Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data

doi:10.1186/1745-6150-2-27

Biology Direct

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Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data

Larry J Wilhelm¹ , H James Tripp¹ , Scott A Givan² , Daniel P Smith¹ and Stephen J Giovannoni¹

¹Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA

²Center for Genome Research and Bioinformatics, Oregon State University, Corvallis, OR, 97331, USA

author email corresponding author email

Biology Direct 2007, 2:27doi:10.1186/1745-6150-2-27


Published:	7 November 2007

Additional files

Additional file 1:

Distribution of expect scores for Pelagibacter syntenic fragments. The values in the plot are taken from the TBLASTN search in which predicted proteins from the HTCC1062 genome were the query genes and the Sargasso Sea metagenomic database was searched (Fig. 2A). The distribution indicates a sharp decline in expect scores approaching the cutoff of 1 × 10^-10. The data are provided as support for this choice of expect score cutoff.

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Additional file 2:

GC content of Pelagibacter syntenic fragments. Histogram of the GC content of metagenomic fragments from the syntenic fragments bin, compared to the mean for the HTCC1062 genome.

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Additional file 3:

Sargasso Sea syntenic fragment plot for Escherichia coli. A syntenic fragment plot using Escherichia coli as the query genome. The data provide a rough measure of the false-positive rate in the syntenic fragment plots.

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Additional file 4:

Syntenic fragment plots of three representative organisms. The bar chart in the upper right corner indicates the number of fragments containing the query organism's 16S rRNA, at the indicated degree of similarity. The horizontal line indicates the average syntenic fragment score.

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Additional file 5:

Syntenic fragments carrying at least three genes. A large portion of the syntenic fragments are not of sufficient length to carry more than three genes. These data show that the general trends of genome coverage and range of amino-acid level identity shown in Fig. 3D hold when the shorter fragments are excluded.

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Additional file 6:

Analysis of assemblies versus unassembled reads. Pelagibacter syntenic fragment analysis performed on unassembled reads (A), and on sequence data containing assemblies as well as unassembled reads (B). The plots are essentially similar.

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Additional file 7:

Enlargement of HVR3 and HVR4. HTCC1062 syntenic fragment plot showing detail in the region of HVR3 and HVR4.

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Additional file 8:

Enlargement of HVR1. HTCC1062 syntenic fragment plot showing detail in the region of HVR1.

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