Advertisement

International Journal of Legal Medicine

, Volume 130, Issue 1, pp 67–71 | Cite as

Whole mitochondrial genome genetic diversity in an Estonian population sample

  • Monika StoljarovaEmail author
  • Jonathan L. King
  • Maiko Takahashi
  • Anu Aaspõllu
  • Bruce Budowle
Original Article

Abstract

Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25 % of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7 % in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85 %, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99 % for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions.

Keywords

Mitochondrial genome (mtGenome) Massively parallel sequencing (MPS) Illumina MiSeq Haplogroup Estonia Power of discrimination 

Notes

Acknowledgments

We would like to thank the Baltic American Freedom Foundation and Council of International Educational Exchange for providing the opportunity for the professional internship of Monika Stoljarova at the University of North Texas Health Science Center.

Supplementary material

414_2015_1249_MOESM1_ESM.xlsx (28 kb)
Supplemental Table 1 (XLSX 27 kb)
414_2015_1249_MOESM2_ESM.xlsx (10 kb)
Supplemental Table 2 (XLSX 10 kb)

References

  1. 1.
    King TE, Fortes GG, Balaresque P, Thomas MG, Balding D, Delser PM, Neumann R, Parson W, Knapp M, Walsh S, Tonasso L, Holt J, Kayser M, Appleby J, Forster P, Ekserdjian D, Hofreiter M, Schurer K (2014) Identification of the remains of King Richard III. Nat Commun 5:5631. doi: 10.1038/ncomms6631 PubMedPubMedCentralCrossRefGoogle Scholar
  2. 2.
    Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P (2013) The first modern human dispersals across Africa. PLoS One 8(11), e80031. doi: 10.1371/journal.pone.0080031 PubMedPubMedCentralCrossRefGoogle Scholar
  3. 3.
    Li CT, Bai YM, Hsieh JC, Lee HC, Yang BH, Chen MH, Lin WC, Tsai CF, Tu PC, Wang SJ, Su TP (2015) Peripheral and central glucose utilizations modulated by mitochondrial DNA 10398A in bipolar disorder. Psychoneuroendocrinology 55C:72–80. doi: 10.1016/j.psyneuen.2015.02.003 CrossRefGoogle Scholar
  4. 4.
    Hagen CM, Aidt FH, Hedley PL, Jensen MK, Havndrup O, Kanters JK, Moolman-Smook JC, Larsen SO, Bundgaard H, Christiansen M (2013) Mitochondrial haplogroups modify the risk of developing hypertrophic cardiomyopathy in a Danish population. PLoS One 8(8), e71904. doi: 10.1371/journal.pone.0071904 PubMedPubMedCentralCrossRefGoogle Scholar
  5. 5.
    Tokutomi T, Takada Y, Kanetake J, Mukaida M (2009) Identification using DNA from skin contact: case reports. Leg Med (Tokyo) 11(Suppl 1):S576-577. doi: 10.1016/j.legalmed.2009.02.004 Google Scholar
  6. 6.
    King JL, LaRue BL, Novroski NM, Stoljarova M, Seo SB, Zeng X, Warshauer DH, Davis CP, Parson W, Sajantila A, Budowle B (2014) High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq. Forensic Sci Int Genet 12:128–135. doi: 10.1016/j.fsigen.2014.06.001 PubMedCrossRefGoogle Scholar
  7. 7.
    Seo SB, Zeng X, King JL, Larue BL, Assidi M, Al-Qahtani MH, Sajantila A, Budowle B (2015) Underlying data for sequencing the mitochondrial genome with the massively parallel sequencing platform ion torrent() PGM (). BMC Genomics 16(1):6938. doi: 10.1186/1471-2164-16-S1-S4 Google Scholar
  8. 8.
    Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S, Lagace R, Irwin J (2013) Reprint of: evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genet 7(6):632–639. doi: 10.1016/j.fsigen.2013.09.007 PubMedCrossRefGoogle Scholar
  9. 9.
    Bodner M, Iuvaro A, Strobl C, Nagl S, Huber G, Pelotti S, Pettener D, Luiselli D, Parson W (2015) Helena, the hidden beauty: resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample. Forensic Sci Int-Gen 15:21–26. doi: 10.1016/j.fsigen.2014.09.012 CrossRefGoogle Scholar
  10. 10.
