Universal global imprints of genome growth and evolution - equivalent length and cumulative mutation density

PLoS ONE

Volumn 5, Issue 4, 2010, Pages

  Chen, Hong Da ^a   Fan, Wen Lang ^a,b   Kong, Sing Guan ^a   Lee, Hoong Chien ^a,c,d  

^a NATIONAL CENTRAL UNIVERSITY   (Taiwan)

^b ACADEMIA SINICA   (Taiwan)

^c CATHAY GENERAL HOSPITAL   (Taiwan)

^d National Center for Theoretical Science   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CHROMOSOME; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI K 12; GENE DUPLICATION; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; GENOME; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM FALCIPARUM; POINT MUTATION; SCHIZOSACCHAROMYCES POMBE; BIOLOGICAL MODEL; ESCHERICHIA COLI; EVOLUTION; GENETICS; KINETICS; SEGMENTAL DUPLICATION;

BIOLOGICAL EVOLUTION; CHROMOSOMES; ESCHERICHIA COLI; GENOME; HUMANS; KINETICS; MODELS, GENETIC; POINT MUTATION; SEGMENTAL DUPLICATIONS, GENOMIC;

EID: 77956306838     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009844     Document Type: Article

References (70)

1. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76: 5269-5273.
2. Li WH (1997) Molecular Evolution Sinauer Associates: Sunderland, MA.
3. Ohno S (1970) Evolution by Gene Duplication Springer-Verlag: Berlin.
4. Hansche PE, Beres V, Lange P (1978) Gene duplication in Saccharomyces cerevisiae. Genetics 88: 673-687.
5. Yamanaka K, Fang L, Inouye M (1998) The CSPA family in Escherichia coli: multiple gene duplication for stress adaptation. Mol Microbiol 27(2): 247-255.
6. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
7. Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, et al. (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
8. Zhang J (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18(6): 292-298.
9. Lewin B (2000) Genes VII Oxford Univ Press. pp 89-115.
10. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
11. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
12. Kleckner N (1981) Transposable elements in prokaryotes. Ann Rev Genet 15: 341-404.
13. Castilho BA, Olfson P, Casadaban MJ (1984) Plasmid insertion mutagenesis and lac gene fusion with mini-mu bacteriophage transposons. J Bacteriol 158(2): 488-495.
14. Levis RW, Ganesan R, Houtchens K, Tolar LA, Sheen FM (1993) Transposons in place of telomeric repeats at a Drosophila telomere. Cell 75(6): 1083-1093.
15. Li WH, Gojobori T, Nei M (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292: 237-239.
16. Vanin EF (1985) Processed pseudogenes: Characteristics and evolution. Annu Rev Genet 19: 253-272.
17. Weiner AM, Deininger PL, Efstratiadis A (1986) Nonviral retroposons: genes, pseudogenes, and trans- posable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55: 631-661.
18. Bensasson D, Zhang DX, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol 16(6): 314-321.
19. McGrath JM, Jancso MM, Pichersky E (1993) Duplicate sequences with a similarity to expressed genes in the genome of Arabidopsis thaliana. Theor Appl Genet 86: 880-888.
20. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE (2001) Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res 11: 1005-1017.
21. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. (2002) Recent segmental duplications in the human genome. Science 297: 1003-1007.
22. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, et al. (2005) Segmental duplications and copy-number variation in the human genome. Am J Human Genet 77: 78-88.
23. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A 94: 6809-6814.
24. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci U S A 95: 1971-1974.
25. Mochizuki K, Fine NA, Fujisawa T, Gorovsky MA (2002) Analysis of a piwirelated gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110: 689-699.
26. Coghlan A, Wolfe KH (2002) Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res 12: 857-867.
27. Pevzner P, Tesler G (2003) Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Res 13: 37-45.
28. Grant D, Cregan P, Shoemaker RC (2000) Genome organization in dicots: Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc Natl Acad Sci U S A 97: 4168-4173.
29. Spring J (2002) Genome duplication strikes back. Nat Genet 31: 128-129.
30. Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome dupli- cation in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
31. Peng CK, Buldyrev SV, Goldberg AL, Havlin S, Simons M, et al. (1993) Finitesize effects on long-range correlations: Implications for analyzing DNA sequences. Phys Rev E 47: 3730-3733.
32. Mantegna RN, Buldyrev SV, Goldberger AL, Havlin S, Peng CK, et al. (1994) Linguistic features of noncoding DNA sequences. Phys Rev Lett 73: 3169-3172.
