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Abstract
BackgroundThe genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores, large and fairly homogeneous stretches of DNA that belong to a small number of families characterized by different average GC levels, by different gene concentration (that increase with GC), different chromatin structures, different replication timing in the cell cycle, and other different properties. A question raised by these basic results concerns how far back in evolution the compartmentalized organization of the eukaryotic genomes arose.ResultsIn the present work we approached this problem by studying the compositional organization of the genomes from the unicellular eukaryotes for which full sequences are available, the sample used being representative. The average GC levels of the genomes from unicellular eukaryotes cover an extremely wide range (19%-60% GC) and the compositional patterns of individual genomes are extremely different but all genomes tested show a compositional compartmentalization.ConclusionsThe average GC range of the genomes of unicellular eukaryotes is very broad (as broad as that of prokaryotes) and individual compositional patterns cover a very broad range from very narrow to very complex. Both features are not surprising for organisms that are very far from each other both in terms of phylogenetic distances and of environmental life conditions. Most importantly, all genomes tested, a representative sample of all supergroups of unicellular eukaryotes, are compositionally compartmentalized, a major difference with prokaryotes.
Highlights
The genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores, large and fairly homogeneous stretches of DNA that belong to a small number of families characterized by different average GC levels, by different gene concentration, different chromatin structures, different replication timing in the cell cycle, and other different properties
Investigations at the sequence level showed that (i) the genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores that belong to a small number of families that are characterized by different GC levels and dinucleotide frequencies [1,2,3,4,5,6]
The results just reported clearly show that the genomes of unicellular eukaryotes range from narrow compositional distributions, as in the case of O. tauri, T. pseudonana, C. neoformans and P. falciparum, P. berghei and P. chabaudi, to more heterogeneous patterns, such as those of S. cerevisiae and T. brucei, while in many other groups such as P
Summary
The genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores, large and fairly homogeneous stretches of DNA that belong to a small number of families characterized by different average GC levels, by different gene concentration (that increase with GC), different chromatin structures, different replication timing in the cell cycle, and other different properties. Investigations at the sequence level showed that (i) the genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores that belong to a small number of families that are characterized by different GC levels and dinucleotide frequencies [1,2,3,4,5,6]. These findings confirmed and extended previous investigations (originally using density gradient ultracentrifugation [7,8,9]) carried out by our laboratory over many years (see [6] for a review). Later work based on sequenced yeast chromosomes showed that some of them consist of alternating large domains of GC-rich
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