The major compositional transitions in the vertebrate genome

Journal of Molecular Evolution

Volumn 44, Issue SUPPL. 1, 1997, Pages

  Bernardi, Giorgio ^a   Hughes, Sandrine ^b   Mouchiroud, Dominique ^b  

^a INSTITUT JACQUES MONOD   (France)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

Base composition; Evolution; Isochores; Orthologous mammalian genes

Indexed keywords

ANIMAL CELL; ARTICLE; CATTLE; CHICKEN; DNA SEQUENCE; EVOLUTION; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; MAMMAL; NONHUMAN; VERTEBRATE; XENOPUS;

ANIMALIA; AVES; BOS TAURUS; DINOSAURIA; GALLUS GALLUS; MAMMALIA; VERTEBRATA;

EID: 0031029793     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/pl00000051     Document Type: Article

References (55)

1. Aïssani B, Bernardi G (1991a) CpG islands: features and distribution in the genome of vertebrates. Gene 106:173-183
2. Aïssani B, Bernards G (1991b) CpG islands, genes and isochores in the genome of vertebrates. Gene 106:185-195
3. Aïssani B, D'Onofrio G, Mouchiroud D, Gardiner K, Gautier C, Bernardi G (1991) The compositional properties of human genes. J Mol Evol 32:497-503
4. Bernardi G (1989) The isochore organization of the human genome. Annu Rev Genet 23:637-661
5. Bernardi G (1993a) The vertebrate genome: isochores and evolution. Mol Biol Evol 10:186-204
6. Bernardi G (1993b) The human genome organization and its evolutionary history: a review. Gene 135:57-66
7. Bernardi G (1995) The human genome: organization and evolutionary history. Annu Rev Genet 29:445-476
8. Bernardi G, Bernardi G (1986) Compositional constraints and genome evolution. J Mol Evol 24:1-11
9. Bernardi G, Bernardi G (1990a) Compositional patterns in the nuclear genomes of cold-blooded vertebrates. J Mol Evol 31:265-281
10. Bernardi G, Bernardi G (1990b) Compositional transitions in the nuclear genomes of cold-blooded vertebrates. J Mol Evol 31:282-293
11. Bernardi G, Bernardi G (1991) Compositional properties of nuclear genes from cold-blooded vertebrates. J Mol Evol 33:57-67
12. Bernardi G, Olofsson B, Filipski J, Zerial M, Saunas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953-958
13. Bernardi G, Mouchiroud D, Gautier C, Bernardi G (1988) Compositional patterns in vertebrate genomes: conservation and change in evolution. J Mol Evol 28:7-18
14. Bush GL, Case SM, Wilson AC, Patton JL (1977) Rapid speciation and chromosomal evolution in mammals. Proc Natl Acad Sci USA 74:3942-3946
15. Caccio S, Perani P, Saccone S, Kadi F, Bernardi G (1994) Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates. J Mol Evol 39:331-339
16. Caccio S, Zoubak S, D'Onofrio G, Bernardi G (1995) Nonrandom frequency patterns of synonymous substitutions of homologous mammalian genes. J Mol Evol 40:280-292
17. Carroll RL (1987) Vertebrate paleontology and evolution. WH Freeman, New York
18. Caspers GJ, Reinders GJ, Leunissen J, Wattel J, de Jong W (1996) Protein sequences indicate that turtles branched off from the amniote tree after mammals. J Mol Evol 42:580-586
19. Clay O, Caccio S, Zoubak S, Mouchiroud D, Bernardi G (1996) Human coding and non-coding DNA: compositional correlations. Mol Phylogenet Evol 5:2-12
20. Cortadas J, Olofsson B, Meunier-Rotival M, Macaya G, Bernardi G (1979) The DNA components of the chicken genome. Eur J Biochem 99:179-186
21. Cross S, Kovarik P, Schmidtke J, Bird A (1991) Non-methylated islands in fish genomes are GC-poor. Nucleic Acids Res 19:1469-1474
22. Dodemont H-J, Soriano P, Quax WJ, Ramaekers F, Lenstra JA, Groenen MAM, Bernardi G, Bloemendal H (1982) The genes coding for the cytoskeletal proteins actin and vimentin in warmblooded vertebrates. EMBO J 1:987-994
23. Duret L, Mouchiroud D, Gouy M (1994) HOVERGEN: homologous vertebrate genes data base. Nucleic Acids Res 22:2360-2363
24. Elgar G (1996) Quality not quantity: the pufferfish genome. Hum Mol Genet 5:1437-1442
25. Freese J (1962) On the evolution of base composition of DNA. J Theor Biol 3:82-101
