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  • 1
    Electronic Resource
    Electronic Resource
    Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 504-510 
    Details
    ISSN: 1432-1432
    Keywords: Human genome ; Amino acids ; Isochores ; Coding sequences ; Introns ; Codon positions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have analyzed the correlation that exists between the GC levels of third and first or second codon position for about 1400 human coding sequences. The linear relationship that was found indicates that the large differences in GC level of third codon positions of human genes are paralleled by smaller differences in GC levels of first and second codon positions. Whereas third codon position differences correspond to very large differences in codon usage within the human genome, the first and second codon position differences correspond to smaller, yet very remarkable, differences in the amino acid composition of encoded proteins. Because GC levels of codon positions are linearly correlated with the GC levels of the isochores harboring the corresponding genes, both codon usage and amino acid composition are different for proteins encoded by genes located in isochores of different GC levels. Furthermore, we have also shown that a linear relationship with a unity slope and a correlation coefficient of 0.77 exists between GC levels of introns and exons from the 238 human genes currently available for this analysis. Introns are, however, about 5% lower in GC, on average, than exons from the same genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102652
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  • 2
    Electronic Resource
    Electronic Resource
    Silent substitutions in mammalian genomes and their evolutionary implications (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 583-589 
    Details
    ISSN: 1432-1432
    Keywords: Isochores ; Mutation rates ; Mammals ; DNA replication ; DNA repair
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An analysis of silent substitutions in pairwise comparisons of homologous genes from different mammals has shown that, in spite of individual fluctuations, their frequencies (which are very strongly correlated with the frequency of substitutions per synonymous site calculated according to Li et al. 1985) do not vary, on the average, with the GC levels of silent positions. This holds in the general case, in which silent positions of pairs of homologous genes share the same composition, namely in the human/other primates, human/artiodactyls, and in the mouse/rat pairs, as well as in the special cases in which the composition of silent positions are different, namely in the human/rabbit and the human/rat (or human/mouse) pairs. A slightly lower frequency found for low GC values in the human/bovine and human/pig pairs seems to be due to the specific gene samples used. These results contradict the previously claimed existence of differences in mutation rates and of mutational biases in third codon positions of coding sequences located in different isochores of mammalian genomes. They also imply that the variations in nucleotide precursor pools through the cell cycle and the differences in replication timing, or in repair efficiency, which were reported for different isochores, do not lead, as claimed, to differences in mutation rates, not in mutational biases in mammals. The differences claimed appear to be due to using small gene samples when individual fluctuations from gene to gene are relatively large.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00182744
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  • 3
    Electronic Resource
    Electronic Resource
    Insect muscle actins differ distinctly from invertebrate and vertebrate cytoplasmic actins (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 406-415 
    Details
    ISSN: 1432-1432
    Keywords: Muscle actin gene ; Cytoplasmic actin gene ; Sequence comparison ; Insect ; Molecular evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Invertebrate actins resemble vertebrate cytoplasmic actins, and the distinction between muscle and cytoplasmic actins in invertebrates is not well established as for vertebrate actins. However, Bombyx and Drosophila have actin genes specifically expressed in muscles. To investigate if the distinction between muscle and cytoplasmic actins evidenced by gene expression analysis is related to the sequence of corresponding genes, we compare the sequences of actin genes of these two insect species and of other Metazoa. We find that insect muscle actins form a family of related proteins characterized by about 10 muscle-specific amino acids. Insect muscle actins have clearly diverged from cytoplasmic actins and form a monophyletic group emerging from a cluster of closely related proteins including insect and vertebrate cytoplasmic actins and actins of mollusc, cestode, and nematode. We propose that muscle-specific actin genes have appeared independently at least twice during the evolution of animals: insect muscle actin genes have emerged from an ancestral cytoplasmic actin gene within the arthropod phylum, whereas vertebrate muscle actin genes evolved within the chordate lineage as previously described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00162997
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  • 4
    Electronic Resource
    Electronic Resource
    The Major Compositional Transitions in the Vertebrate Genome (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S044 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Base composition — Evolution — Isochores — Orthologous mammalian genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000051
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  • 5
    Electronic Resource
