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Eukaryote Genomes

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Introduction to Evolutionary Genomics

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

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Abstract

General overviews of eukaryote genomes are first discussed, including organelle genomes, introns, and junk DNAs. We then discuss the evolutionary features of eukaryote genomes, such as genome duplication, C-value paradox, and the relationship between genome size and mutation rates. Genomes of multicellular organisms, plants, fungi, and animals are then briefly discussed.

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References

  1. Kryukov, K., Sumiyama, K., Ikeo, K., Gojobori, T., & Saitou, N. (2012). A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses. Genome Biology and Evolution, 4, 501–512.

    Article  Google Scholar 

  2. Carballido-López, R. (2006). The Bacterial actin-like cytoskeleton. Microbiology and Molecular Biology Reviews, 70, 888–909.

    Article  Google Scholar 

  3. Andersson, S. G., et al. (1998). The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature, 396, 133–140.

    Article  Google Scholar 

  4. Martin, W., & Muller, M. (1998). The hydrogen hypothesis for the first eukaryote. Nature, 392, 37–41.

    Article  Google Scholar 

  5. Harish, A., & Kurland, C. G. (2017). Mitochondria are not captive bacteria. Journal of Theoretical Biology, 434, 88–98.

    Article  Google Scholar 

  6. Wolstenholme, D. R., & Jeon, K. W. (Eds.). (1992). Mitochondrial genome. Cambridge: Academic Press Inc.

    Google Scholar 

  7. Sakai, M., & Sakaizumi, M. (2012). The complete mitochondrial genome of Dugesia japonica (Platyhelminthes; order Tricladida). Zoological Science, 29, 672–680.

    Article  Google Scholar 

  8. Sugiyama, Y., Watase, Y., Nagase, M., Makita, M., Yagura, S., Hirai, A., et al. (2005). The complete nucleotide sequence of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants and multipartite organization. Molecular and General Genomics, 272, 603–615.

    Article  Google Scholar 

  9. Bergthorsson, U., Adams, K. L., Thomason, B., & Palmer, J. (2003). Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature, 424, 197–201.

    Article  Google Scholar 

  10. Rodriguez-Moreno, L., Benjak, A., Marti, M. C., Puigdomenech, P., Aranda, M. A., & Garcia-Mas, J. (2011). Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin. BMC Genomics, 12, 424.

    Article  Google Scholar 

  11. Lilly, J. W., & Havey, M. J. (2001). Small, repetitive DNAs contribute significantly to the expanded mitochondrial genome of cucumber. Genetics, 159, 317–328.

    Google Scholar 

  12. Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., et al. (1986). The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO Journal, 5, 2043–2049.

    Article  Google Scholar 

  13. Oldenburg, D. J., & Bendich, A. J. (2004). Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize. Journal of Molecular Biology, 344, 1311–1330.

    Article  Google Scholar 

  14. Woischnik, M., & Moraes, C. T. (2002). Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Research, 12, 885–893.

    Article  Google Scholar 

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

    Google Scholar 

  16. Graur, D. (2017) Rubbish DNA: The functionless fraction of the human genome. In: N. Saitou (Ed.) The evolution of the human genome, Chapter 2, Tokyo: Springer.

    Chapter  Google Scholar 

  17. The Nobel Prize in Physiology or Medicine 1993, http://www.nobelprize.org/nobel_prizes/medicine/laureates/1993/press.html.

  18. Gilbert, W. (1978). Why genes in pieces? Nature, 271, 501.

    Article  Google Scholar 

  19. Kenmochi N. (2012) Introns. In Encyclopedia of Evolution. Kyoritsu Shuppan (in Japanese).

    Google Scholar 

  20. Sheth, N., Roca, X., Hastings, M. L., Roeder, T., Krainer, A. R., & Sachidanandam, R. (2006). Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Research, 34, 3955–3967.

    Article  Google Scholar 

  21. Tycowski, K. T., Kolev, N. G., Conrad, N. K., Fok, V., Steitz, J. A. (2006). The ever-growing world of small nuclear ribonucleoproteins. In R. F. Gesteland, T. R. Cech, J. F. Atkins (Eds.) The RNA World, 3rd edn. (pp. 327–368) Cold Spring Harbor Laboratory Press.

