Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads - A baiting and iterative mapping approach

Nucleic Acids Research

Volumn 41, Issue 13, 2013, Pages

  Hahn, Christoph ^a   Bachmann, Lutz ^a   Chevreux, Bastien ^b  

^a UNIVERSITY OF OSLO   (Norway)

^b DSM NUTRITIONAL PRODUCTS LTD   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ACCURACY; ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER MODEL; CONTROLLED STUDY; DNA BARCODING; ECTOPARASITE; GENETIC ALGORITHM; GENETIC DISTANCE; GENETIC SIMILARITY; GYRODACTYLUS DERJAVINOIDES; GYRODACTYLUS THYMALLI; HELMINTH; MEMORY; METAGENOMICS; MITOCHONDRIAL BAITING AND ITERATIVE MAPPING; MITOCHONDRIAL GENOME; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RAINBOW TROUT; SEQUENCE ANALYSIS; TELEOST;

ANIMALS; CHROMOSOME MAPPING; COMPUTER SIMULATION; ELECTRON TRANSPORT COMPLEX IV; FISHES; GENOME, MITOCHONDRIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; PLATYHELMINTHS; SEQUENCE ANALYSIS, DNA;

EID: 84880527958     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt371     Document Type: Article

References (51)

1. Avise, J.C. (1994) Molecular Markers, Natural History and Evolution. Chapman and Hall, New York and London.
2. Hajibabaei, M., Singer, G.A.C., Hebert, P.D.N. and Hickey, D.A. (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet., 23, 167-172. (Pubitemid 46497507)
3. Avise, J.C., Arnold, J., Ball, R.M., Berminham, E., Lamb, T., Neigel, J.E., Reeb, C.A. and Saunders, N.C. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst., 18, 489-522.
4. Avise, J.C. (1998) The history and purview of phylogeography: a personal reflection. Mol. Ecol., 7, 371-379. (Pubitemid 28226686)
5. Green, R.E., Malaspinas, A.S., Krause, J., Briggs, A.W., Johnson, P.L., Uhler, C., Meyer, M., Good, J.M., Maricic, T., Stenzel, U. et al. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell, 134, 416-426.
6. Krause, J., Fu, Q., Good, J.M., Viola, B., Shunkov, M.V., Derevianko, A.P. and Paabo, S. (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature, 464, 894-897.
7. Rogaev, E.I., Moliaka, Y.K., Malyarchuk, B.A., Kondrashov, F.A., Derenko, M.V., Chumakov, I. and Grigorenko, A.P. (2006) Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol., 4, e73.
8. 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. et al. (2010) A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius). PLoS One, 5, e9255.
9. 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. et al. (2009) The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res., 19, 213-220.
10. Lindqvist, C., Schuster, S.C., Sun, Y., Talbot, S.L., Qi, J., Ratan, A., Tomsho, L.P., Kasson, L., Zeyl, E., Aars, J. et al. (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl Acad. Sci. USA, 107, 5053-5057.
11. Miller, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., Zhao, F., Lim Kim, H., Burhans, R.C., Drautz, D.I., Wittekindt, N.E. et al. (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl Acad. Sci. USA, 109, E2382-E2390.
12. Huyse, T., Plaisance, L., Webster, B.L., Mo, T.A., Bakke, T.A., Bachmann, L. and Littlewood, D.T.J. (2007) The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogen of Atlantic salmon (Salmo salar). Parasitology, 134, 739-747. (Pubitemid 46841602)
13. Plaisance, L., Huyse, T., Littlewood, D.T.J., Bakke, T.A. and Bachmann, L. (2007) The complete mitochondrial DNA sequence of the monogenean Gyrodactylus thymalli, a parasite of grayling (Thymallus thymallus). Mol. Biochem. Parasitol., 154, 190-194. (Pubitemid 47042206)
14. Jex, A.R., Waeschenbach, A., Littlewood, D.T.J., Hu, M. and Gasser, R.B. (2008) The mitochondrial genome of Toxocara canis. PLoS Negl. Trop. Dis., 2, e273.
15. Driscoll, C.A., Yamaguchi, N., Bar-Gal, G.K., Roca, A.L., Luo, S., Macdonald, D.W. and O'Brien, S.J. (2009) Mitochondrial phylogeography illuminates the origin of the extinct caspian tiger and its relationship to the Amur Tiger. PLoS One, 4, e4125.
16. Liu, G.H., Lin, R.Q., Li, M.W., Liu, W., Liu, Y., Yuan, Z.G., Song, H.Q., Zhao, G.H., Zhang, K.X. and Zhu, X.Q. (2011) The complete mitochondrial genomes of three cestode species of Taenia infecting animals and humans. Mol. Biol. Rep., 38, 2249-2256.
17. Jia, W.Z., Yan, H.B., Guo, A.J., Zhu, X.Q., Wang, Y.C., Shi, W.G., Chen, H.T., Zhan, F., Zhang, S.H., Fu, B.Q. et al. (2010) Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis additional molecular markers for a tapeworm genus of human and animal health significance. BMC Genomics, 11, 447.
18. Achilli, A., Olivieri, A., Soares, P., Lancioni, H., Hooshiar Kashani, B., Perego, U.A., Nergadze, S.G., Carossa, V., Santagostino, M., Capomaccio, S. et al. (2012) Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc. Natl Acad. Sci. USA, 109, 2449-2454.
19. Jex, A.R., Littlewood, D.T.J. and Gasser, R.B. (2010) Toward next-generation sequencing of mitochondrial genomes-focus on parasitic worms of animals and biotechnological implications. Biotechnol. Adv., 28, 151-159.