    Electronic Resource
    Compositional patterns in vertebrate genomes: Conservation and change in evolution (1988)
    Springer
    Journal of molecular evolution 28 (1988), S. 7-18 
    Details
    ISSN: 1432-1432
    Keywords: Compositional patterns ; Compositional shifts ; Genome evolution ; Isochores ; Vertebrates ; Selection ; Neutral theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The evolution of vertebrate genomes can be investigated by analyzing their regional compositional patterns, namely the compositional distributions of large DNA fragments (in the 30–100-kb size range), of coding sequences, and of their different codon positions. This approach has shown the existence of two evolutionary modes. In the conservative mode, compositional patterns are maintained over long times (many million years), in spite of the accumulation of enormous numbers of base substitutions. In the transitional, or shifting, mode, compositional patterns change into new ones over much shorter times. The conservation of compositional patterns, which has been investigated in mammalian genomes, appears to be due in part to some measure of compositional conservation in the base substitution process, and in part to negative selection acting at regional (isochore) levels in the genome and eliminating deviations from a narrow range of values, presumably corresponding to optimal functional properties. On the other hand, shifts of compositional patterns, such as those that occurred between cold-blooded and warm-blooded vertebrates, appear to be due essentially to both negative and positive selection again operating at the isochore level, largely under the influence of changes in environmental conditions, and possibly taking advantage of mutational biases in the replication/repair enzymes and/or in the enzyme make-up of nucleotide precursor pools. Other events (like translocations and changes in chromosomal structure) also play a role in the transitional mode of genome evolution. The present findings (1) indicate that isochores, which correspond to the DNA segments of individual or contiguous chromatin domains, represent selection units in the vertebrate genome; and (2) shed new light on the selectionist-neutralist controversy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02143493
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  • 6
    Electronic Resource
    Electronic Resource
    Codon usage changes and sequence dissimilarity between human and rat (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 81-91 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Evolutionary rate ; Isochores ; Silent dissimilarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary This paper reports on the relationship between the number of silent differences and the codon usage changes in the lineages leading to human and rat. Examination of 102 pairs of homologous genes gives rise to four main conclusions: (1) We have previously demonstrated the existence of a codon usage change (called the minor shift) between human and rat; this was confirmed here with a larger sample. For genes with extreme C+G frequencies, the C+G level in the third codon position is less extreme in rat than in human. (2) Protein similarity and percentage of positive differences are the two main factors that discriminate homologous genes when characterized by differences between rat and human. By definition, positive differences result from silent changes between A or T and C or G with a direction implying a C+G content variation in the same direction as the overall gene variation. (3) For genes showing both codon usage change and low protein similarity, a majority of amino acid replacements contributes to C+G level variation in positions I and II in the same direction as the variation in position III. This is thus a new example of protein evolution due to constraints acting at the DNA level. (4) In heavy isochores (high C+G content) no direct correlation exists between codon usage change (measured by the dissymmetry of differences) and silent dissimilarity. In light isochores the opposite situation is observed: modification of codon usage is associated with a high synonymous dissimilarity. This result shows that, in some cases, modification of constraints acting at the DNA level could accelerate divergence between genomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109477
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  • 7
    Electronic Resource
    Electronic Resource
    Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 107-113 
    Details
    ISSN: 1432-1432
    Keywords: DNA repair ; DNA replication ; DNA transcription ; Isochores
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The frequencies of synonymous substitutions of mammalian genes cover a much wider range than previously thought. We report here that the different frequencies found in homologous genes from a given mammalian pair are correlated with those in the same homologous genes from a different mammalian pair. This indicates that the frequencies of synonymous substitutions are gene-specific (as are the frequencies of nonsynonymous substitutions), or, in other words, that “fast” and “slow” genes in one mammal are fast and slow, respectively, in any other one. Moreover, the frequencies of synonymous substitutions are correlated with the frequencies of nonsynonymous substitution in the same genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00166602
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  • 8
    Electronic Resource
    Electronic Resource
    The compositional patterns of the avian genomes and their evolutionary implications (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 544-551 
    Details
    ISSN: 1432-1432
