The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Hung, Chih Ming ^a,b   Lin, Rong Chien ^b   Chu, Jui Hua ^b   Yeh, Chia Fen ^b   Yao, Chiou Ju ^c   Li, Shou Hsien ^b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b NATIONAL TAIWAN NORMAL UNIVERSITY   (Taiwan)

^c NATIONAL MUSEUM OF NATURAL SCIENCE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DEAMINATION; DNA DEGRADATION; ECTOPISTES MIGRATORIUS; FEMALE; GENE SEQUENCE; GENETIC PROCEDURES; MALE; MITOCHONDRIAL GENOME; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PIGEON; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; ANIMAL; BASE PAIRING; DNA CONTAMINATION; DNA SEQUENCE; GENE FREQUENCY; GENETICS; METAGENOME; METHODOLOGY; PIGEONS AND DOVES; POSTMORTEM CHANGE; SPECIES EXTINCTION;

DNA;

ANIMALS; BASE PAIRING; BASE SEQUENCE; COLUMBIDAE; DNA; DNA CONTAMINATION; EXTINCTION, BIOLOGICAL; GENE FREQUENCY; GENOME, MITOCHONDRIAL; METAGENOME; POSTMORTEM CHANGES; SEQUENCE ANALYSIS, DNA;

EID: 84874267094     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0056301     Document Type: Article

References (42)

1. Nee S, May RM, (1997) Extinction and the loss of evolutionary history. Science 278: 692-694.
2. Pääbo S, Poinar H, Serre D, Jaenicke-Després, Hebler J, et al. (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38: 645-679.
3. Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM, (2008) New developments in ancient genomics. Trends Ecol Evol 23: 386-393.
4. Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, et al. (2002) Flight of the Dodo. Science 295: 1683.
5. Gilbert MTP, Drautz DI, Lesk AM, Ho SYW, Qi J, et al. (2008) Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci USA 105: 8327-8332.
6. Lambert DM, Ritchie PA, Millar CD, Holland B, Drummond AJ, et al. (2002) Rates of evolution in ancient DNA from Adélie penguins. Science 295: 2270-2273.
7. Leonard JA, (2008) Ancient DNA application for wildlife conservation. Mol Ecol 17: 4186-4196.
8. Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, et al. (2004) Rise and fall of the Beringian steppe bison. Science 306: 1561-1565.
9. Dalén L, Nyström V, Valdiosera C, Germonpré M, Sablin M, et al. (2007) Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox. Proc Natl Acad Sci USA 104: 7626-6729.
10. Poulakakis N, Glaberman S, Russello M, Beheregaray LB, Ciof C, et al. (2008) Historical DNA analysis reveal living descendants of an extinct species of Galápagos tortoise. Proc Natl Acad Sci USA 105: 15464-15469.
11. Rowe KC, Singhal S, MacManes MD, Ayroles JF, Morelli TL, et al. (2011) Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Mol Ecol Resour 11: 1082-1092.
12. Rohland N, Siedel H, Hofreiter M, (2004) Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. BioTechniques 36: 814-821.
13. Ho SYW, Gilbert MTP, (2010) Ancient mitogenomics. Mitochondrion 10: 1-11.
14. Lopez JV, Yuhki N, Masuda R, Modi W, O'Brien SJ, (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39: 174-190.
15. Collura RV, Stewart C-B, (1995) Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominolds. Nature 378: 485-489.
16. Gilbert MTP, Hansen AJ, Willerslev E, Rudbeck L, Barnes I, et al. (2003) Characterization of genetic Miscoding lesions caused by postmortem damage. Am J Hum Genet 72: 48-61.
17. Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, et al. (2007) Novel high-resolution characterization of ancient DNA reveals C>U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res 35: 5717-5728.
18. Axelsson E, Willerslev E, Gilbert MTP, Nielsen R, (2008) The effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol 25: 2181-2187.
19. Knapp M, Hofreiter M, (2010) Next generation sequencing of ancient DNA: requirements, strategies and perspective. Genes 1: 227-243.
20. Gilbert MTP, Tomsho LP, Rendulic S, Packard M, Drautz DI, et al. (2007) Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science 317: 1927-1930.
21. Schorger AW (1955) The passenger pigeon. Madison: University of Wisconsin Press.
22. Catling PM, (2001) Extinction and importance of history and dependence in conservation. Biodiversity 2: 2-14.
23. Cassista S, (2009) A discussion of theories relating to population dynamics of passenger pigeon population: abundance and extinction. Undergraduate J Anthropol 1: 141-149.
24. Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, et al. (2012) Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res 20: 908-916.
25. Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M, (2009) Direct multiplex sequencing (DMPS)-a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res 19: 1843-1848.
26. Moraes-Barros Nd, Morgante JS, (2007) A simple protocol for the extraction and sequence analysis of DNA from study skin of museum collections. Genet Mol Biol 30: 1181-1185.
27. Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, et al. (2010) Characterization of the complete mitochondrial genome of the rock pigeon, Columba livia (Columbiformes: Columbidae). Genet Mol Res 9: 1234-1249.
28. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, et al. (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456: 387-390.
29. Gregory TR (2005) Animal Genome Size Database. Available: http://www.genomesize.com. Accessed 2012 June 8.
30. Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, et al. (2011) Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol Biol Evol 28: 1927-1942.
31. Poinar HN, Schwarz C, Qi J, Shapiro B, MacPhee RDE, et al. (2006) Metagenomics to Paleogenomics: large-scale sequencing of mammoth DNA. Science 311: 392-394.
32. Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, et al. (2009) The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res 19: 213-220.
33. Edwards CJ, Magee DA, Park SDE, McGettigan PA, Lohan AJ, et al. (2010) A compete mitochondrial genome sequence from a Mesolithic wild aurochs (Bos primigenius). Plos One 5: e9255.
34. Lindqvist C, Schuster SC, Sun Y, Talbot SL, Qi 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.
35. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, et al. (2008) A large genome center's improvements to the Illumina sequencing system. Nat Methods 5: 1005-1010.
36. Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT, (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. Plos One 7: e30087.
37. Krause J, Dear PH, Pollack JL, Slatkin M, Spriggs H, et al. (2005) Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439: 724-727.
38. Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, et al. (2008) Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr Biol 18: 1687-1693.
39. Briggs AW, Good JM, Green RE, Krause J, Maricic T, et al. (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325: 318.
40. Binladen J, Gilbert MTP, Bollback JP, Pantiz F, Bendixen C, et al. (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. Plos One 2: e197.
41. Rawlence NJ, Wood JR, Armstrong KN, Cooper A, (2009) DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa. Proc R Soc B 276: 3395-3402.
42. Oskam CL, Haile J, McLay E, Rigby P, Allentoft ME, et al. (2010) Fossil avian eggshell preserves ancient DNA. Proc R Soc B 277: 1991-2000.