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Open Access Highly Accessed Research article

Compositional patterns in the genomes of unicellular eukaryotes

Maria Costantini1*, Fernando Alvarez-Valin2, Susan Costantini3, Rosalia Cammarano1 and Giorgio Bernardi4

Author Affiliations

1 Laboratory of Animal Physiology and Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy

2 Sección Biomatemática, Facultad de Sciencias, Universidad de la Repùblica, Montevideo, Uruguay

3 INT “G. Pascale” - CROM (Oncology Research Centre of Mercogliano), Mercogliano, Italy

4 Biology Department, Rome 3 University, Viale Marconi 446, Rome, Italy

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BMC Genomics 2013, 14:755  doi:10.1186/1471-2164-14-755

Published: 5 November 2013

Abstract

Background

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. A question raised by these basic results concerns how far back in evolution the compartmentalized organization of the eukaryotic genomes arose.

Results

In 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.

Conclusions

The 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.

Keywords:
Compositional organization; Genome; Unicellular eukaryotes