26. Gardiner K (1995) Human genome organization. Curr Opin Genet Dev 5:315-322
27. Gouy M, Gautier L, Attimonelli M, Lanave C, di Paola G (1985) ACNUC - a portable retrieval system for nucleic acid sequence database: logical and physical design and usage. Comput Appl Biosci 1:167-172
28. Haeckel E (1866) Generelle Morphologie der Organismen. G. Reiner, Berlin
29. Hedges SB, Maxson LR (1996) Molecular and morphology in amniote phylogeny. Mol Phylogenet Evol 6:311-314
30. Hudson AP, Cuny G, Cortadas J, Haschemeyer AEV, Bernardi G (1980) An analysis of fish genomes by density gradient centrifugation. Eur J Biochem 112:203-210
31. Kadi F, Mouchiroud D, Sabeur G, Bernardi G (1993) The compositional patterns of the avian genomes and their evolutionary implications. J Mol Evol 37:544-551
32. Lövtrup S (1977) The phylogeny of vertebrates. Wiley, London
33. Macaya G, Thiery JP, Bernardi G (1976) An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108:237-254
34. Mouchiroud D, Bernardi B (1993) Compositional properties of coding sequences and mammalian phylogeny. J Mol Evol 37:109-116
35. Mouchiroud D, Fichant G, Bernardi G (1987) Compositional compartmentalization and gene composition in the genome of vertebrates. J Mol Evol 26:198-204
36. Mouchiroud D, D'Onofrio G, Aïssani B, Macaya G, Gautier C, Bernardi G (1991) The distribution of genes in the human genome. Gene 100:181-187
37. Ohta T (1996) The current significance and standing of neutral and nearly neutral theories. Bioessays 18:673-677
38. Olofsson B, Bernardi G (1983) Organization of nucleotide sequences in the chicken genome. Eur J Biochem 130:241-245
39. Owen R (1866) On the anatomy of vertebrates, vol 1. Longmans, London
40. Perrin P, Bernardi G (1987) Directional fixation of mutations in vertebrate evolution. J Mol Evol 26:301-310
41. Pizon V, Cuny G, Bernardi G (1984) Nucleotide sequence organization in the very small genome of a tetraodontid fish. Arothron diadematus. Evol J Biochem 140:25-30
42. Saccone S, De Sario A, Delia Valle G, Bernardi G (1992) The highest gene concentrations in the human genome are in T-bands of metaphases chromosomes. Proc Natl Acad Sci USA 89:4913-4917
43. Saccone S, De Sario A, Wiegant J, Raap AK, Delia Valle G, Bernardi G (1993) Correlation between isochores and chromosomal bands in the human genome. Proc Natl Acad Sci USA 90:11929-11933
44. Saccone S, Caccio S, Kusuda J, Andreozzi L, Bernardi G (1996) Identification of the gene-richest bands in human chromosomes. Gene 174:85-94
45. Sabeur G, Macaya G, Kadi F, Bernardi G (1993) The isochore patterns of mammalian genomes and their phylogenetic implications. J Mol Evol 37:93-108
46. Salinas J, Zerial M, Filipski J, Bernardi G (1986) Gene distribution and nucleotide sequence organization in the mouse genome. Eur J Biochem 160:469-478
47. Sueoka N (1962) On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci USA 48:582-592
48. Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85:2563-2567
49. Sueoka N (1992) Directional mutation pressure, selective constraints, and genetic equilibria. J Mol Evol 34:95-114
50. Sueoka N (1993) Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J Mol Evol 37:137-153
51. Thiery JP, Macaya G, Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 108:219-235
52. Walter RB, Robig RL, Kozak KA, McEntire B, Morizot DC, Nairn RS (1993) Cloning and gene map assignment of the Xiphophorus DNA ligase 1 gene. Mol Biol Evol 10:1227-1238
53. Zerial M, Salinas J, Filipski J, Bernardi G (1986) Gene distribution and nucleotide sequence organization in the human genome. Eur J Biochem 160:479-485
54. Zoubak S, D'Onofrio G, Caccio S, Bernardi G, Bernardi G (1995) Specific compositional patterns of synonymous positions in homologous mammalian genes. J Mol Biol 40:293-307
55. Zoubak S, Clay O, Bernardi G (1996) The gene distribution of the human genome. Gene 174:95-102