Genome complexity and repetitive DNA in metazoans from extreme marine environments

Gene

Volumn 362, Issue 1-2, 2005, Pages 98-108

  Fielman, Kevin T ^a,b   Marsh, Adam G ^a  

^a UNIVERSITY OF DELAWARE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Antarctic; Cot; Genomics; Hydrothermal vent; Shannon index

Indexed keywords

DNA;

ARTICLE; ASTERIAS; CORRELATION ANALYSIS; DNA CONTENT; DNA SEQUENCE; GENOME ANALYSIS; GENOME SIZE; HABITAT STRUCTURE; HYBRIDIZATION; HYDROTHERMAL VENT; KINETICS; LARVA; LIMULUS; MARINE ENVIRONMENT; NONHUMAN; OYSTER; POLYCHAETA; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SEA URCHIN; SNAIL; TEMPERATURE; THERMOSTABILITY; WORM;

ANIMALS; ENVIRONMENT; GENOME; MARINE BIOLOGY; MICROSCOPY, FLUORESCENCE; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID RENATURATION; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID; STATISTICS; TEMPERATURE;

ALVINELLA POMPEJANA; ASTERIAS; BOS TAURUS; ECHINOIDEA; EUKARYOTA; GASTROPODA; ILYANASSA OBSOLETA; INVERTEBRATA; LIMULUS; LIMULUS POLYPHEMUS; METAZOA; ODONTASTER VALIDUS; OSTREIDAE; POLYCHAETA; SACCHAROMYCES CEREVISIAE; STERECHINUS NEUMAYERI; STREBLOSPIO BENEDICTI;

EID: 28244472834     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.06.035     Document Type: Article

References (63)

