Advertisement

Analysis of Whole Mitogenomes from Ancient Samples

  • Gloria Gonzales Fortes
  • Johanna L. A. PaijmansEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1347)

Abstract

Ancient mitochondrial DNA has been used in a wide variety of paleontological and archeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based on the analysis of short fragments from the mitochondrial control region, analyzed using PCR coupled with Sanger sequencing. With the introduction of high-throughput sequencing, as well as new enrichment technologies, the recovery of full mitochondrial genomes (mitogenomes) from ancient specimens has become significantly less complicated. Here we present a protocol to build ancient extracts into Illumina high-throughput sequencing libraries, and subsequent Agilent array-based capture to enrich for the desired mitogenome. Both are based on previously published protocols, with the introduction of several improvements aimed to increase the recovery of short DNA fragments, while keeping the cost and effort requirements low. This protocol was designed for enrichment of mitochondrial DNA in ancient or other degraded samples. However, the protocols can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.

Key words

Ancient DNA (aDNA) Next-Generation Sequencing Targeted enrichment DNA capture Mitogenome 

References

  1. 1.
    Pääbo S, Poinar H, Serre D et al (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38:645–679CrossRefPubMedGoogle Scholar
  2. 2.
    Gilbert MTP, Bandelt H-J, Hofreiter M et al (2005) Assessing ancient DNA studies. Trends Ecol Evol 20:541–544CrossRefPubMedGoogle Scholar
  3. 3.
    Rasmussen M, Li Y, Lindgreen S et al (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757–762PubMedCentralCrossRefPubMedGoogle Scholar
  4. 4.
    Rasmussen M, Guo X, Wang Y et al (2011) An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science 334:94–98PubMedCentralCrossRefPubMedGoogle Scholar
  5. 5.
    Keller A, Graefen A, Ball M et al (2012) New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. Nat Commun 3:698CrossRefPubMedGoogle Scholar
  6. 6.
    Green RE, Krause J, Briggs AW et al (2010) A Draft Sequence of the Neandertal Genome. Science 328:710–722CrossRefPubMedGoogle Scholar
  7. 7.
    Reich D, Green RE, Kircher M et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060PubMedCentralCrossRefPubMedGoogle Scholar
  8. 8.
    Meyer M, Kircher M, Gansauge M-T et al (2012) A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 338:222–226PubMedCentralCrossRefPubMedGoogle Scholar
  9. 9.
    Orlando L, Ginolhac A, Raghavan M et al (2011) True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res 21:1705–1719PubMedCentralCrossRefPubMedGoogle Scholar
  10. 10.
    Paijmans JLA, Gilbert MTP, Hofreiter M (2013) Mitogenomic analyses from ancient DNA. Mol Phylogenet Evol 69:404–416CrossRefPubMedGoogle Scholar
  11. 11.
    Dabney J, Knapp M, Glocke I et al (2013) Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci 201314445Google Scholar
  12. 12.
    Meyer M, Fu Q, Aximu-Petri A et al (2013) A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505:403–406CrossRefPubMedGoogle Scholar
  13. 13.
    Zhang H, Paijmans JLA, Chang F et al (2013) Morphological and genetic evidence for early Holocene cattle management in northeastern China. Nat Commun 4:2755PubMedGoogle Scholar
  14. 14.
    Thalmann O, Shapiro B, Cui P et al (2013) Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs. Science 342:871–874CrossRefPubMedGoogle Scholar
  15. 15.
    Poinar HN, Schwarz C, Qi J et al (2006) Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA. Science 311:392–394CrossRefPubMedGoogle Scholar
  16. 16.
    Gilbert MTP, Tomsho LP, Rendulic S et al (2007) Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts. Science 317:1927–1930CrossRefPubMedGoogle Scholar
  17. 17.
    Summerer D (2009) Enabling technologies of genomic-scale sequence enrichment for targeted high-throughput sequencing. Genomics 94:363–368CrossRefPubMedGoogle Scholar
  18. 18.
    Mamanova L, Coffey AJ, Scott CE et al (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7:111–118CrossRefPubMedGoogle Scholar
  19. 19.
    Hodges E, Xuan Z, Balija V et al (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39:1522–1527CrossRefPubMedGoogle Scholar
  20. 20.
    Fu Q, Meyer M, Gao X et al (2013) DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci 110:2223–2227PubMedCentralCrossRefPubMedGoogle Scholar
  21. 21.
    Ávila-Arcos MC, Cappellini E, Romero-Navarro JA et al (2011) Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Sci Rep 1:74PubMedCentralCrossRefPubMedGoogle Scholar
  22. 22.
    Burbano HA, Hodges E, Green RE et al (2010) Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture. Science 328:723–725PubMedCentralCrossRefPubMedGoogle Scholar
  23. 23.
    Burbano HA, Green RE, Maricic T et al (2012) Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes. PLoS One 7, e32877PubMedCentralCrossRefPubMedGoogle Scholar
  24. 24.
    Bos KI, Schuenemann VJ, Golding GB et al (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature 478:506–510PubMedCentralCrossRefPubMedGoogle Scholar
  25. 25.
    Meyer M., Kircher M. (2010) Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing. Cold Spring Harb Protoc 2010, doi:10.1101/pdb.prot5448.Google Scholar
  26. 26.
    Hodges E, Rooks M, Xuan Z et al (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc 4:960–974PubMedCentralCrossRefPubMedGoogle Scholar
  27. 27.
    Rohland N, Siedel H, Hofreiter M (2010) A rapid column-based ancient DNA extraction method for increased sample throughput. Mol Ecol Resour 10:677–683CrossRefPubMedGoogle Scholar
  28. 28.
    Briggs AW., Heyn P. (2012) Preparation of Next-Generation Sequencing Libraries from Damaged DNA. In: Shapiro B, Hofreiter M (eds.) Anc. DNA. Humana Press, New York pp 143–154Google Scholar
  29. 29.
    Bowman SK, Simon MD, Deaton AM et al (2013) Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics 14:466PubMedCentralCrossRefPubMedGoogle Scholar
  30. 30.
    Gansauge M-T, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8:737–748CrossRefPubMedGoogle Scholar
  31. 31.
    Craig DW, Pearson JV, Szelinger S et al (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5:887–893PubMedCentralCrossRefPubMedGoogle Scholar
  32. 32.
    Kircher M, Sawyer S, Meyer M (2011) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 1–8Google Scholar
  33. 33.
    Rohland N, Reich D (2012) Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res 22:939–946PubMedCentralCrossRefPubMedGoogle Scholar
  34. 34.
    Li C, Hofreiter M, Straube N et al (2013) Capturing protein-coding genes across highly divergent species. Biotechniques 54:321–326PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Gloria Gonzales Fortes
    • 1
  • Johanna L. A. Paijmans
    • 1
    Email author
  1. 1.Institute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany

Personalised recommendations