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slides13 - onday Oct 29 - Andersson and Moran readings...

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Systems Microbiology Monday Oct 29 - Andersson and Moran readings Genome Evolution & Ecology LGT & Genome Evolution Genomics of Genomics of Endosymbionts Endosymbionts Environmental Genomics Environmental Genomics
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Mechanisms and consequences of Lateral Gene Transfer Redfield, Nat. Rev. Genet. 2001 A B C Organismal phylogeny A B C gene phylogeny Transduction: via a virus (bacteriophage) Transformation: integration of free DNA Conjugation: direct contact (plasmid) Microscopic photographs of phage and bacterial conjugation removed due to copyright restrictions. DNA transfer by transduction DNA transfer by conjugation Phage-infected donor Recipient Recipient Recipient Donor Common Rare Hfr Donor Dead Donor Competent recipient Gene transfer by competence F A B C Figure by MIT OCW.
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POPULATION GENETICS OF PATHOGENS UROPATHOGENIC & ENTEROHAEMORRHAGIC “HOT-SPOTS” Welch, R. A. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 17020-17024 585 7.6% MG1655 (K-12) Non-Pathogenic CFT073 Uropathogenic EDL933 (O157:H7) Enterohaemorrhagic 514 6.7% 204 2.6% 1623 21.2% 1346 17.6% 193 2.5% 2996 39.2% Total proteins = 7638 2996 (39.2%) in all 3 911 (11.9%) in 2 out of 3 3554 (46.5%) in 1 out of 3 Figure by MIT OCW.
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POPULATION GENETICS OF PATHOGENS UROPATHOGENIC & ENTEROHAEMORRHAGIC “HOT-SPOTS” Welch, R. A. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 17020-17024 100 Kb aspV aspV thrW serX serX serW serU serU argW argW ssrA ssrA metV selC (pap) pheU selC (LEE) leuX leuX (pap-hly) pheV pheV asnT,V thrW ** * * * * * * ** 100 Kb CFT073 EDL933 Figure by MIT OCW.
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1. Construct multiple alignment of sequences 2. Construct table listing all pairwise differences (dist matrix) 3. Construct tree from pairwise distances Gorilla : ACGT CGTA Human : ACGTTCCT Chimpanzee : ACGTT T C G - Ch 2 - Hu 4 4 - Go Ch Hu Go Go Hu Ch 2 1 1 1 Molecular Phylogenetics : Inferring Evolutionary Relationships
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Lateral Gene Transfer and molecular phylogenetics “Gene tree” assumes similarity by descent
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But what if there is extensive lateral gene transfer between bacteria ??? “true” tree based on Gene ‘Y’ Gene “X” laterally transfered Gene “X” tree looks like this
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Example of genome dynamics over time due to Lateral Gene Transfer Gene uptake In gamma- Proteobacteria E. Lerat et al 03 S. typhimurium E. coli Y. pestis KIM CO92 W. brevipalpis B. aphidicola P. multocida H. influenzae V. cholerae P. aeruginosa X. fastidiosa X. campestris X. axonopodis Many genes in most genomes arrived via LGT after the common ancestor. Most genes arriving via LGT come from distant sources (not in this group) Many persist as vertically transmitted genes within the descendant clade. ---but many are lost quickly (many present only in tips of tree)
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Detecting Horizontal Transfers 1. Unexpected ranking of sequence similarity among homologs 2. Unexpected phylogenetic tree topology 3. Unusual phyletic pattern 4. Conservation of gene order 5. Anomalous DNA composition
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slides13 - onday Oct 29 - Andersson and Moran readings...

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