    McElhoe JA, Holland MM, Makova KD, Su MS, Paul IM, Baker CH, Faith SA, Young B (2014) Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq. Forensic Sci Int Genet 13:20–29. doi: 10.1016/j.fsigen.2014.05.007 PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    European DNA Profiling Group (EDNAP) (1999–2015) EMPOP. www.empop.org. Accessed 19 Mar 2015
  12. 12.
    Parson W, Dur A (2007) EMPOP—a forensic mtDNA database. Forensic Sci Int Genet 1(2):88–92. doi: 10.1016/j.fsigen.2007.01.018 PubMedCrossRefGoogle Scholar
  13. 13.
    Just RS, Scheible MK, Fast SA, Sturk-Andreaggi K, Higginbotham JL, Lyons EA, Bush JM, Peck MA, Ring JD, Diegoli TM, Rock AW, Huber GE, Nagl S, Strobl C, Zimmermann B, Parson W, Irwin JA (2014) Development of forensic-quality full mtGenome haplotypes: success rates with low template specimens. Forensic Sci Int Genet 10:73–79. doi: 10.1016/j.fsigen.2014.01.010 PubMedCrossRefGoogle Scholar
  14. 14.
    Just RS, Scheible MK, Fast SA, Sturk-Andreaggi K, Rock AW, Bush JM, Higginbotham JL, Peck MA, Ring JD, Huber GE, Xavier C, Strobl C, Lyons EA, Diegoli TM, Bodner M, Fendt L, Kralj P, Nagl S, Niederwieser D, Zimmermann B, Parson W, Irwin JA (2015) Full mtGenome reference data: development and characterization of 588 forensic-quality haplotypes representing three U.S. populations. Forensic Sci Int Genet 14:141–155. doi: 10.1016/j.fsigen.2014.09.021 PubMedCrossRefGoogle Scholar
  15. 15.
    Nelis M, Esko T, Magi R, Zimprich F, Zimprich A, Toncheva D, Karachanak S, Piskackova T, Balascak I, Peltonen L, Jakkula E, Rehnstrom K, Lathrop M, Heath S, Galan P, Schreiber S, Meitinger T, Pfeufer A, Wichmann HE, Melegh B, Polgar N, Toniolo D, Gasparini P, D’Adamo P, Klovins J, Nikitina-Zake L, Kucinskas V, Kasnauskiene J, Lubinski J, Debniak T, Limborska S, Khrunin A, Estivill X, Rabionet R, Marsal S, Julia A, Antonarakis SE, Deutsch S, Borel C, Attar H, Gagnebin M, Macek M, Krawczak M, Remm M, Metspalu A (2009) Genetic structure of Europeans: a view from the North-East. PLoS One 4(5), e5472. doi: 10.1371/journal.pone.0005472 PubMedPubMedCentralCrossRefGoogle Scholar
  16. 16.
    Lappalainen T, Laitinen V, Salmela E, Andersen P, Huoponen K, Savontaus ML, Lahermo P (2008) Migration waves to the Baltic Sea region. Ann Hum Genet 72(Pt 3):337–348. doi: 10.1111/j.1469-1809.2007.00429.x PubMedCrossRefGoogle Scholar
  17. 17.
    Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, Rengo C, Sellitto D, Cruciani F, Kivisild T, Villems R, Thomas M, Rychkov S, Rychkov O, Rychkov Y, Golge M, Dimitrov D, Hill E, Bradley D, Romano V, Cali F, Vona G, Demaine A, Papiha S, Triantaphyllidis C, Stefanescu G, Hatina J, Belledi M, Di Rienzo A, Novelletto A, Oppenheim A, Norby S, Al-Zaheri N, Santachiara-Benerecetti S, Scozari R, Torroni A, Bandelt HJ (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67(5):1251–1276PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Pliss L, Tambets K, Loogvali EL, Pronina N, Lazdins M, Krumina A, Baumanis V, Villems R (2006) Mitochondrial DNA portrait of Latvians: towards the understanding of the genetic structure of Baltic-speaking populations. Ann Hum Genet 70(Pt 4):439–458. doi: 10.1111/j.1469-1809.2005.00238.x PubMedCrossRefGoogle Scholar
  19. 19.
    Illumina (2015) Nextera XT DNA Library preparation guideGoogle Scholar
  20. 20.
    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079. doi: 10.1093/bioinformatics/btp352 PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, Genomes Project Analysis G (2011) The variant call format and VCFtools. Bioinformatics 27(15):2156–2158. doi: 10.1093/bioinformatics/btr330 PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303. doi: 10.1101/gr.107524.110 PubMedPubMedCentralCrossRefGoogle Scholar
  23. 23.
    Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23(2):147. doi: 10.1038/13779 PubMedCrossRefGoogle Scholar
  24. 24.
    King JL, Sajantila A, Budowle B (2014) mitoSAVE: mitochondrial sequence analysis of variants in Excel. Forensic Sci Int Genet 12:122–125. doi: 10.1016/j.fsigen.2014.05.013 PubMedCrossRefGoogle Scholar
  25. 25.
    Stoneking M, Hedgecock D, Higuchi RG, Vigilant L, Erlich HA (1991) Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 48(2):370–382PubMedPubMedCentralGoogle Scholar
  26. 26.
    Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3):585–595PubMedPubMedCentralGoogle Scholar
  27. 27.
    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729. doi: 10.1093/molbev/mst197 PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Kloss-Brandstatter A, Pacher D, Schonherr S, Weissensteiner H, Binna R, Specht G, Kronenberg F (2011) HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum Mutat 32(1):25–32. doi: 10.1002/humu.21382 PubMedCrossRefGoogle Scholar
  29. 29.
    van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386–E394. doi: 10.1002/humu.20921 PubMedCrossRefGoogle Scholar
  30. 30.
    Bandelt HJ, Salas A (2012) Current next generation sequencing technology may not meet forensic standards. Forensic Sci Int Genet 6(1):143–145. doi: 10.1016/j.fsigen.2011.04.004 PubMedCrossRefGoogle Scholar
  31. 31.
    Naue J, Horer S, Sanger T, Strobl C, Hatzer-Grubwieser P, Parson W, Lutz-Bonengel S (2015) Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA. Mitochondrion 20:82–94. doi: 10.1016/j.mito.2014.12.002 PubMedCrossRefGoogle Scholar
  32. 32.
    Achilli A, Rengo C, Magri C, Battaglia V, Olivieri A, Scozzari R, Cruciani F, Zeviani M, Briem E, Carelli V, Moral P, Dugoujon JM, Roostalu U, Loogvali EL, Kivisild T, Bandelt HJ, Richards M, Villems R, Santachiara-Benerecetti AS, Semino O, Torroni A (2004) The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 75(5):910–918. doi: 10.1086/425590 PubMedPubMedCentralCrossRefGoogle Scholar
  33. 33.
    Ottoni C, Ricaut FX, Vanderheyden N, Brucato N, Waelkens M, Decorte R (2011) Mitochondrial analysis of a Byzantine population reveals the differential impact of multiple historical events in South Anatolia. Eur J Hum Genet: EJHG 19(5):571–576. doi: 10.1038/ejhg.2010.230 PubMedPubMedCentralCrossRefGoogle Scholar
  34. 34.
    Tambets K, Rootsi S, Kivisild T, Help H, Serk P, Loogvali EL, Tolk HV, Reidla M, Metspalu E, Pliss L, Balanovsky O, Pshenichnov A, Balanovska E, Gubina M, Zhadanov S, Osipova L, Damba L, Voevoda M, Kutuev I, Bermisheva M, Khusnutdinova E, Gusar V, Grechanina E, Parik J, Pennarun E, Richard C, Chaventre A, Moisan JP, Barac L, Pericic M, Rudan P, Terzic R, Mikerezi I, Krumina A, Baumanis V, Koziel S, Rickards O, De Stefano GF, Anagnou N, Pappa KI, Michalodimitrakis E, Ferak V, Furedi S, Komel R, Beckman L, Villems R (2004) The western and eastern roots of the Saami—the story of genetic “outliers” told by mitochondrial DNA and Y chromosomes. Am J Hum Genet 74(4):661–682. doi: 10.1086/383203 PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Rogalla U, Perkova M, Dambueva I, Zakharov I (2010) Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. PLoS One 5(12), e15214. doi: 10.1371/journal.pone.0015214 PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Lembring M, van Oven M, Montelius M, Allen M (2013) Mitochondrial DNA analysis of Swedish population samples. Int J Legal Med 127(6):1097–1099. doi: 10.1007/s00414-013-0908-6 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of Gene TechnologyTallinn University of TechnologyTallinnEstonia
  2. 2.Institute of Applied Genetics, Department of Molecular and Medical GeneticsUniversity of North Texas Health Science CenterFort WorthUSA

Personalised recommendations