Research
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria
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* Corresponding author: Frédéric Partensky partensky@sb-roscoff.fr
- † Equal contributors
1 Université Paris 6 and CNRS, UMR 7144, Station Biologique, 29682 Roscoff, France
2 Université Rennes 1, UMR 6553 EcoBio, IFR90/FR2116, CAREN, 35042 Rennes, France
3 Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
4 Scripps Institution of Oceanography, UCSD, San Diego, CA 92093, USA
5 Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia 2109
6 Institut Pasteur, Dépt de Microbiologie, Unité des Cyanobactéries, URA 2172 CNRS, Paris, France
7 Genoscope (CEA) and UMR 8030 CNRS-Genoscope-Université d'Evry, 91057 Evry, France
8 J Craig Venter Institute, Rockville, MD 20850, USA
9 The Interuniversity Institute for Marine Science, Hebrew University, Eilat 88103, Israel
10 University of Freiburg, Faculty of Biology, D-79104 Freiburg, Germany
Genome Biology 2008, 9:R90 doi:10.1186/gb-2008-9-5-r90
Published: 28 May 2008Additional files
Additional data file 1:
The 70 Synechococcus-specific genes.
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Additional data file 2:
All accessory protein families found in 2-10 Synechococcus strains, including the 61 families shared only by the euryhaline Synechococcus spp. strains WH5701 and RS9917.
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Additional data file 3:
Genomes have been re-aligned so that they all start at dnaN. For other details, see the legend of Figure 3.
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Additional data file 4:
Core genome segments surrounding the islands are connected by yellow shading. Genes shared specifically by Synechococcus spp. WH7803 and CC9902 are connected by gray shading.
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Additional data file 5:
Island coordinates and island gene composition in the 14 genomes of marine picocyanobacteria used in this study.
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Additional data file 6:
NJ tree based on concatenated alignment of the core genome rooted with the freshwater cyanobacterium Synechocystis sp. PCC6803 (863 proteins, 263,424 amino acid positions, gene families with paralogs excluded).
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Additional data file 7:
The 122 core protein families showing a phylogeny divergent from the consensus core protein distance tree shown in Figure 4a (that is, for which at least one event of LGT has occurred), with bipartition supported by bootstrap values ≥ 99%.
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Additional data file 8:
This enzyme is part of the GS/GOGAT pathway, which is involved in the assimilation of NH4+. This tree suggests at least two transfers between clades III and V (represented by WH7803 and WH8102, respectively) and between clades II and X (represented by RS9916 and CC9605, respectively).
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