Abstract
The vertebrate genome underwent two major compositional transitions, between therapsids and mammals and between dinosaurs and birds. These transitions concerned a sizable part (roughly one-third) of the genome, the gene-richest part of it, and consisted in an increase in GC levels (GC is the molar fraction of guanine + cytosine in DNA) which affected both coding sequences (especially third codon positions) and noncoding sequences. These major transitions were studied here by comparing GC3 levels (GC3 is the GC of third codon positions) of orthologous genes from Xenopus, chicken, calf, and man.
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Aïssani B, Bernardj G (1991a) CpG islands: features and distribution in the genome of vertebrates. Gene 106:173–183
Aïssani B, Bernardi G (1991b) CpG islands, genes and isochores in the genome of vertebrates. Gene 106:185–195
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
Bernardi G (1989) The isochore organization of the human genome. Annu Rev Genet 23:637–661
Bernardi G (1993a) The vertebrate genome: isochores and evolution. Mol Biol Evol 10:186–204
Bernardi G (1993b) The human genome organization and its evolutionary history: a review. Gene 135:57–66
Bernardi G (1995) The human genome: organization and evolutionary history. Annu Rev Genet 29:445–476
Bernardi G, Bernardi G (1986) Compositional constraints and genome evolution. J Mol Evol 24:1–11
Bernardi G, Bernardi G (1990a) Compositional patterns in the nuclear genomes of cold-blooded vertebrates. J Mol Evol 31:265–281
Bernardi G, Bernardi G (1990b) Compositional transitions in the nuclear genomes of cold-blooded vertebrates. J Mol Evol 31:282–293
Bernardi G, Bernardi G (1991) Compositional properties of nuclear genes from cold-blooded vertebrates. J Mol Evol 33:57–67
Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warmblooded vertebrates. Science 228:953–958
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
Bush GL, Case SM, Wilson AC, Patton JL (1977) Rapid speciation and chromosomal evolution in mammals. Proc Natl Acad Sci USA 74:3942–3946
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
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
Carroll RL (1987) Vertebrate paleontology and evolution. WH Freeman, New York
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
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
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
Cross S, Kovarik P, Schmidtke J, Bird A (1991) Non-methylated islands in fish genomes are GC-poor. Nucleic Acids Res 19:1469–1474
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
Duret L, Mouchiroud D, Gouy M (1994) HOVERGEN: homologous vertebrate genes data base. Nucleic Acids Res 22:2360–2363
Elgar G (1996) Quality not quantity: the pufferfish genome. Hum Mol Genet 5:1437–1442
Freese J (1962) On the evolution of base composition of DNA. J Theor Biol 3:82–101
Gardiner K (1995) Human genome organization. Curr Opin Genet Dev 5:315–322
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
Haeckel E (1866) Generelle Morphologie der Organismen. G. Reiner, Berlin
Hedges SB, Maxson LR (1996) Molecular and morphology in amniote phylogeny. Mol Phylogenet Evol 6:311–314
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
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
Lövtrup S (1977) The phylogeny of vertebrates. Wiley, London
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
Mouchiroud D, Bernardi B (1993) Compositional properties of coding sequences and mammalian phylogeny. J Mol Evol 37:109–116
Mouchiroud D, Fichant G, Bernardi G (1987) Compositional compartmentalization and gene composition in the genome of vertebrates. J Mol Evol 26:198–204
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
Ohta T (1996) The current significance and standing of neutral and nearly neutral theories. Bioessays 18:673–677
Olofsson B, Bernardi G (1983) Organization of nucleotide sequences in the chicken genome. Eur J Biochem 130:241–245
Owen R (1866) On the anatomy of vertebrates, vol 1. Longmans, London
Perrin P, Bernardi G (1987) Directional fixation of mutations in vertebrate evolution. J Mol Evol 26:301–310
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
Saccone S, De Sario A, Delia Valle G, Bernardi G (1992) The highest gene concentrations in the human genome are in T-bands of meta-phases chromosomes. Proc Natl Acad Sci USA 89:4913–4917
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
Saccone S, Caccio S, Kusuda J, Andreozzi L, Bernardi G (1996) Identification of the gene-richest bands in human chromosomes. Gene 174:85–94
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
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
Sueoka N (1962) On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci USA 48:582–592
Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85:2563–2567
Sueoka N (1992) Directional mutation pressure, selective constraints, and genetic equilibria. J Mol Evol 34:95–114
Sueoka N (1993) Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J Mol Evol 37:137–153
Thiery JP, Macaya G, Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 108:219–235
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
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
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
Zoubak S, Clay O, Bernardi G (1996) The gene distribution of the human genome. Gene 174:95–102
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Bernardi, G., Hughes, S. & Mouchiroud, D. The major compositional transitions in the vertebrate genome. J Mol Evol 44 (Suppl 1), S44–S51 (1997). https://doi.org/10.1007/PL00000051
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DOI: https://doi.org/10.1007/PL00000051