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Open Access Highly Accessed Research article

Gene copy number variation and its significance in cyanobacterial phylogeny

Bettina E Schirrmeister12*, Daniel A Dalquen34, Maria Anisimova34 and Homayoun C Bagheri1

Author Affiliations

1 Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland

2 School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK

3 Computational Biochemistry Research Group, Swiss Federal Institute of Technology, Universitätstrasse 6, 8092 Zurich, Switzerland

4 , Swiss Institute of Bioinformatics, Universitätstrasse 6, 8092 Zurich, Switzerland

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BMC Microbiology 2012, 12:177  doi:10.1186/1471-2180-12-177

Published: 15 August 2012

Additional files

Additional file 1:

Identified gene copies. The sheet contains Information on 41 gene copies and their presence in 22 cyanobacterial species. Amino acid sequences of the coded proteins exhibit 98% similarity within a genome and 50% across species.

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Additional file 2:

16S rRNA gene copy data including data from the rrndb-database. Table with information on 16S rRNA copy numbers including data received from the rrnDB database [45] marked (*).

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Additional file 3:

Distribution of 16S rRNA copy numbers using additional data from rrndb3. Boxplot representations of the 16S rRNA gene copy number distribution across the previously defined morphological groups. Additional data on 16S rRNA copy numbers were received from the rrndb-database [45]. Spearman’s rank correlation coefficient (ρ) and Pearson’s correlation coefficient (R) are displayed above the graph. A strong correlation of 16S rRNA gene copies to terminally differentiated cyanobacteria is supported.

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Additional file 4:

Distribution of mean distances within species of bootstrap samples for the different eubacterial phyla. The distribution of mean distances of the bootstrap samples presented as a histogram. The 95% confidence intervals between cyanobacteria and Chloroflexi, Spirochaetes and Bacteroidetes do not overlap. Cyanobacterial 16S rRNA gene sequence variation within species is significantly lower.

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Additional file 5:

Distribution of mean distances between species of bootstrap samples for the different eubacterial phyla. The distribution of mean distances of the bootstrap samples presented as a histogram. The 95% confidence intervals between cyanobacteria and the other eubacterial phyla do not overlap. Cyanobacterial 16S rRNA gene sequence variation between species are significantly lower.

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Open Data

Additional file 6:

Phylogenetic tree and distance matrix of Spirochaetes. (A) Phylogenetic tree of the eubacterial phylum Spirochaetes including all 16S rRNA gene copies, reconstructed using Bayesian analysis. On the nodes posterior probabilities >0.90 are displayed. The letter “R” denote gene copies that are positioned on the reverse DNA strand. (B) Distance matrix of Spirochaetes. Genetic distances have been estimated according to the K80 substitution model. White lines separate sequence copies of different species.

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Open Data

Additional file 7:

Phylogenetic tree of Bacteroidetes. Phylogenetic tree of the eubacterial phylum Bacteroidetes including all 16S rRNA gene copies, reconstructed using Bayesian analysis. On the nodes posterior probabilities >0.90 are displayed.The letter “R” denote gene copies that are positioned on the reverse DNA strand.

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Additional file 8:

Distance matrix of Bacteroidetes. Genetic distances have been estimated according to the K80 substitution model. White lines separate sequence copies of different species.

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Open Data

Additional file 9:

Distance matrix of cyanobacterial ITS-region. Distance matrix of the internal transcribed spacer sequence region in cyanobacteria. Genetic distances have been estimated according to the K80 substitution model. White lines separate sequence copies of different species. Distances ≥5.7 are displayed by the same blue color.

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Additional file 10:

Data of 16S rRNA gene sequences of the different eubacterial phyla. Species nomenclature, genome sizes, 16S rRNA gene copy numbers and accession numbers from the eubacterial taxa used in this study.

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