    Google Scholar 

  22. Cavalier-Smith, T. (1991). Intron phylogeny: A new hypothesis. Trends in Genetics, 7, 145–148.

    Article  Google Scholar 

  23. Marck, C., & Grosjean, H. (2002). tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189–1232.

    Article  Google Scholar 

  24. Simoens, C. R., Gielen, J., Van Montagu, M., & Inze, D. (1988). Characterization of highly repetitive sequences of Arabidopsis thaliana. Nucleic Acids Research, 16, 6753–6766.

    Article  Google Scholar 

  25. Murata, M., Ogura, Y., & Mototoshi, F. (1994). Centromeric repetitive sequences in Arabidopsis thaliana. Japanese Journal of Genetics, 69, 361–370.

    Article  Google Scholar 

  26. Yamada, K., et al. (2002). Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302, 842–846.

    Article  Google Scholar 

  27. The ENCODE Project Consortium. (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 

  28. 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 

  29. Yoshiura, K., et al. (2006). A SNP in the ABCC11 gene is the determinant of human earwax type. Nature Genetics, 38, 324–330.

    Article  Google Scholar 

  30. Wolfe, K. H., & Shields, D. C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387, 708–713.

    Article  Google Scholar 

  31. Ma, L.-J., et al. (2009). Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genetics, 5, e1000549.

    Article  Google Scholar 

  32. Aury, J. M., et al. (2006). Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature, 444, 171–178.

    Article  Google Scholar 

  33. Nossa, C. W., et al. (2014). Joint assembly and genetic mapping of theAtlantic horseshoe crab genome reveals ancient whole genome duplication. GigaScience, 3, 9.

    Article  Google Scholar 

  34. Williams, T. A., et al. (2016). A recent whole-genome duplication divides populations of a globally distributed microsporidian. Molecular Biology and Evolution, 33, 2002–2015.

    Article  Google Scholar 

  35. Swaiger, E. E., et al. (2017). The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biology, 15, 62.

    Article  Google Scholar 

  36. Lynch, M., & Conery, J. S. (2000). The evolutionary fate and consequences of duplicated genes. Science, 302, 1401–1404.

    Article  Google Scholar 

  37. Gregory, T. R., & DeSalle, R. (2005). Comparative genomics in prokaryotes. In T. R. Gregory (Ed.), The evolution of the genome, Chapter 10, Burlington: Elsevier.

    Chapter  Google Scholar 

  38. Gott, J. M., & Emeson, R. B. (2000). Functions and mechanisms of RNA editing. Annual Review of Genetics, 34, 499–531.

    Article  Google Scholar 

  39. Tillich, M., Lehwark, P., Morton, B. R., & Maier, U. G. (2006). The evolution of chloroplast RNA editing. Molecular Biology and Evolution, 23, 1912–1921.

    Article  Google Scholar 

  40. How, G. F., Venkatesh, B., & Brenner, S. (1996). Conserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor. Genome Research, 6, 1185–1191.

    Article  Google Scholar 

  41. Hardison, R. C. (2000). Conserved noncoding sequences are reliable guides to regulatory elements. Trends in Genetics, 16, 369–372.

    Article  Google Scholar 

  42. Levy, S., Hannenhalli, S., & Workman, C. (2001). Enrichment of regulatory signals in con- served non-coding genomic sequence. Bioinformatics, 17, 871–877.

    Article  Google Scholar 

  43. Carroll, S. B. (2005). Evolution at two level: On genes and form. PLoS Biology, 3, e245.

    Article  Google Scholar 

  44. Siepel, A., et al. (2005). Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research, 15, 1034–1050.

    Article  Google Scholar 

  45. Kaplinsky, N. J., Braun, D. M., Penterman, J., Goff, S. A., & Freeling, M. (2002). Utility and distribution of conserved noncoding sequences in the grasses. Proceedings of the National Academy of Sciences USA, 99, 6147–6151.

