.; Green, R.E.; Krause, J.; Maricic, T.; Stenzel, U.; Pääbo, S. Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources. J. Vis. Exp. 2009, 31, doi: 10.3791/1573.
57. Meyer, M.; Stenzel, U.; Hofreiter, M. Parallel tagged sequencing on the 454 platform. Nat. Protoc. 2008, 3, 267-278.
58. Shapiro, B.; Hofreiter, M. Analysis of ancient human genomes. Bioessays 2010, 32, 388-391.