The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations

Genome Biology and Evolution

Volumn 6, Issue 12, 2014, Pages 3122-3136

  Bai, Haihua ^a   Guo, Xiaosen ^b,c   Zhang, Dong ^d   Narisu, Narisu ^e   Bu, Junjie ^b,f   Jirimutu, Jirimutu ^a   Liang, Fan ^b   Zhao, Xiang ^b   Xing, Yanping ^d   Wang, Dingzhu ^a   Li, Tongda ^b,g   Zhang, Yanru ^d   Guan, Baozhu ^h   Yang, Xukui ^b   Yang, Zili ^d   Shuangshan, Shuangshan ^a,i   Su, Zhe ^b   Wu, Huiguang ^a   Li, Wenjing ^b   Chen, Ming ^a,j   Zhu, Shilin ^b   Bayinnamula, Bayinnamula ^a   Chang, Yuqi ^b   Gao, Ying ^a   Lan, Tianming ^b   Suyalatu, Suyalatu ^a   Huang, Hui ^b   Su, Yan ^b   Chen, Yujie ^a   Li, Wenqi ^b   Yang, Zu ^b   Feng, Qiang ^b,c   Wang, Jian ^b,k   Yang, Huanming ^b,f,k   Wang, Jun ^b,c,l,m   Wu, Qizhu ^a   Yin, Ye ^b   Zhou, Huanmin ^d   more..

^a INNER MONGOLIA UNIVERSITY FOR NATIONALITIES   (China)

^b BGI SHENZHEN   (China)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d INNER MONGOLIA AGRICULTURAL UNIVERSITY   (China)

^e NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^f UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^g SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^h Inner Mongolia International Mongolian Hospital   (China)

ⁱ BAOTOU TEACHERS COLLEGE   (China)

^j ZHEJIANG UNIVERSITY   (China)

^k James D Watson Institute of Genome Science   (China)

^l KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^m AARHUS UNIVERSITY   (Denmark)

more..

Author keywords

De novo assembly; Genetic imprints; Genetic variations; Mongolian genome; Patrilineal origin

Indexed keywords

CARNITINE;

ASIAN CONTINENTAL ANCESTRY GROUP; DEFICIENCY; GENE DELETION; GENE EXPRESSION REGULATION; GENE FLOW; GENETICS; HUMAN; HUMAN GENOME; MALE; MOLECULAR EVOLUTION; MONGOLIA; POPULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ASIAN CONTINENTAL ANCESTRY GROUP; CARNITINE; EVOLUTION, MOLECULAR; GENE DELETION; GENE FLOW; GENOME, HUMAN; HUMANS; MALE; MONGOLIA; MUTAGENESIS, INSERTIONAL; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION;

EID: 84938503872     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu242     Document Type: Article

References (70)

