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Human Genome

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Introduction to Evolutionary Genomics

Part of the book series: Computational Biology ((COBO,volume 17))

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Abstract

The human genome can be considered as the representative of mammalian genomes. Basic characteristics of the human genome, such as the overall structure, protein coding genes, and RNA genes, are first discussed. Personal genome sequencing and genomic heterogeneity are described next. We then discuss genetic changes to produce humanness. At the end, ancient human genomes are briefly reviewed.

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References

  1. Gregory, T. R. (Ed.). (2005). The evolution of the genome. Burlington: Elsevier Academic.

    Google Scholar 

  2. Bickmore, W. A. (2001). Karyotype analysis and chromosome banding. Encyclopedia of Life Sciences (http://web.udl.es/usuaris/e4650869/docencia/segoncicle/genclin98/recursos_classe_%28pdf%29/revisionsPDF/bandmethods2.pdf)

  3. International Human Genome Sequencing Consortium. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921.

    Article  Google Scholar 

  4. Venter, J. C., and others (2001). The sequence of the human genome. Science, 291, 1304–1351.

    Google Scholar 

  5. Brown, T. A. (2007). Figure 7.13, genomes 3. New York: Garland Science Publishing.

    Google Scholar 

  6. International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature, 431, 931–945.

    Article  Google Scholar 

  7. Imanishi, T., et al. (2004). Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology, 2, 856–875.

    Article  Google Scholar 

  8. Clamp, M., et al. (2007). Distinguishing protein-coding and noncoding genes in the human genome. PNAS, 104, 19428–19433.

    Article  Google Scholar 

  9. Mi, H., Muruganujan, A., Thomas, P. D., et al. (2013). PANTHER in 2013: Modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acid Research, 41, D377–D386.

    Article  Google Scholar 

  10. Nozawa, M., Kawahara, Y., & Nei, M. (2007). Genomic drift and copy number variation of sensory receptor genes in humans. PNAS, 104, 20421–20426.

    Article  Google Scholar 

  11. http://gtrnadb.ucsc.edu

  12. www.ensembl.org/biomart/

  13. The ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74.

    Article  Google Scholar 

  14. Thurman, R. E., et al. (2012). The accessible chromatin landscape of the human genome. Nature, 489, 75–82.

    Article  Google Scholar 

  15. Neph, S., et al. (2012). An expansive human regulatory lexicon encoded in transcription factor footprints. Nature, 489, 83–90.

    Article  Google Scholar 

  16. Gestein, M. B. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91–100.

    Article  Google Scholar 

  17. Djebali, S., et al. (2012). Landscape of transcription in human cells. Nature, 489, 101–108.

    Article  Google Scholar 

  18. Birney, E., et al. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799–816.

    Article  Google Scholar 

  19. van Bakel, H., Nislow, C., Blencowe, B. J., & Hughes, T. R. (2010). Most “Dark Matter” transcripts are associated with known genes. Plos Biology, 8, e1000371.

    Article  Google Scholar 

  20. Pennisi, E. (2012). ENCODE project writes eulogy for Junk DNA. Science, 337, 1159–1161.

    Article  MathSciNet  Google Scholar 

  21. Eddy, S. (2012). The C-value paradox, junk DNA and ENCODE. Current Biology, 22, R898.

    Article  Google Scholar 

  22. Graur, D., Zheng, Y., Price, N., Azevedo, R. B. R., Zufall, R. A., & Elhaik, E. (2013). On the immortality of television sets: function in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution, 5(3), 578–590. (published online on February 20, 2013).

    Google Scholar 

  23. Ohno, S. (1972). So much “junk” DNA in our genome. Brookhaven Symposium in Biology, 23, 366–370.

    Google Scholar 

  24. Levy, S., et al. (2007). The diploid genome sequence of an individual human. PLoS Biology, 5, e254.

    Article  Google Scholar 

  25. http://huref.jcvi.org/

  26. Wheeler, D. A., et al. (2008). The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872–876.

    Article  Google Scholar 

  27. http://jimwastonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/

  28. Bentley, D. R., et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53–59.

    Article  Google Scholar 

  29. Wang, J., et al. (2008). The diploid genome sequence of an Asian individual. Nature, 456, 60–66.

    Article  Google Scholar 

  30. http://yh.genomics.org.cn/

  31. Ley, T. J., et al. (2008). DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456, 66–72.

    Article  Google Scholar 

  32. Ahn, S. M., et al. (2009). The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Research, 19, 1622–1629.

    Article  Google Scholar 

  33. Kim, J.-I., et al. (2009). A highly annotated whole-genome sequence of a Korean individual. Nature, 460, 1011–1015.

    Google Scholar 

  34. Fujimoto, A., et al. (2010). Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nature Genetics, 42, 931–936.

    Article  Google Scholar 

  35. Ng, P. C., Levy, S., Huang, J., Stockwell, T. B., Walenz, B. P., Li, K., Axelrod, N., Busam, D. A., Strausberg, R. L., & Venter, J. C. (2008). Genetic variation in an individual human exome. PLoS Genetics, 4, e1000160.

    Article  Google Scholar 

  36. Schster, S. C., et al. (2010). Complete Khoisan and Bantu genomes from southern Africa. Nature, 463, 943–947.

    Article  Google Scholar 

  37. Ju, Y.-S., et al. (2011). Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nature Genetics, 42, 931–936.

    Google Scholar 

  38. Roach, J. C., et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science, 328, 636–639.

    Article  Google Scholar 

  39. The 1000 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.

    Article  Google Scholar 

  40. Conrad, D. F., et al. (2011). Variation in genome-wide mutation rates within and between human families. Nature Genetics, 43, 712–714.

