Bio524_10_Lecture5_ComparativeGenomics_PAIs (1)

Bio524_10_Lecture5_ComparativeGenomics_PAIs (1) - islands =...

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What’s the conceptual basis of the “pan-genome” Discuss Core versus Dispensible genes PAIs are defined by: Different G +C content than chr. DNA Association with mobile DNA elements Absence from non-pathogenic strains Presence of known or suspected Vir genes Insertion into tRNA, or duplicated, genes
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How are genes on PAIs regulated?
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Enterobacteria Diverse lifestyles Diverse hosts Diverse pathogenicity Diverse genomes
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A core set of genes are derived from the common ancestor of all enterobacteria. Genome Size Number of Genes Shared with E. coli K-12 E. coli K-12 4.64 Mb 4405 - E. coli O157:H7 5.54 5416 3840 (71%) Shigella flexneri 4.60 4084 3030 (74%) Salmonella typhi 4.79 4459 3094 (69%) Yersinia pestis 4.60 4198 2254 (54%) Buchnera aphidicola 0.64 564 560 (99%) 8 genomes of enterobacteria compared using Mauve
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Much of the difference in gene content among enterobacterial genomes appears to be due to horizontal gene transfer offset by deletions. E. coli O157:H7 EDL933 vs. K-12 MG1655 MG1655
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Unformatted text preview: islands = 0.6 Mb EDL933 islands = 1.5 Mb Hypervariable Backbone = 4.1 Mb Uropath Hemorag We are still discovering new genes as we continue to sequence genomes K O C = 3.59 Mb Ci = 1.35 Mb Ki=0.51 Mb K C = 0.15 Mb O C =0.14 Mb K O =0.39 Mb O=1.40 Mb Three E. coli Genomes K (MG1655) O (EDL933) C (CFT073) We are still discovering new combinations of genes in the population Evolutionary model of the emergence of Escherichia coli O157:H7 Adapted from Lathem et al. J Infect Dis, 2003;187:1907-1914 Genes where all three strains differ from EDL933: Putative Fimbrial Operon Urease / Tellurite Resisitance O-Antigen Biosynthesis Cryptic Prophage Many Unknowns Genes where ECOR37 differs from the others: Putative invasin Other Notable Clusters: 18 Kb known deletion in DEC5A A closer look at an alignment of 6 E. coli genomes A closer look at an alignment of 6 E. coli genomes Iron Uptake Dehydrogenase Sulfatase Fimbrae...
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This note was uploaded on 10/24/2010 for the course BIOL 524 taught by Professor Dangl during the Fall '10 term at UNC.

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Bio524_10_Lecture5_ComparativeGenomics_PAIs (1) - islands =...

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