Abstract
To review the general consideration about the different compositional structure of warm and cold-blooded vertebrates genomes, we used of the increasing number of genetic sequences, including coding (exons) and non-coding (introns) regions, that have been deposited on the databases throughout last years. The nucleotide distributions of the third codon positions (GC3) have been analyzed in 1510 coding sequences (CDS) of fish, 1414 CDS of amphibians and 320 CDS of reptiles. Also, the relationship between GC content of 74, 56 and 25 CDS of fish, amphibians and reptiles, respectively and that of their corresponding introns (GCI) have been considerated. In accordance with recent data, sequence analysis showed the presence of very GC3-rich CDS in these poikilotherm vertebrates. However, very high diversity in compositional patterns among different orders of fish, amphibians and reptiles was found. Significant positive correlations between GC3 and GCI was also confirmed for the genes analyzed. Nevertheless, introns resulted to be poorer in GC than their corresponding CDS, this difference being larger than in human genome. Because the limited number of available sequences including exons and introns we must be cautious about the results derived from them. However, the indicious of higher GC richness of coding sequences than of their corresponding introns could aid to understand the discrepancy of sequence analysis with the ultracentrifugation studies in cold-blooded vertebrates that did not predict the existence of GC-rich isochores.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- CDS:
-
Coding Sequences
- GC3:
-
Guanine and cytosine content on the third codon position
- GCI:
-
Guanine and cytosine content on the intron sequences
References
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
Belle E, Smith N, Eyre-Walker A (2002) Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J Mol Evol 55:356–363
Bernardi G (1995) The human genome: Organization and evolutionary history. Ann Rev Genet 29:445–476
Bernardi G, Bernardi G (1990) Compositional patterns in the nuclear genome of cold-blooded vertebrates. J Mol Evol 31:265–281
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 warm-blooded vertebrates. Science 228:953–958
Bucciarelli G, Bernardi G, Bernardi G (2002) An ultracentrifugation analysis of two hundred fishes genomes. Gene 295:153–162
Clay O, Caccaio S, Zoubak S, Mouchiroud D, Bernardi G (1996) Human coding and non-coding DNA: compositional correlations. Mol Phylogenet Evol 5:2–12
D´Onofrio G, Jabbari K, Musto H, Alvarez F-Valin, Cruviller S, Bernardi GG (1999) Evolutionary genomics of vertebrates and its implications. Ann N Y Acad Sci 870:81–94
D’Onofrio G, Mouchiroud D, Aïssani B (1991) Correlations between the compositional properties of human genes, codon usage and aminoacid composition of proteins. J Mol Evol 32:504–510
Duret L, Mourchiroud D, Gouy M (1994) HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res 22:2360–2365
Duret L, Mouchiroud D, Gouy M (1995) Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J Mol Evol 40:308–317
Hamada K, Horiike T, Kanaya S, Nakamura H, Ota H, Yatogo T, Okada K, Shinozawa T (2002) Changes in body temperature pattern in vertebrates do not influence the codon usages of alpha-globin genes. Genes Genet Syst 77(3):197–207
Hughes S, Clay O, Bernardi G (2002) Compositional patterns in reptilian genomes. Gene 295:323–329
Hughes S, Zelus D, Mouchiroud D (1999) Warm-blooded isochore structure in Nile crocodile and turtle. Mol Biol Evol 16:1521–1527
Kadi F, Mouchiroud D, Sauber G, Bernardi G (1993) The compositional patterns of the avian genomes and their evolutionary implications. J Mol Evol 37:544–551
Mouchiroud D, D’Onofrio G, Aissani B, Macaya G, Gautier C, Bernardi G (1991) The distribution of genes in the human genome. Gene 100:181–187
Nekrutenko A, Li WH (2000) Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res 10(12):1896–1995
Nelson JS (1994) Fishes of the world, 3rd edn. John Wiley and sons, New York
Ream R, Johns G, Somero G (2003) Base compositions of gene encoding α-Actin and Lactate Dehydrogenase-A from differently adapted vertebrates show no temperature-adaptative variation in G + C content. Mol Biol Evol 20(1):105–110
Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16(6):276–277
Robinson M, Gautier C, Mouchiroud D (1997) Evolution of isochores in rodents. Mol Biol Evol 14(8):823–828
Vinogradov A (2001) Within-intron correlation with base composition of adjacent exons in different genomes. Gene 276:143–151
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fortes, G.G., Bouza, C., Martínez, P. et al. Diversity in isochore structure among cold-blooded vertebrates based on GC content of coding and non-coding sequences. Genetica 129, 281–289 (2007). https://doi.org/10.1007/s10709-006-0009-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10709-006-0009-2