High-throughput sequencing of a South American Amerindian

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Ribeiro dos Santos, André M ^a   De Souza, Jorge Estefano Santana ^b,c   Almeida, Renan ^c   Alencar, Dayse O ^a   Barbosa, Maria Silvanira ^a   Gusmão, Leonor ^a,d   Silva Jr , Wilson A ^b   De Souza, Sandro J ^c,e   Silva, Artur ^a   Ribeiro dos Santos, Ândrea ^a   Darnet, Sylvain ^a   Santos, Sidney ^a  

^a FEDERAL UNIVERSITY OF PARÁ   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c Institute of Bioinformatics and Biotechnology   (Brazil)

^d UNIVERSITY OF PORTO   (Portugal)

^e FEDERAL UNIVERSITY OF RIO GRANDE DO NORTE   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AMERICAN INDIAN; ARTICLE; CLUSTER ANALYSIS; GENETIC LINKAGE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; INDEL MUTATION; MOLECULAR GENETICS; POPULATION GENETICS; POPULATION GROUP; SINGLE NUCLEOTIDE POLYMORPHISM;

CLUSTER ANALYSIS; DNA, MITOCHONDRIAL; GENETIC LINKAGE; GENETICS, POPULATION; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDEL MUTATION; INDIANS, SOUTH AMERICAN; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION GROUPS;

EID: 84893621863     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0083340     Document Type: Article

References (55)

1. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59. doi:10.1038/nature07517.
2. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. doi:10.1038/nature03959. (Pubitemid 41613494)
3. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, et al. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19: 1527-1541. doi:10.1101/gr.091868.109.
4. Gibbs RA, Belmont JW, Hardenbol P, Willis TD, Yu F (2003) The International HapMap Project. Nature 426: 789-796. doi:10.1038/nature02168.
5. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. doi:10.1038/nature09534.
6. Ahn SM, Kim TH, Lee S, Kim DS, Ghang H, et al. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome 19: 1622-1629. doi:10.1101/gr.092197.109.
7. Kim J-I, Ju YS, Park H, Kim S, Lee S, et al. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 460: 1011-1015. doi:10.1038/nature08211.
8. Tong P, Prendergast JGD, Lohan AJ, Farrington SM, Cronin S, et al. (2010) Sequencing and analysis of an Irish human genome. Genome Biol 11: R91. doi:10.1186/gb-2010-11-9-r91.
9. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, et al. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463: 943-947. doi:10.1038/nature08795.
10. Shapiro B, Hofreiter M (2010) Analysis of ancient human genomes. BioEssays 32: 388-391. doi:10.1002/bies.201000026.
11. Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, et al. (2010) Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet 42: 931-936. doi:10.1038/ng.691.
12. Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, et al. (2011) An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334: 94-98. doi:10.1126/science.1211177.
13. Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, et al. (2012) Systematic analysis and functional annotation of variations in the genome of an Indian individual. Hum Mutat 33: 1133-1140. doi:10.1002/humu.22091.
14. Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, et al. (2012) Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics 13: 440. doi:10.1186/1471-2164-13-440.
15. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65. doi:10.1038/nature07484.
16. Gonzaga-Jauregui C, Lupski JR, Gibbs R a (2012) Human Genome Sequencing in Health and Disease. Annu Rev Med 63: 35-61. doi:10.1146/annurev-med-051010- 162644.
17. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, et al. (2010) Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328: 723-725. doi:10.1126/science.1188046.
18. Fagundes NJR, Kanitz R, Bonatto SL (2008) A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization of Beringia. PLoS One 3: e3157. doi:10.1371/journal.pone.0003157.
19. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722. doi:10.1126/science.1188021.
20. O'Rourke DH, Raff JA (2010) The human genetic history of the Americas: the final frontier. Curr Biol 20: R202-7. doi:10.1016/j.cub.2009.11.051.
21. Forster P, Harding R, Torroni A, Bandelt HJ (1996) Origin and evolution of Native American mtDNA variation: a reappraisal. Am J Hum Genet 59: 935-945. (Pubitemid 26328092)
22. Rothhammer F, Dillehay TD (2009) The late Pleistocene colonization of South America: An interdisciplinary perspective. Ann Hum Genet 73: 540-549.
23. Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, et al. (2012) Reconstructing Native American population history. Nature 488: 370-374. doi:10.1038/nature11258.
24. Bisso-Machado R, Bortolini MC, Salzano FM (2012) Uniparental genetic markers in South Amerindians. Genet Mol Biol 35: 365-387. doi:10.1590/S1415- 47572012005000027.
25. Silva Jr WA, Bonatto SL, Holanda AJ, Ribeiro-dos-Santos AK, Paixão BM, et al. (2002) Mitochondrial Genome Diversity of Native Americans Supports a Single Early Entry of Founder Populations into America. Am J Hum Genet 71: 187-192. (Pubitemid 34734722)
26. Van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386-94. doi:10.1002/humu.20921.
27. Smith DG, Malhi RS, Eshleman J, Lorenz JG, Kaestle FA (1999) Distribution of mtDNA haplogroup X among Native North Americans. Am J Phys Anthropol 110: 271-284. doi:10.1002/(SICI)1096-8644(199911)110:3〈271::AID-AJPA2〉3.0. CO;2-C. (Pubitemid 29504073)
28. Kong Q-P, Bandelt H-J, Sun C, Yao Y-G, Salas A, et al. (2006) Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15: 2076-2086. doi:10.1093/hmg/ddl130. (Pubitemid 43923397)
29. Starikovskaya EB, Sukernik RI, Derbeneva OA, Volodko N V, Ruiz-Pesini E, et al. (2005) Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of Native American haplogroups. Ann Hum Genet 69: 67-89. doi:10.1046/j.1529-8817.2003.00127.x. (Pubitemid 40202009)
30. Ribeiro-Dos-Santos AKC, Santos SEB, L MA, Guapindaia V, Zago MA (1996) Heterogeneity of mitochondrial DNA haplotypes in Pre-Columbian natives of the Amazon region. Am J Phys Anthropol 101: 29-37. doi:10.1002/(SICI)1096- 8644(199609)101:1〈29::AID-AJPA3〉3.0.CO;2-8. (Pubitemid 26295311)
31. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, et al. (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18: 830-838. doi:10.1101/gr.7172008. (Pubitemid 351645073)
32. Santos SE, Ribeiro-dos-Santos AK, Meyer D, Zago MA (1996) Multiple founder haplotypes of mitochondrial DNA in Amerindians revealed by RFLP and sequencing. Ann Hum Genet 60: 305-319. (Pubitemid 26283447)
33. Rodriguez-Delfin LA, Rubin-de-Celis VE, Zago MA (2001) Genetic diversity in an Andean population from Peru and regional migration patterns of Amerindians in South America: data from Y chromosome and mitochondrial DNA. Hum Hered 51: 97-106. doi:22964.
34. Zegura SL, Karafet TM, Zhivotovsky LA, Hammer MF (2004) High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas. Mol Biol Evol 21: 164-175. doi:10.1093/molbev/msh009. (Pubitemid 38233530)
35. Roewer L, Nothnagel M, Gusmão L, Gomes V, González M, et al. (2013) Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans. PLoS Genet 9: e1003460. doi:10.1371/journal.pgen.1003460.
36. Bailliet G, Ramallo V, Muzzio M, García A, Santos MR, et al. (2009) Brief communication: Restricted geographic distribution for Y-Q* paragroup in South America. Am J Phys Anthropol 140: 578-582. doi:10.1002/ajpa.21133.
37. Toscanini U, Gusmão L, Berardi G, Gomes V, Amorim A, et al. (2011) Male lineages in South American native groups: evidence of M19 traveling south. Am J Phys Anthropol 146: 188-196. doi:10.1002/ajpa.21562.
38. Bortolini MC, Salzano FM, Thomas MG, Stuart S, Nasanen SPK, et al. (2003) Y-chromosome evidence for differing ancient demographic histories in the Americas. Am J Hum Genet 73: 524-539. doi:10.1086/377588. (Pubitemid 37076267)
39. Demarchi DA, Mitchell RJ (2004) Genetic structure and gene flow in Gran Chaco populations of Argentina: evidence from Y-chromosome markers. Hum Biol 76: 413-429. (Pubitemid 39274412)
40. Sala A, Argüelles CF, Marino ME, Bobillo C, Fenocchio A, et al. (2010) Genetic analysis of six communities of Mbyá-Guaraní inhabiting northeastern Argentina by means of nuclear and mitochondrial polymorphic markers. Hum Biol 82: 433-456. doi:10.3378/027.082.0406.
41. Blanco-Verea A, Jaime JC, Brión M, Carracedo A (2010) Y-chromosome lineages in native South American population. Forensic Sci Int Genet 4: 187-193. doi:10.1016/j.fsigen.2009.08.008.
42. Dos Santos SEB, Rodrigues JD, Ribeiro-dos-Santos AK, Zago MA (1999) Differential contribution of indigenous men and women to the formation of an urban population in the Amazon region as revealed by mtDNA and Y-DNA. Am J Phys Anthropol 109: 175-180. doi:10.1002/(SICI)1096-8644(199906)109:2〈175::AID- AJPA3〉3.0.CO;2. (Pubitemid 29256788)
43. Gonçalves VF, Stenderup J, Rodrigues-Carvalho C, Silva HP, Gonçalves-Dornelas H, et al. (2013) Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil. Proc Natl Acad Sci U S A 110: 6465-6469. doi:10.1073/pnas.1217905110.
44. Balter M (2008) Archaeology. Ancient algae suggest sea route for first Americans. Science 320: 729. doi:10.1126/science.320.5877.729.
45. Smit AFA, Hubley R, Green P. (n.d.) RepeatMasker Open-3.0.
46. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi:10.1093/bioinformatics/btp352.
47. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311. (Pubitemid 32054478)
48. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290: 457-465. (Pubitemid 11159074)
49. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147. doi:10.1038/13779. (Pubitemid 29455385)
50. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567. doi:10.1111/j.1755-0998.2010.02847.x.
51. Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27: 3070-3071. doi:10.1093/bioinformatics/ btr521.
52. R Core Team (2013) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
53. Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461: 489-494. doi:10.1038/nature08365.
54. Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8: e1002967. doi:10.1371/journal.pgen.1002967.
55. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7: 574-578. doi:10.1111/j.1471-8286.2007.01758.x. (Pubitemid 47035522)