1. 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
2. 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491:56-65.
3. Albers CA, et al. 2011. Dindel: accurate indel calls from short-read data. Genome Res. 21:961-973.
4. Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19:1655-1664.
5. Anderson S, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
6. Andrews RM, et al. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 23:147.
7. Attwood TK, Beck ME, Bleasby AJ, Parry-Smith DJ. 1994. PRINTS- A database of protein motif fingerprints. Genome Res. 22:3590-3596.
8. Bairoch A, Apweiler R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Genome Res. 28:45-48.
9. Barrett J, Fry B, Maller J, Daly M. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
10. Behar DM, et al. 2010. The genome-wide structure of the Jewish people. Nature 466:238-242.
11. Behar DM, et al. 2012. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet. 90:675-684.
12. Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
13. Birney E, Clamp M, Durbin R. 2004. GeneWise and genomewise. Genome Res. 14:988-995.
14. Bru C, et al. 2005. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 33:D212-D215.
15. Burge C, Karlin S. 1997. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 268:78-94.
16. Deng W, et al. 2004. Evolution and migration history of the Chinese population inferred from Chinese Y-chromosome evidence. J Hum Genet. 49:339-348.
17. De Pristo MA, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 43:491-498.
18. Derenko M, et al. 2007. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet. 81:1025-1041.
19. Finn RD, et al. 2010. the Pfam protein families database. Nucleic Acids Res. 38:D211-D222.
20. Genome of the Netherlands Consortium. 2014. Whole-genome sequence variation, population structure and demographic history of Dutch population. Nat Genet. 46:818-825.
21. Green RE, et al. 2010. A draft sequence of the Neandertal genome. Science 328:710-722.
22. Harris RS. 2007. Improved pairwise alignment of genomic DNA [PhD thesis]. The Pennsylvania State University.
23. Hulo N, et al. 2006. The PROSITE database. Nucleic Acids Res. 34:D227-D230.
24. Karafet TM, et al. 2008. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 18:830-838.
25. Katoh T, et al. 2005. Genetic features of Mongolian ethnic groups revealed by Y-chromosomal analysis. Gene 346:63-70.
26. Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12:656-664.
27. Koizumi A, Nozaki J, Ohura T, Kayo T, Wada Y, et al. 1999. Genetic epidemiology of the carnitine transporter OCTN2 gene in a Japanese population and phenotypic characterization in Japanese pedigrees with primary systemic carnitine deficiency. Hum Mol Genet. 8:2247-2254.
28. Kolman CJ, Sambuughin N, Bermingham E. 1996. Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders. Genetics 142:1321-1334.
29. Komatsu F, et al. 2006. Investigation of oxidative stress and dietary habits in Mongolian people, compared to Japanese people. Nutr Metab (Lond). 3:21.
30. Komatsu F, et al. 2008. Dietary habits of Mongolian people, and their influence on lifestyle-related diseases and early aging. Curr Aging Sci. 1:84-100.
31. Komatsu F, Kagawa Y, Kawabata T, Kaneko Y, Ishiguro K. 2009. Relationship of dietary habits and obesity to oxidative stress in Palauan people: compared with Japanese and Mongolian people. Curr Aging Sci. 2:214-222.
32. Kurtz S, et al. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12.
33. Letunic I, Doerks T, Bork P. 2012. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 40:D302-D305.
34. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
35. Li H, Handsaker B, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
36. Li JZ, et al. 2008. Worldwide human relationships inferred from genomewide patterns of variation. Science 319:1100-1104.
37. Li R, Fan W, et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature 463:311-317.
38. Li R, Li Y, et al. 2009. SNP detection for massively parallel whole-genome resequencing. Genome Res. 19:1124-1132.
39. Li R, Li Y, et al. 2010. Building the sequence map of the human pangenome. Nat Biotechnol. 28:57-63.
40. Li Y, et al. 2011. Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol. 29:723-730.
41. Longo N, Amat Di San Filippo C, Pasquali M. 2006. Disorders of carnitine transport and the carnitine cycle. Am J Med Genet C Semin Med Genet. 142C:77-85.
42. Luo R, et al. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18.
43. McKenna A, et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-1303.
44. Merriwether DA, Hall WW, Vahlne A, Ferrell RE. 1996. mtDNA variation indicates Mongolia may have been the source for the founding population for the New World. Am J Hum Genet. 59:204-212.
45. Ogata H, et al. 1999. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27:29-34.
46. Purcell S, et al. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 81:559-575.
47. Rasmussen M, et al. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94-98.
48. Reich D, et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.
49. Reich D, et al. 2012. Reconstructing Native American population history. Nature 488:370-374.
50. Reich D, Thangaraj K, Patterson N, Price AL, Singh L. 2009. Reconstructing Indian population history. Nature 461:489-494.
51. Richards JF. 1993. The Mughal Empire. The New Cambridge History of India. Cambridge: Cambridge University Press.
52. Shi H, et al. 2008. Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biol. 6:45.
53. Stanke M, Tzvetkova A, Morgenstern B. 2006. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol. 7:S11-S11.
54. Starikovskaya EB, 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.
55. Su B, et al. 1999. Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age. Am J Hum Genet. 65:1718-1724.
56. Svobodova H, et al. 2007. Apolipoprotein E gene polymorphism in the Mongolian population. Folia Biol (Praha). 53:138-142.
57. Tanaka M, et al. 2004. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res. 14:1832-1850.
58. Tsunoda K, Harihara S, Tanabe Y, Dashnyam B. 2012. Polymorphism of the apolipoprotein B gene and association with plasma lipid and lipoprotein levels in the Mongolian Buryat. Biochem Genet. 50:249-268.
59. Twitchett D, Fairbank JK. 1994. Alien regimes and borders states. In: Twitchett DC, Franke H, editors. The Cambridge History of China, Vol. 6. Cambridge: Cambridge University Press. p. 321-489.
60. Tylor NP, et al. 2006. MLH3 mutation in endometrial cancer. Cancer Res. 66:7502-7508.
61. Wang J, et al. 2008. The diploid genome sequence of an Asian individual. Nature 456:60-65.
62. Wang K, Li M, Hakonarson H. 2010. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38:e164.
63. Weatherford J. 2005. The Mongol world war: 1121-1261. Genghis Khan and the making of the modern world. New York: Crown Publisher. p. 84-207.
64. Xing J, et al. 2013. Genomic analysis of natural selection and phenotypic variation in high-altitude Mongolians. PLoS Genet. 9:e1003634.
65. Yoon YA, et al. 2012. SLC22A5 mutations in a patient with systemic primary canitine deficiency: the first Korean case confirmed by biological and molecular investigation. Ann Clin Lab Sci. 42:424-428.
66. Zdobnov EM, Apweiler R. 2001. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847-848.
67. Zerjal T, et al. 2003. The genetic legacy of the Mongols. Am J Hum Genet. 72:717-721.
68. Zheng L, Han Z, Lu S, Li Y, Shuyuan L. 2002. Morphological traits in peoples of Mongolian nationality of the Hulunbuir league, Inner Mongolia, China. Anthropol Anz. 60:175-185.
69. Zheng LY, et al. 2011. Genome-wide patterns of genetic variation in sweet ang grain sorghum (Sorghum bicolor). Genome Biol. 12:R114.
70. Zhong H, et al. 2010. Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet. 55:428-435.