Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence

1. Green RE et al (2010) A draft sequence of the Neandertal genome. Science 328:710–722

   Article  CAS  Google Scholar 

2. Meyer M et al (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338:222–226

   Article  CAS  Google Scholar 

3. Schubert M et al (2014) Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A 111:E5661–E5669

   Article  CAS  Google Scholar 

4. Palkopoulou E et al (2015) Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr Biol 25:1395–1400

   Article  CAS  Google Scholar 

5. Węcek K et al (2016) Complex admixture preceded and followed the extinction of wisent in the wild. Mol Biol Evol. https://doi.org/10.1093/molbev/msw254

6. Barnett R et al (2016) Mitogenomics of the extinct cave lion, Panthera spelaea (Goldfuss, 1810), resolve its position within the Panthera cats. Open Quaternary 2:4

   Article  Google Scholar 

7. Lindqvist C et al (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci U S A 107:5053–5057

   Article  CAS  Google Scholar 

8. Llamas B et al (2016) Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. Sci Adv 2:e1501385

   Article  Google Scholar 

9. Hervella M et al (2016) The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Sci Rep 6:25501

   Article  CAS  Google Scholar 

10. Soubrier J et al (2016) Early cave art and ancient DNA record the origin of European bison. Nat Commun 7:13158

    Article  Google Scholar 

11. Paijmans JLA, Gilbert MTP, Hofreiter M (2013) Mitogenomic analyses from ancient DNA. Mol Phylogenet Evol 69:404–416

    Article  CAS  Google Scholar 

12. Soares AER et al (2016) Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation. BMC Evol Biol 16:230

    Article  Google Scholar 

13. Gansauge M-T, Meyer M (2014) Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Res 24:1543–1549

    Article  CAS  Google Scholar 

14. Carpenter ML et al (2013) Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet 93:852–864

    Article  CAS  Google Scholar 

15. Nagarajan N, Pop M (2013) Sequence assembly demystified. Nat Rev Genet 14:157–167

    Article  CAS  Google Scholar 

16. Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res 41(13):e129

    Article  CAS  Google Scholar 

17. Chevreux B, Wetter T, Suhai S et al (1999) Genome sequence assembly using trace signals and additional sequence information. German Conf Bioinformatics 99:45–56

    Google Scholar 

18. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771

    Article  CAS  Google Scholar 

19. Arnason U et al (2008) Mitogenomic relationships of placental mammals and molecular estimates of their divergences. Gene 421:37–51

    Article  CAS  Google Scholar 

20. Camacho C et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421

    Article  Google Scholar 

21. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  CAS  Google Scholar 

22. Milne I et al (2013) Using tablet for visual exploration of second-generation sequencing data. Brief Bioinform 14:193–202

    Article  CAS  Google Scholar 

23. Rogaev EI et al (2006) Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol 4:e73

    Article  Google Scholar 

24. Lavrov DV, Pett W (2016) Animal mitochondrial DNA as we do not know it: mt-genome organization and evolution in nonbilaterian lineages. Genome Biol Evol 8:2896–2913

    Article  CAS  Google Scholar 

25. Bernt M et al (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–319

    Article  Google Scholar 

26. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191

    Article  CAS  Google Scholar 

27. Larsson A (2014) AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30:3276–3278

    Article  CAS  Google Scholar 

28. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  Google Scholar 

29. Robinson JT et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26

    Article  CAS  Google Scholar 

30. Hunter SS et al (2015) Assembly by reduced complexity (ARC): a hybrid approach for targeted assembly of homologous sequences. bioRxiv 014662. doi:10.1101/014662

    Google Scholar 

31. Green RE et al (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134:416–426

    Article  CAS  Google Scholar 

32. Brankovics B et al (2016) GRAbB: selective assembly of genomic regions, a new niche for genomic research. PLoS Comput Biol 12:e1004753

    Article  Google Scholar 

33. Diercksens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45:e18

    Article  Google Scholar 

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