The GC-heterogeneity of teleost fishes

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Melodelima, Christelle ^a   Gautier, Christian ^b  

^a UNIVERSITÉ JOSEPH FOURIER   (France)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

ARTICLE; EXON; FISH; FISH GENETICS; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME ANALYSIS; HIDDEN MARKOV MODEL; INTRON; ISOCHORE; MOSAICISM; NONHUMAN; ORTHOLOGY; TELEOST; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; CHICKEN; CHROMOSOME MAP; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; GENOME; HUMAN; PROBABILITY; ZEBRA FISH;

ACTINOPTERYGII; AVES; CROCODYLIDAE (ALL CROCODILES); MAMMALIA; PISCES; SARCOPTERYGII; SAUROPSIDA; TELEOSTEI; TESTUDINES; VERTEBRATA;

ANIMALS; BASE COMPOSITION; BAYES THEOREM; CHICKENS; CHROMOSOME MAPPING; FISHES; GENOME; HUMANS; ISOCHORES; MARKOV CHAINS; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA; ZEBRAFISH;

EID: 61949197289     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-632     Document Type: Article

References (23)

1. Bernardi G Isochores and the evolutionary genomics of vertebrates Gene 2000, 241(1):3-17. 10.1016/S0378-1119(99)00485-0 10607893
2. Eyre-Walker A Hurst LD The evolution of isochores Nat Rev Genet 2001, 2(7):549-555. 10.1038/35080577 11433361
3. Nekrutenko A Li WH Assessment of compositional heterogeneity within and between eukaryotic genomes Genome Res 2000, 10(12):1986-1995. 313050 11116093 10.1101/gr.10.12.1986
4. Barakat A Matassi G Bernardi G Distribution of genes in the genome of Arabidopsis thaliana and its implications for the genome organization of plants Proc Natl Acad Sci USA 1998, 95(17):10044-10049. 21458 9707597 10.1073/pnas.95.17.10044
5. Oliver JL Bernaola-Galvan P Carpena P Roman-Roldan R Isochore chromosome maps of eukaryotic genomes Gene 2001 276, 1-2:47-56. 10.1016/ S0378-1119(01)00641-2 11591471
6. Zhang CT Zhang R Isochore structures in the genome of the plant Arabidopsis thaliana J Mol Evol 2004, 59:227-238. 10.1007/ s00239-004-2617-8 15486696
7. Bernardi G Bernardi G Compositional patterns in the nuclear genome of cold-blooded vertebrates J Mol Evol 1990, 31(4):265-281. 10.1007/ BF02101122 2124275
8. Bernardi G The vertebrate genome: Isochores and evolution Mol Biol Evol 1993, 10(1):186-204. 8450755
9. Hughes S Zelus D Mouchiroud D Warm-blooded isochore structure in Nile crocodile and turtle Mol Biol Evol 1999, 16(11):1521-1527. 10555283
10. Hamada K Horiike T Kanaya S Nakamura H Ota H Yatogo T Okada K Nakamura H Shinozawa T Changes in body temperature pattern in vertebrates do not influence the codon usages of alpha-globin genes Genes Genet Syst 2002, 77(3):197-207. 10.1266/ggs.77.197 12207041
11. Hamada K Horiike T Ota H Mizuno K Shinozawa T Presence of isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of coding regions Genes Genet Syst 2003, 78(2):195-198. 10.1266/ggs.78.195 12773820
12. Fortes GG Bouza C Martinez P Sanchez L Diversity in isochore structure among cold-blooded vertebrates based on GC content of coding and non-coding sequences Genetica 2006. 16897446
13. Chojnowski JL Franklin J Katsu Y Iguchi T Guillette LJ Jr Kimball RT Braun EL Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes J Mol Evol 2007, 65(3):259-266. 10.1007/s00239-007-9003-2 17674077
14. Kuraku S Ishijima J Nishida-Umehara C Agata K Kuratani S Matsuda Y cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids Chromosome Res 2006, 14(2):187-202. 10.1007/s10577-006-1035-8 16544192
15. Jaillon O Aury JM Brunet F Petit JL Stange-Thomann N Mauceli E Bouneau L Fischer C Ozouf-Costaz C Bernot A et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype Nature 2004, 431(7011):946-957. 10.1038/nature03025 15496914
16. Mouchiroud D D'Onofrio G Aissani B Macaya G Gautier C Bernardi G The distribution of genes in the human genome Gene 1991, 100:181-187. 10.1016/0378-1119(91)90364-H 2055469
17. Lander ES Linton LM Birren B Nusbaum C Zody MC Baldwin J Devon K Dewar K Doyle M FitzHugh W et al Initial sequencing and analysis of the human genome Nature 2001, 409(6822):860-921. 10.1038/35057062 11237011
18. Duret L Mouchiroud D Gautier C Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores J Mol Evol 1995, 40(3):308-317. 10.1007/BF00163235 7723057
19. Aparicio S Chapman J Stupka E Putnam N Chia JM Dehal P Christoffels A Rash S Hoon S Smit A et al Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes Science 2002, 297(5585):1301-1310. 10.1126/ science.1072104 12142439
20. Melodelima C Gueguen L Piau D Gautier C A computational prediction of isochores based on hidden Markov models Gene 2006, 385:41-49. 10.1016/ j.gene.2006.04.032 17020791
21. Jørgensen FG Schierup MH Clark AG Heterogeneity in Regional GC Content and Differential Usage of Codons and Amino Acids in GC-Poor and GC-Rich Regions of the Genome of Apis mellifera Mol Biol Evol 2007, 24(2):611-619. 10.1093/molbev/msl190 17150976
22. Pizon V Cuny G Bernardi G Nucleotide sequence organization in the very small genome of a tetraodontid fish, Arothron diadematus Eur J Biochem 1984, 140(1):25-30. 10.1111/j.1432-1033.1984.tb08062.x 6705796
23. Gueguen L Sarment: Python modules for HMM analysis and partitioning of sequences Bioinformatics 2005, 21(16):3427-3428. 10.1093/bioinformatics/ bti533 15947017