1. R.C. Angerer, E.H. Davidson, and R.J. Britten DNA sequence organization in mollusk Aplysia californica Cell 6 1975 29 40
2. R.C. Angerer, E.H. Davidson, and R.J. Britten Single copy DNA and structural gene sequence relationships among 4 sea-urchin species Chromosoma 56 1976 213 226
3. G. Bernardi Chromatography of nucleic acids on hydroxyapatite Nature 206 1965 779 783
4. G. Bernardi Compositional transitions in the nuclear genomes of cold-blooded vertebrates J. Mol. Evol. 31 1990 282 293
5. G. Bernardi Isochores and the evolutionary genomics of vertebrates Gene 241 2000 3 17
6. R.J. Britten, and E.H. Davidson Repetitive and non-repetitive DNA sequences and a speculation on origins of evolutionary novelty Q. Rev. Biol. 46 1971 111 138
7. R.J. Britten, and D.E. Kohne Repeated sequences in DNA Science 161 1968 529 540
8. V.A. Brykov, V.G. Volfson, and V.I. Vorobev Genome structure and divergence of nucleotide-sequences in echinodermata Chromosoma 74 1979 105 124
9. S.C. Cary, T. Shank, and J. Stein Worms bask in extreme temperatures Nature 391 1998 545 546
10. M. Ceccarelli Genome plasticity in Festuca arundinacea: direct response to temperature changes by redundancy modulation of interspersed DNA repeats Theor. Appl. Genet. 104 2002 901 907
11. M.S. Clark Antarctic genomics Compar. Funct. Genom. 5 2004 230 238
12. E.H. Davidson, B.R. Hough, M.E. Chamberlin, and R.J. Britten Sequence repetition in DNA of Nassaria (Ilyanassa) obsoleta Dev. Biol. 25 1971 445 463
13. D.R. Dixon, L.R.J. Dixon, P.L. Pascoe, and J.T. Wilson Chromosomal and nuclear characteristics of deep-sea and hydrothermal-vent organisms: correlates of increased growth rates Mar. Biol. 139 2001 251 255
14. A. Eyre-Walker, and L.D. Hurst The evolution of isochores Nat. Rev., Genet. 2 2001 549 555
15. M.J. Fazzari, and J.M. Greally Epigenomics: beyond CpG islands Nat. Rev., Genet. 5 2004 446 455
16. M.E. Feder, and T. Mitchell-Olds Evolutionary and ecological functional genomics Nat. Rev., Genet. 4 2003 651 657
17. G.A. Galau, M.E. Chamberlain, B.R. Hough, R.J. Britten, and E.H. Davidson Evolution of repetitive and nonrepetitive DNA Molecular Evolution 1978 Sinauer Associates, Inc. Massachusetts 200 262
18. R.B. Goldberg Sequence organization in genomes of 5 marine invertebrates Chromosoma 51 1975 225 251
19. D.E. Graham, B.R. Neufeld, E.H. Davidson, and R.J. Britten Interspersion of repetitive and non-repetitive DNA sequences in sea-urchin genome Cell 1 1974 127 137
20. Gregory, T.R., 2001a. Animal Genome Size Database. http://www.genomesize. com.
21. T.R. Gregory Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma Biol. Rev. 76 2001 65 101
22. T.R. Gregory Genome size and developmental parameters in the homeothermic vertebrates Genome 45 2002 833 838
23. T.R. Gregory Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approch to the C-value enigma Biol. J. Linn. Soc. 79 2003 329 339
24. B. Helmuth, C.D.G. Harley, P.M. Halpin, M. O'Donnell, G.E. Hofmann, and C.A. Blanchette Climate change and latitudinal patterns of intertidal thermal stress Science 298 2002 1015 1017
25. G.E. Hofmann, B.A. Buckley, S. Airaksinen, J.E. Keen, and G.N. Somero Heat-shock protein expression is absent in the Antarctic fish Trematomus bernacchii (family Nototheniidae) J. Exp. Biol. 203 2000 2331 2339
26. R.B. Jackson, C.R. Linder, M. Lynch, M. Purugganan, S. Somerville, and S.S. Thayer Linking molecular insight and ecological research Trends Ecol. Evol. 17 2002 409 414
27. R. Kalendar, J. Tanskanen, S. Immonen, E. Nevo, and A.H. Schulman Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence Proc. Natl. Acad. Sci. U. S. A. 97 2000 6603 6607
28. J.C. Kamalay, J.V. Ruderman, and R.B. Goldberg DNA sequence repetition in the genome of the American oyster Biochim. Biophys. Acta, Nucleic Acids Protein Synth. 432 1976 121 128
29. Y. Kashi, and M. Soller Functional roles of microsatellites and minisatellites D.B. Goldstein C. Schlotterer Microsatellites. Evolution and Applications 1999 Oxford University Press New York 10 23
30. H.H. Kazazian Mobile elements: drivers of genome evolution Science 303 2004 1626 1632
31. M. Kloc, and B. Zagrodzinska Chromatin elimination-an oddity or a common mechanism in differentiation and development? Differentiation 68 2001 84 91
32. J. Kozlowski, M. Konarzewski, and A.T. Gawelczyk Cell size as a link between noncoding DNA and metabolic rate scaling Proc. Natl. Acad. Sci. U. S. A. 100 2003 14080 14085