20. Morin, P.A., Archer, F.I., Foote, A.D., Vilstrup, J., Allen, E.E., Wade, P., Durban, J., Parsons, K., Pitman, R., Li, L. et al. (2010) Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res., 20, 908-916.
21. Horn, S., Durka, W., Wolf, R., Ermala, A., Stubbe, A., Stubbe, M. and Hofreiter, M. (2011) Mitochondrial genomes reveal slow rates of molecular evolution and the timing of speciation in beavers (Castor), one of the largest rodent species. PLoS One, 6, e14622.
22. Jex, A.R., Hall, R.S., Littlewood, D.T.J. and Gasser, R.B. (2010) An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res., 38, 522-533.
23. Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H., Kumar, A., Howard, E., Shendure, J. and Turner, D.J. (2010) Target-enrichment strategies for next-generation sequencing. Nat. Methods, 7, 111-118.
24. Li, M., Schroeder, R., Ko, A. and Stoneking, M. (2012) Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Res., 40, e137.
25. Zerbino, D. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Res., 18, 821-829. (Pubitemid 351645072)
26. Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J. and Birol, I. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
27. Simpson, J.T. and Durbin, R. (2011) Efficient de novo assembly of large genomes using compressed data structures. Genome Res., 22, 549-556.
28. Gnerre, S., Maccallum, I., Przybylski, D., Ribeiro, F.J., Burton, J.N., Walker, B.J., Sharpe, T., Hall, G., Shea, T.P., Sykes, S. et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA, 108, 1513-1518.
29. Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert, K.H., Remington, K.A. et al. (2000) A whole-genome assembly of Drosophila. Science, 287, 2196-2204. (Pubitemid 30177014)
30. Earl, D., Bradnam, K., St John, J., Darling, A., Lin, D., Fass, J., Yu, H.O., Buffalo, V., Zerbino, D.R., Diekhans, M. et al. (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res., 21, 2224-2241.
31. Salzberg, S.L., Phillippy, A.M., Zimin, A., Puiu, D., Magoc, T., Koren, S., Treangen, T.J., Schatz, M.C., Delcher, A.L., Roberts, M. et al. (2012) GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res., 22, 557-567.
32. Tsai, I., Otto, T. and Berriman, M. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol., 11, R41.
33. Hebert, P.D., Cywinska, A., Ball, S.L. and deWaard, J.R. (2003) Biological identifications through DNA barcodes. Proc. Biol. Sci., 270, 313-321. (Pubitemid 36228536)
34. Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y. et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience., 1, 18.
35. Chevreux, B., Wetter, T. and Suhai, S. (1999) Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB).
36. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009). 1000 Genome Project Data Processing Subgroup. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
37. Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F. and Marshall, D. (2010) Tablet-next generation sequence assembly visualization. Bioinformatics, 26, 401-402.
38. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. (Pubitemid 24354800)
39. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol., 28, 2731-2739.
40. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
41. Zhang, Z., Schwartz, S., Wagner, L. and Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7, 203-214. (Pubitemid 30412170)
42. Bernt, M., Donath, A., Juhling, F., Externbrink, F., Florentz, C., Fritzsch, G., Putz, J., Middendorf, M. and Stadler, P.F. (2012) MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol., in press, doi: 10.1016/j.ympev.2012.08.023.
43. Pell, J., Hintze, A., Canino-Koning, R., Howe, A., Tiedje, J.M. and Brown, C.T. (2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc. Natl Acad. Sci. USA, 109, 13272-13277.
44. Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W.J., Wang, X., Xie, B., Ni, P. et al. (2009) The genome of the cucumber, Cucumis sativus L., Nat. Genet., 41, 1275-1281.
45. Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y. et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
46. Haiminen, N., Kuhn, D.N., Parida, L. and Rigoutsos, I. (2011) Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. PLoS One, 6, e24182.
47. Meinila, M., Kuusela, J., Zietara, M.S. and Lumme, J. (2004) Initial steps of speciation by geographic isolation and host switch in salmonid pathogen Gyrodactylus salaris (Monogenea: Gyrodactylidae). Int. J. Parasitol., 34, 515-526. (Pubitemid 38317175)
48. Tsang, W.Y. and Lemire, B.D. (2002) Mitochondrial genome content is regulated during nematode development. Biochem. Biophys. Res. Commun., 291, 8-16. (Pubitemid 34681130)
49. Robin, E.D. and Wong, R. (1988) Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J. Cell Physiol., 136, 507-513.
50. Olson, P.D., Zarowiecki, M., Kiss, F. and Brehm, K. (2012) Cestode genomics-progress and prospects for advancing basic and applied aspects of flatworm biology. Parasite Immunol., 34, 130-150.
51. Berriman, M., Haas, B.J., LoVerde, P.T., Wilson, R.A., Dillon, G.P., Cerqueira, G.C., Mashiyama, S.T., Al-Lazikani, B., Andrade, L.F., Ashton, P.D. et al. (2009) The genome of the blood fluke Schistosoma mansoni. Nature, 460, 352-358.