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Comparison of sequenced Bacterial Genomes
Comparative Microbial Genomics Group
Dave Ussery
Advanced Bioinformatics course lecture
21 November, 2003
overview
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OverviewLast week: DNA structures in Bacterial Genomes
Today: How do you cp. 150 genomes?
1. Introduction & a look at 4 Pseudomonas genomes
2. 5 epsilon Proteobacteria (Campylobacter, Helicobacter, and Related Organisms)
3. Comparison of 5 Clostridium genomes
title
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Part 1: Introduction
And A look at 4 Pseudomonas genomes
OVERVIEW
1. Introduction to Bacterial Genome cp.
2. An example of “Current methods” (Bordetella)
3. Comparison of Four Pseudomonas Species
[CBS tools for bacterial genome comparison]
overview
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3 Bordetella genomes
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Introduction Example: 3 Bordetella genomes
Parkhill et al., Nature Genetics, 35:32-40, (2003).
Wheel plots
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Genome alignment
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circles
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Comparing Genomes
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Comparing genomes:
2. Atlas plots for visualisation of the whole chromosome
• Genome Alignment (sometimes useful)
1. Table for comparisons
3. Proteome comparisons
Cp 100 genomes
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Comparative Microbial Genomics Group
How do you compare more than 100 bacterial genomes?
Organism perAT lengthPseudomonas aeruginosa, strain PAO1 33.4 6,264,403Pseudomonas fluorescens SBW25 40.0 6,703,654Pseudomonas putida KT2440 38.5 6,181,863P. syringae pv. tomato strain DC3000 41.0 6,397,126Average of 150 genomes 52.8 3,004,048
http://www.cbs.dtu.dk/services/GenomeAtlas/Bacteria
Comparison tool #1 - The table
Repeats table
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Organism Global Direct Global InvertedLocal Direct Local InvertedP. aeruginosa PAO1 3.6 2.5 12.1 7.7P. fluorescens SBW25 3.8 3.2 6.5 4.5P. putida KT2440 4.7 3.8 7.1 5P. syringae DC3000 6.9 6.2 5.2 3.8Average of 150 genomes 4.1 2.9 8.3 6.1
repeats
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Purine stretches
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Genome Letters
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Di and Tetranucleotides
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GL tables 1 and 2
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REP REPREPREP
Repetative sequences
REP logos
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GL Figure 10
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GL Table 3
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Know your insects
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Paer. Genome atlas
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Comparison tool #2 - DNA atlases
Pput Genome Atlas
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Psyr. Genome Atlas
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3 genome alignment
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Table 2
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Organism perAT length rRNA operons # genes # sigmasPseudomonas aeruginosa, strain PAO1 33.4 6,264,403 4 5566 23Pseudomonas fluorescens SBW25 40.0 6,703,654 5 5480 29Pseudomonas putida KT2440 38.5 6,181,863 7 5350 23P. syringae pv. tomato strain DC3000 41.0 6,397,126 5 5471 14Average of 150 genomes 52.8 3,004,048 3 2890 8
sigmas
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Sig70 tree
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Blast table
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Comparison tool #3 - Proteome cp.
Blast atlas
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Paer blast atlas
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Pput blast atlas
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Psyr blast atlas
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zoom
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Table 3.1
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Phylome 1 atlas
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phylome2atlas
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An aside
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An aside…
Bacteria has a periodicity of 11
Archaea has a periodicity of 10
Peder Worning et al., Nucl. Acids Res., 28:706-709, 2000
E.coli autocorrel.
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E.coli autocorrel
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Fourier transform
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E.coli O157
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E.coli periodicity
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Haemophilus
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C. jejuni
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H.pylori J99
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M. janasschii
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T. maritima
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Cp. 3 genomes
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Pseudomonas periodicity
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Summary
1. Table (gives single-value, general features)
summary
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2. DNA Atlases (circular maps of the whole chromosome)
3 ways to compare genomes:
3. Proteome comparison (Blast, Phylome-atlas, etc.)