    Article  Google Scholar 

  46. Guo, H., & Moose, S. P. (2003). Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell, 15, 1143–1158.

    Article  Google Scholar 

  47. Inada, D. C., et al. (2003). Conserved noncoding sequences in the grasses. Genome Research, 13, 2030–2041.

    Article  Google Scholar 

  48. Thomas, B. C., Rapaka, L., Lyons, E., Pedersen, B., & Freeling, M. (2007). Arabidopsis intragenomic conserved noncoding sequence. Proceedings of the National Academy of Sciences USA, 104, 3348–3353.

    Article  Google Scholar 

  49. D’Hont, A., et al. (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488, 213–217.

    Article  Google Scholar 

  50. Kritsas, K., Samuel, E., Wuest, S. E., Hupalo, D., Kern, A. D., Wicker, T., et al. (2012). Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Research, 22, 2455–2466.

    Article  Google Scholar 

  51. Hettiarachchi, N., & Saitou, N. (2014). Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning. Genome Biology and Evolution, 6, 2527–2542.

    Article  Google Scholar 

  52. Rajic, Z. A., Jankovic, G. M., Vidovic, A., Milic, N. M., Skoric, D., Pavlovic, M., et al. (2005). Size of the protein-coding genome and rate of molecular evolution. Journal of Human Genetics, 50, 217–229.

    Article  Google Scholar 

  53. Sanjuan, R., Nebot, M. R., Chirico, N., Mansky, L. M., & Belshaw, R. (2010). Viral mutation rates. Journal of Virology, 84, 9733–9748.

    Article  Google Scholar 

  54. Lynch, M. (2006). The origins of eukaryotic gene structure. Molecular Biology and Evolution, 23, 450–468.

    Article  Google Scholar 

  55. Lynch, M. (2010). Evolution of the mutation rate. Trends in Genetics, 26, 345–352.

    Article  Google Scholar 

  56. Drake, J. W., Charlesworth, B., Charlesworth, D., & Crow, J. F. (1998). Rates of spontaneous mutation. Genetics, 148, 1667–1686.

    Google Scholar 

  57. Mewes, H. W., et al. (1997). Overview of the yeast genome. Nature, 387, 7–65.

    Article  Google Scholar 

  58. Lynch, M. (2007). Origin of genome architecture. Sunderland: Sinaur Associates.

    Google Scholar 

  59. https://www.ncbi.nlm.nih.gov/genome/browse/#!/eukaryotes/.

  60. Martin, F., et al. (2010). Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature, 464, 1033–1038.

    Article  Google Scholar 

  61. Arabidopsis Genome Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796–815.

    Article  Google Scholar 

  62. Hu, T. T., et al. (2011). The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics, 43, 476–481.

    Article  Google Scholar 

  63. Goff, S. A., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92–100.

    Article  Google Scholar 

  64. Yu, J., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92.

    Article  Google Scholar 

  65. Londo, J. P., et al. (2006). Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proceedings of the National Academy of Sciences USA, 103, 9578–9583.

    Article  Google Scholar 

  66. Yang, C.-C., Kawahara, Y., Mizuno, H., Wu, J., Matsumoto, T., & Itoh, T. (2012). Independent domestication of Asian rice followed by gene flow from japonica to indica. Molecular Biology and Evolution, 29, 1471–1479.

    Article  Google Scholar 

  67. The Rice Annotation Project. (2007). Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research, 17, 175–183.

    Article  Google Scholar 

  68. The International Wheat Genome Sequencing Consortium (IWGSC). (2014). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 345(6194), 1251788.

    Google Scholar 

  69. http://www.nobelprize.org/nobel_prizes/medicine/laureates/1995/lewis.html.

  70. Gehring, W. J. (1999). Master control genes in development and evolution: The homeobox story. New Haven: Yale University Press.

    Google Scholar 

  71. Carroll, S. B., Grenier, J. K., & Weatherbee, S. D. (2005). From DNA to diversity. Malden: Blackwell Publishing.

    Google Scholar 

  72. Matsunami, M., Sumiyama, K., & Saitou, N. (2010). Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis. Journal of Molecular Evolution, 71, 427–436.

    Article  Google Scholar 

  73. Foronda, D., de Navas, L. F., Garaulet, D. L., & Sanchez-Herrero, E. (2009). Function and specificity of Hox genes. International Journal of Developmental Biology, 53, 1409–1419.