    Keywords: Isochores ; DNA ; Coding sequences ; Birds ; Mammals ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The compositional distributions of large (main-band) DNA fragments from eight birds belonging to eight different orders (including both paleognathous and neognathous species) are very broad and extremely close to each other. These findings, which are paralleled by the compositional similarity of homologous coding sequences and their codon positions, support the idea that birds are a monophyletic group. The compositional distribution of third-codon positions of genes from chicken, the only avian species for which a relatively large number of coding sequences is known, is very broad and bimodal, the minor GC-richer peak reaching 100% GC. The very high compositional heterogeneity of avian genomes is accompanied (as in the case of mammalian genomes) by a very high speciation rate compared to cold-blooded vertebrates which are characterized by genomes that are much less heterogeneous. The higher GC levels attained by avian compared to mammalian genomes might be correlated with the higher body temperature (41–43°C) of birds compared to mammals (37°C). A comparison of GC levels of coding sequences and codon positions from man and chicken revealed very close average GC levels and standard deviations. Homologous coding sequences and codon positions from man and chicken showed a surprisingly high degree of compositional similarity which was, however, higher for GC-poor than for GC-rich sequences. This indicates that GC-poor isochores of warm-blooded vertebrates reflect the composition of the isochores of the genome of the common reptilian ancestor of mammals and birds, which underwent only a small compositional change at the transition from cold- to warm-blooded vertebrates. In contrast, the GC-rich isochores of birds and mammals are the result of large compositional changes at the same evolutionary transition, where were in part different in the two classes of warm-blooded vertebrates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160434
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  • 9
    Electronic Resource
    Electronic Resource
    Compositional compartmentalization and gene composition in the genome of vertebrates (1987)
    Springer
    Journal of molecular evolution 26 (1987), S. 198-204 
    Details
    ISSN: 1432-1432
    Keywords: Genome ; Isochores ; Gene composition ; Coding sequences ; Vertebrates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The compositional distribution of coding sequences from five vertebrates (Xenopus, chicken, mouse, rat, and human) is shifted toward higher GC values compared to that of the DNA molecules (in the 35–85-kb size range) isolated from the corresponding genomes. This shift is due to the lower GC levels of intergenic sequences compared to coding sequences. In the cold-blooded vertebrate, the two distributions are similar in that GC-poor genes and GC-poor DNA molecules are largely predominant. In contrast, in the warm-blooded vertebrates, GC-rich genes are largely predominant over GC-poor genes, whereas GC-poor DNA molecules are largely predominant over GC-rich DNA molecules. As a consequence, the genomes of warm-blooded vertebrates show a compositional gradient of gene concentration. The compositional distributions of coding sequences (as well as of DNA molecules) showed remarkable differences between chicken and mammals, and between mouse (or rat) and human. Differences were also detected in the compositional distribution of housekeeping and tissue-specific genes, the former being more abundant among GC-rich genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099852
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  • 10
    Electronic Resource
    Electronic Resource
    The compositional distribution of coding sequences and DNA molecules in humans and murids (1988)
    Springer
    Journal of molecular evolution 27 (1988), S. 311-320 
    Details
    ISSN: 1432-1432
    Keywords: Genome composition ; Coding sequences ; Isochores ; Humans ; Murids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The compositional distributions of coding sequences and DNA molecules (in the 50-100-kb range) are remarkably narrower in murids (rat and mouse) compared to humans (as well as to all other mammals explored so far). In murids, both distributions begin at higher and end at lower GC values. A comparison of homologous coding sequences from murids and humans revealed that their different compositional distributions are due to differences in GC levels in all three codon positions, particularly of genes located at both ends of the distribution. In turn, these differences are responsible for differences in both codon usage and amino acids. When GC levels at first+second codon positions and third codon positions, respectively, of murid genes are plotted against corresponding GC levels of homologous human genes, linear relationships (with very high correlation coefficients and slopes of about 0.78 and 0.60, respectively) are found. This indicates a conservation of the order of GC levels in homologous genes from humans and murids. (The same comparison for mouse and rat genes indicates a conservation of GC levels of homologous genes.) A similar linear relationship was observed when plotting GC levels of corresponding DNA fractions (as obtained by density gradient centrifugation in the presence of a sequence-specific ligand) from mouse and human. These findings indicate that orderly compositional changes affecting not only coding sequences but also noncoding sequences took place since the divergence of murids. Such directional fixations of mutations point to the existence of selective pressures affecting the genome as a whole.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101193
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