33. Forsdyke D (1995) Relative roles of primary sequence and (G+C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J Mol Evol 41: 573-581.
34. Karlin S, Mrazek J (1997) Compositional differences within and between eukaryotic genomes. Proc Natl Acad Sci U S A 94: 10227-10232.
35. Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B (1999) Genomic signature: characterization and classiffication of species assessed by chaos game representation of sequences. Mol Biol Evol 16(10): 1391-1399.
36. Hao BL, Lee HC, Zhang SY (2000) Fractals related to long DNA sequences and complete genomes. Chaos, Solitons and Fractals 11: 825-836.
37. Ochman H, Elwyn S, Moran NA (1999) Calibrating bacterial evolution. Proc Natl Acad Sci U S A 96: 12638-12643.
38. Nachman MW, Crowell SL (2000) Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
39. Liu G, Program NCS, Zhao S, Bailey JA, Sahinalp SC, et al. (2003) Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res 13: 358-368.
40. Voss RF (1996) Comment on "Linguistic features of noncoding DNA sequences". Phys Rev Lett 76: 1978.
41. Bonhoeffer S, Herz AV, Boerlijst MC, Nee S, Nowak MA, et al. (1996) No signs of hidden language in noncoding DNA. Phys Rev Lett 76: 1977.
42. Israeloff NE, Kagalenko M, Chan K (1996) Can Zipf distinguish language from noise in noncoding DNA? Phys Rev Lett 76: 1976.
43. Mantegna RN, Buldyrev SV, Goldberger AL, Halvin S, Peng CK, et al. (1996) Mantegna et al. reply:. Phys Rev Lett 76: 1979-1981.
44. Peng CK, Buldyrev SV, Havlin S, Simons M, Stanley HE, et al. (1994) Mosaic organization of DNA nucleotides. Phys Rev E 49: 1685-1689.
45. Bernaola-Galvffan P, Carpena P, Roman-Roldan R, Oliver JL (2002) Study of statistical correlations in DNA sequences. Gene 300: 105-115.
46. Messer PW, Arndt PF, Lassig M (2005) Solvable sequence evolution models and genomic correlations. Phys Rev Lett 94: 138103.
47. Fickett JW, Torney DC, Wolf DR (1992) Base compositional structure of genomes. Genomics 13: 1056-1064.
48. Xie HM, Hao BL (2002) Visualization of k-tuple distribution in procaryote complete genomes and their randomized counterparts. In: Proceedings of the IEEE Computer Society Bioinformatics Conference. pp 31-42.
49. Hsieh LC, Luo LF, Lee HC (2003) Genomes are large systems with small-system statistics: Seg- mental duplication in the growth of microbial chromosomes. AAPPS Bulletin 13: 22-27.
50. Chen TY, Hsieh LC, Lee HC (2005) Shannon information and self-similarity in complete chromosomes. Comput Phys Commun 169: 218-221.
51. Zhou F, Olman V, Xu Y (2008) Barcodes for genomes and applications. BMC Bioinformatics 9: 546.
52. Kong SG, Chen HD, Fan WL, Wigger J, Torda AE, et al. (2009) Quantitative measure of random- ness and order for complete genomes. Phys Rev E 79: 061911.
53. Bapteste E, Boucher Y, Leigh J, Doolittle WF (2004) Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 12: 406-411.
54. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375.
55. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302: 1401-1404.
56. Coghlan A, Eichler EE, Oliver SG, Paterson AH, Stein L (2005) Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet 21: 673-682.
57. Messer PW, Bundschuh R, Vingron M, Arndt PF (2007) Effects of long-range correlations in DNA on sequence alignment score statistics. J Comput Biol 14: 655-668.
58. Bartel DP (2004) Micrornas: Genomics, biogenesis, mechanism, and function. Bioinformatics 116: 281-297.
59. Doolittle WF (1997) Fun with genealogy. Proc Natl Acad Sci U S A 94: 12751-12753.
60. Feng DF, Cho G, Doolittle RF (1997) Determining divergence times with a protein clock: Update and reevaluation. Proc Natl Acad Sci U S A 94: 13028-13033.
61. Hedges SB (2002) The origin and evolution of model organisms. Nat Rev Genet 3: 838-849.
62. Woese CR (1998) The universal ancestor. Proc Natl Acad Sci U S A 95: 6854-6859.
63. Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci U S A 99: 8742-8747.
64. Glansdorff N, Xu Y, Labedan B (2008) The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct 3: 29.
65. Drake JW, Charlesworth B, Charlesworth D, Crow JF (1998) Rates of spontaneous mutation. Genetics 148: 1667-1686.
66. Denver DR, Morris K, Lynch M, Thomas WK (2004) High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 430: 679-682.
67. Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, et al. (2007) Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature 445: 82-85.
68. GenBank (2009) The genbank genome database. URL http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome.
69. Rudner R, Karkas JD, Chargaff E (1968) Separation of B. subtilis DNA into complementary strands. iii. direct analysis. Proc Natl Acad Sci U S A 60: 921-922.
70. Chen HD, Chang CH, Hsieh LC, Lee HC (2005) Divergence and Shannon information in genomes. Phys Rev Lett 94: 178103.