    Article  Google Scholar 

  74. Aruga, J., et al. (2006). A wide-range phylogenetic analysis of Zic proteins: Implications for correlations between protein structure conservation and body plan complexity. Genomics, 87, 783–792.

    Article  Google Scholar 

  75. C. elegans Sequencing Consortium. (1998). Genome sequence of the nematode C. elegans: A platform for investigating biology. Science, 282, 2012–2018.

    Article  Google Scholar 

  76. Meldal, B. H. M., et al. (2007). An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa. Molecular Phylogenetics and Evolution, 42, 622–636.

    Article  Google Scholar 

  77. Brenner, S. (1974). The genetics of Caenorhabditis elegans. Genetics, 77, 71–94.

    Google Scholar 

  78. Chalfie, M. (Ed.) WormBook—The online review of C. elegans biology, http://www.wormbook.org/.

  79. Adams, M. D., et al. (2000). The genome sequence of Drosophila melanogaster. Science, 287, 2185–2195.

    Article  Google Scholar 

  80. Drosophila 12 Genomes Consortium. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203–218.

    Article  Google Scholar 

  81. Gall, J. G. (1981). Chromosome structure and the C-value paradox. Journal of Cell Biology, 91, 3s–14s.

    Article  Google Scholar 

  82. Vendrely, R., & Vendrely, C. (1948). La teneur du noyau cellulaire en acide désoxyribonuclé- ique à travers les organes, les individus et les espèces animales. Cellular and Molecular Life Sciences, 4, 434–436. (in French).

    Article  Google Scholar 

  83. Pollister, A. W., & Ris, H. (1947). Nucleoprotein determination in cytological preparations. Cold Spring Harbor Symposia on Quantitative Biology, 12, 147–157.

    Article  Google Scholar 

  84. Swift, H. (1950). The constancy of deoxyribose nucleic acid in plant nuclei. Proceedings of the National Academy of Sciences USA, 36, 643–654.

    Article  Google Scholar 

  85. Koonin, E. V. (2006). The origin of introns and their role in eukaryogenesis: A compromise solution to the introns-early versus introns-late debate? Biology Direct, 1, 22.

    Article  Google Scholar 

  86. Roy, S. W., & Gilbert, W. (2006). The evolution of spliceosomal introns: Patterns, puzzles and progress. Nature Reviews Genetics, 7, 211–221.

    Google Scholar 

  87. Doolittle, W. F. (1978). Genes in pieces: Were they ever together? Nature, 272, 581–582.

    Article  Google Scholar 

  88. Cavalier-Smith, T. (1978). Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. Journal of Cell Science, 34, 247–278.

    Google Scholar 

  89. Logsdon, J. M., Jr. (1998). The recent origins of spliceosomal introns revisited. Current Opinion in Genetics & Development, 8, 637–648.

    Article  Google Scholar 

  90. Go, M. (1981). Correlation of DNA exonic regions with protein structural units in haemoglobin. Nature, 291, 90–92.

    Article  Google Scholar 

  91. Rogozin, I. B., Wolf, Y. I., Sorokin, A. V., Mirkin, B. G., & Koonin, E. V. (2003). Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Current Biology, 13, 1512–1517.

    Article  Google Scholar 

  92. Nguyen, D. H., Yoshihama, M., & Kenmochi, N. (2005). New maximum likelihood estimators for eukaryotic intron evolution. PLoS Computational Biology, 1, e79.

    Article  Google Scholar 

  93. Yoshihama, M., Nakao, A., Nguyen, H. D., & Kenmochi, N. (2006). Analysis of ribosomal protein gene structures: Implications for intron evolution. PLoS Genetics, 2, 237–242.

    Article  Google Scholar 

  94. Yoshihama, M., Nguyen, H. D., & Kenmochi, N. (2007). Intron dynamics in ribosomal protein genes. PLoS ONE, 1, e141.

    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. (2018). Eukaryote Genomes. In: Introduction to Evolutionary Genomics. Computational Biology, vol 17. Springer, Cham. https://doi.org/10.1007/978-3-319-92642-1_9

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  • DOI: https://doi.org/10.1007/978-3-319-92642-1_9

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