33. A. La Terza, C. Miceli, and P. Luporini The gene for the heat-shock protein 70 of Euplotes focardii, an Antarctic psychrophilic ciliate Antarct. Sci. 16 2004 23 28
34. Z. Lippman Role of transposable elements in heterochromatin and epigenetic control Nature 430 2004 471 476
35. M. Lynch, and J.S. Conery The origins of genome complexity Science 302 2003 1401 1404
36. A.G. Marsh, P.K.K. Leong, and D.T. Manahan Energy metabolism during embryonic development and larval growth of an Antarctic sea urchin J. Exp. Biol. 202 1999 2041 2050
37. A.G. Marsh, R.E. Maxson, and D.T. Manahan High macromolecular synthesis with low metabolic cost in Antarctic sea urchin embryos Science 291 2001 1950 1952
38. J.S. Mattick RNA regulation: a new genetics? Nat. Rev., Genet. 5 2004 316 323
39. K.W. McLean, and A.H. Whiteley Characteristics of DNA from oyster, Crassostrea-gigas Biochim. Biophys. Acta 335 1974 35 41
40. A. Nekrutenko, and W.H. Li Assessment of compositional heterogeneity within and between eukaryotic genomes Genome Res. 10 2000 1986 1995
41. C.E. Nelson, B.M. Hersh, and S.B. Carroll The regulatory content of intergenic DNA shapes genome architecture Genome Biol. 5 2004 R25.1 R25.15
42. J. Paces, R. Zika, V. Paces, A. Pavlicek, O. Clay, and G. Bernardi Representing GC variation along eukaryotic chromosomes Gene 333 2004 135 141
43. D.G. Peterson Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery Genome Res. 12 2002 795 807
44. D.G. Peterson, S.R. Wessler, and A.H. Paterson Efficient capture of unique sequences from eukaryotic genomes Trends Genet. 18 2002 547 550
45. D.A. Petrov Evolution of genome size: new approaches to an old problem Trends Genet. 17 2001 23 28
46. N.B. Petrov, A.B. Poltaraus, and A.S. Antonov The genome of the pogonophoran Siboglinum-fiordicum-characteristics of its organization and divergence from the genomes of several representative invertebrate animals Mol. Biol. 14 1980 340 348
47. S. Porebski, L.G. Bailey, and B.R. Baum Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components Plant. Mol. Biol. Report. 15 1997 8 15
48. M. Purugganan, and G. Gibson Merging ecology, molecular evolution, and functional genetics Mol. Ecol. 12 2003 1109 1112
49. C. Schlotterer Evolutionary dynamics of microsatellite DNA Chromosoma 109 2000 365 371
50. C.E. Shannon A mathematical theory of communication Bell Syst. Tech. J. 27 1948 623 656
51. V.L. Singer, L.J. Jones, S.T. Yue, and R.P. Haugland Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation Anal. Biochem. 249 1997 228 238
52. D.J. Small, T. Moylan, M.E. Vayda, and B.D. Sidell The myoglobin gene of the Antarctic icefish, Chaenocephalus aceratus, contains a duplicated TATAAAA sequence that interferes with transcription J. Exp. Biol. 206 2003 131 139
53. M.L. Smith, and R. Boal DNA-sequence organization in common pacific starfish Pisaster-ochraceous Can. J. Biochem. 56 1978 1048 1054
54. M.J. Smith, A. Lui, K.K. Gibson, and J.K. Etzkorn DNA-sequence organization in the starfish Dermasterias-imbricata Can. J. Biochem. 58 1980 352 360
55. M.B. Soares, M.D. Bonaldo, P. Jelene, L. Su, L. Lawton, and A. Efstratiadis Construction and characterization of a normalized cDNA library Proc. Natl. Acad. Sci. U. S. A. 91 1994 9228 9232
56. I.F. Spellerberg, and P.J. Fedor A tribute to Claude Shannon (1916-2001) and a plea for more rigorous use of species richness, species diversity and the 'Shannon-Wiener' Index Glob. Ecol. Biogeogr. 12 2003 177 179
57. M.A. Thomas, and R. Klaper Genomics for the ecological toolbox Trends Ecol. Evol. 19 2004 439 445
58. S. Tweedie, J. Charlton, V. Clark, and A. Bird Methylation of genomes and genes at the invertebrate-vertebrate boundary Mol. Cell. Biol. 17 1997 1469 1475
59. C.L. Van Dover The Ecology of Deep-sea Hydrothermal Vents 2000 Princeton University Press Princeton
60. C. Vieira, and C. Biemont Transposable element dynamics in two sibling species: Drosophila melanogaster and Drosophila simulans Genetica 120 2004 115 123
61. V.I. Vorobev, and G.N. Kosjuk Distribution of repetitive and non-repetitive nucleotide-sequences in DNA of sea-urchin FEBS Lett. 47 1974 43 46
62. J.G. Wetmur, and N. Davidson Kinetics of renaturation of DNA J. Mol. Biol. 31 1968 349 370
63. G.A. Wray The evolution of transcriptional regulation in eukaryotes Mol. Biol. Evol. 20 2003 1377 1419