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Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium

Lionel Frangeul1, Philippe Quillardet2, Anne-Marie Castets2, Jean-François Humbert23, Hans CP Matthijs4, Diego Cortez5, Andrew Tolonen102, Cheng-Cai Zhang6, Simonetta Gribaldo5, Jan-Christoph Kehr7, Yvonne Zilliges7, Nadine Ziemert7, Sven Becker8, Emmanuel Talla6, Amel Latifi6, Alain Billault9, Anthony Lepelletier1, Elke Dittmann7, Christiane Bouchier1 and Nicole Tandeau de Marsac2*

Author Affiliations

1 Institut Pasteur, Pasteur Genopole ®, F-75015, Paris, France

2 Institut Pasteur, Unité des Cyanobactéries; CNRS, URA2172, F-75015, Paris, France

3 INRA, UMR CARRTEL, BP 511, 74203 Thonon cedex, France

4 Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Nieuwe Achtergracht 127, 1018 WS Amsterdam, The Netherlands

5 Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles; F-75015, Paris, France

6 Université d'Aix-Marseille, Laboratoire de Chimie Bactérienne, CNRS-UPR9043, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France

7 Humboldt-Universität zu Berlin, Institut für Biologie, Molekulare Ökologie, Chausseestr. 117, 10115 Berlin, Germany

8 Netherlands Institute of Ecology NIOO-KNAW, Centre for Limnology, Rijksstraatweg 6, 3631 AC Nieuwersluis, The Netherlands

9 Genoscope – Centre National de Séquençage, 2 rue Gaston Crémieux CP5706 91057 Evry cedex, France

10 Department of Genetics, Harvard Medical School, Boston MA 02115, USA

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BMC Genomics 2008, 9:274  doi:10.1186/1471-2164-9-274

Published: 5 June 2008



The colonial cyanobacterium Microcystis proliferates in a wide range of freshwater ecosystems and is exposed to changing environmental factors during its life cycle. Microcystis blooms are often toxic, potentially fatal to animals and humans, and may cause environmental problems. There has been little investigation of the genomics of these cyanobacteria.


Deciphering the 5,172,804 bp sequence of Microcystis aeruginosa PCC 7806 has revealed the high plasticity of its genome: 11.7% DNA repeats containing more than 1,000 bases, 6.8% putative transposases and 21 putative restriction enzymes. Compared to the genomes of other cyanobacterial lineages, strain PCC 7806 contains a large number of atypical genes that may have been acquired by lateral transfers. Metabolic pathways, such as fermentation and a methionine salvage pathway, have been identified, as have genes for programmed cell death that may be related to the rapid disappearance of Microcystis blooms in nature. Analysis of the PCC 7806 genome also reveals striking novel biosynthetic features that might help to elucidate the ecological impact of secondary metabolites and lead to the discovery of novel metabolites for new biotechnological applications. M. aeruginosa and other large cyanobacterial genomes exhibit a rapid loss of synteny in contrast to other microbial genomes.


Microcystis aeruginosa PCC 7806 appears to have adopted an evolutionary strategy relying on unusual genome plasticity to adapt to eutrophic freshwater ecosystems, a property shared by another strain of M. aeruginosa (NIES-843). Comparisons of the genomes of PCC 7806 and other cyanobacterial strains indicate that a similar strategy may have also been used by the marine strain Crocosphaera watsonii WH8501 to adapt to other ecological niches, such as oligotrophic open oceans.