Cammarano R et al. (2009), The isochore patterns of invertebrate genomes.

ECB-ART-50178

BMC Genomics 2009 Nov 18;10:538. doi: 10.1186/1471-2164-10-538.

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The isochore patterns of invertebrate genomes.

Cammarano R , Costantini M , Bernardi G .

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BACKGROUND: Previous investigations from our laboratory were largely focused on the genome organization of vertebrates. We showed that these genomes are mosaics of isochores, megabase-size DNA sequences that are fairly homogeneous in base composition yet belong to a small number of families that cover a wide compositional spectrum. A question raised by these results concerned how far back in evolution an isochore organization of the eukaryotic genome arose. RESULTS: The present investigation deals with the compositional patterns of the invertebrates for which full genome sequences, or at least scaffolds, are available. We found that (i) a mosaic of isochores is the long-range organization of all the genomes that we investigated; (ii) the isochore families from the invertebrate genomes matched the corresponding families of vertebrates in GC levels; (iii) the relative amounts of isochore families were remarkably different for different genomes, except for those from phylogenetically close species, such as the Drosophilids. CONCLUSION: This work demonstrates not only that an isochore organization is present in all metazoan genomes analyzed that included Nematodes, Arthropods among Protostomia, Echinoderms and Chordates among Deuterostomia, but also that the isochore families of invertebrates share GC levels with the corresponding families of vertebrates.

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References [+] :

Bernardi, The neoselectionist theory of genome evolution. 2007, Pubmed

	Figure 1. The location of the species investigated in these genomes are reported in the approximate tree presented. This is derived from Dunn et al. [7], to which the reader is addressed for the precise tree.
	Figure 2. Distribution of isochores according to GC levels. The first three histograms, shown for the sake of comparison, display the distribution (by weight) of isochores as pooled in bins of 0.5% GC of some vertebrates: human [9], chicken [11] and zebrafish [10]. The bottom panels show the isochore pattern of C. intestinalis and of C. elegans. The total amount of DNA calculated from the sums of isochores, GC % and the number of isochores are reported. Colors represent the five isochore families of the human genome. Notice the different scales on the ordinate axis.
	Figure 3. The distribution of isochores according to GC levels is displayed for D. melanogaster, D. simulans, D. yakuba, A. gambiae. The histogram of stickleback is shown for the sake of comparison. For other details see legend of Figure 2.
	Figure 4. The scaffolds of B. floridae, S. purpuratus, A. aegypti, T. castaneum and D. pulex and are pooled in bins of 1% GC. The gene density (genes/Mb) is calculated on the scaffolds.
	Figure 5. Observed/expected frequencies A) for dinucleotides in 100-kb DNA segments in the isochore families from C. intestinalis and C. elegans. and B) for dinucleotides in 100-kb DNA segments in the scaffolds of B. floridae, S. purpuratus, A. aegypti, T. castaneum and D. pulex.
	Figure 6. Observed/expected frequencies for dinucleotides in 100-kb DNA segments isochore families from the Drosophilids, A. gambiae and T. castaneum.
	Figure 7. The histograms represent the gene density in the isochore families. The gene concentrations of D. melanogaster and A. gambiae increase with increasing GC in isochore families, as in the case of the genomes from human and stickleback.