    Article  Google Scholar 

  41. The International SNP Map Working Group. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409, 928–933.

    Google Scholar 

  42. International HapMap Consortium. (2005). The haplotype map of the human genome. Nature, 437, 1299–1320.

    Article  Google Scholar 

  43. Rosenberg, N. A., et al. (2002). Genetic structure of human populations. Science, 298, 2381–2385.

    Article  Google Scholar 

  44. Yamaguchi-Kabata, Y., Nakazono, K., Takahashi, A., Saito, S., Hosono, N., Kubo, M., Nakamura, Y., & Kamatani, N. (2008). Population structure of Japanese based on SNP genotypes from 7,001 individuals in comparison to other ethnic groups: Effects on population-based association studies. American Journal of Human Genetics, 83, 445–456.

    Article  Google Scholar 

  45. Pinkel, D., et al. (1998). High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics, 20, 207–211.

    Article  Google Scholar 

  46. Sebat, J., et al. (2004). Large-scale copy number polymorphism in the human genome. Science, 305, 525–528.

    Article  Google Scholar 

  47. Redon, R., et al. (2006). Global variation in copy number in the human genome. Nature, 444, 444–454.

    Article  Google Scholar 

  48. Milles, R. E., et al. (2006). An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Research, 16, 1182–1190.

    Article  Google Scholar 

  49. The 1000 Genomes Project Consortium. (2010). A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.

    Article  Google Scholar 

  50. Saitou, N., & Ueda, S. (1994). Evolutionary rate of insertions and deletions in non-coding nucleotide sequences of primates. Molecular Biology and Evolution, 11, 504–512.

    Google Scholar 

  51. Saitou, N. (2005). Evolution of hominoids and the search for a genetic basis for creating humanness. Cytogenetic and Genome Research, 108, 16–21.

    Article  Google Scholar 

  52. Fujiyama, A., et al. (2002). Construction and analysis of a human-chimpanzee comparative clone map. Science, 295, 131–134.

    Article  Google Scholar 

  53. The Chimpanzee Sequencing and Analysis Consortium. (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437, 69–87.

    Article  Google Scholar 

  54. Clark, A. G., et al. (2003). Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science, 302, 1960–1963.

    Article  Google Scholar 

  55. Zhang, J. (2003). Frequent false detection of positive selection by the likelihood method with branch-site models. Molecular Biology and Evolution, 21, 1332–1339.

    Article  Google Scholar 

  56. Kitano, T., Liu, Y.-H., Ueda, S., & Saitou, N. (2004). Human specific amino acid changes found in 103 protein coding genes. Molecular Biology and Evolution, 21, 936–944.

    Article  Google Scholar 

  57. Prabhakar, S., et al. (2008). Human-specific gain of function in a developmental enhancer. Science, 321, 1346–1350.

    Article  Google Scholar 

  58. Duret, L., & Galtier, N. (2009). Comment on “Human-specific gain of function in a developmental enhancer”. Science, 323, 714.

    Article  Google Scholar 

  59. Sumiyama, K., & Saitou, N. (2011). Loss-of–function mutation in a repressor module of human-specifically activated enhancer HACNS1. Molecular Biology and Evolution, 28, 3005–3007.

    Article  Google Scholar 

  60. Noonan, J. P., et al. (2006). Sequencing and analysis of Neanderthal genomic DNA. Science, 314, 1113–1118.

    Article  Google Scholar 

  61. Green, R. E., et al. (2006). Analysis of one million base pairs of Neanderthal DNA. Nature, 444, 330–336.

    Article  Google Scholar 

  62. Wall, J. D., & Kim, S. K. (2007). Inconsistencies in Neanderthal genomic DNA sequences. PLoS Genetics, 3, 1862–1866.

    Article  Google Scholar 

  63. Green, R., et al. (2010). A draft sequence of the Neanderthal genome. Science, 328, 710–722.

    Article  Google Scholar 

  64. Yotova, V., et al. (2011). An X-linked haplotype of Neanderthal origin is present among all non-African populations. Molecular Biology and Evolution, 28, 1957–1962.

    Article  Google Scholar 

  65. Eriksson, A., & Manica, A. (2012). Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences of the United States of America, 109, 13956–13960.

    Article  Google Scholar 

  66. Reich, D., et al. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468, 1053–1060.

    Article  Google Scholar 

  67. Meyer M. et al. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science, Aug. 31, 2012, (epub ahead of print).

    Google Scholar 

  68. Reich, D., et al. (2011). Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American Journal of Human Genetics, 89, 1–13.

    Article  Google Scholar 

  69. Rasmussen, M., et al. (2010). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature, 463, 757–762.

    Article  Google Scholar 

  70. Rasmussen, M., et al. (2011). An Aboriginal Australian genome reveals separate human dispersals into Asia. Science, 334, 94–98.

    Article  Google Scholar 

  71. Keller, A., et al. (2012). New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. Nature Communications, 3, 698.

    Article  Google Scholar 

  72. Skoglund, P., et al. (2012). Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science, 336, 466–469.

    Article  Google Scholar 

  73. Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., Cann, H. M., Barsh, G. S., Feldman, M., Cavalli-Sforza, L. L., & Myers, R. M. (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science, 319, 1100–1104.

    Article  Google Scholar 

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Authors and Affiliations

  1. Division of Population Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan

    Naruya Saitou

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  1. Naruya Saitou
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Saitou, N. (2013). Human Genome. In: Introduction to Evolutionary Genomics. Computational Biology, vol 17. Springer, London. https://doi.org/10.1007/978-1-4471-5304-7_10

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  • DOI: https://doi.org/10.1007/978-1-4471-5304-7_10

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  • Print ISBN: 978-1-4471-5303-0

  • Online ISBN: 978-1-4471-5304-7

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