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Olga Zhaxybayeva, J. Peter Gogarten, Robert L. Charlebois, W. Ford Doolittle and R. Thane Papke

Journal Club 10-10-06. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Olga Zhaxybayeva, J. Peter Gogarten, Robert L. Charlebois, W. Ford Doolittle and R. Thane Papke Genome Res . 2006 16: 1099-1108. Presented by Song Yang. Cyanobacteria.

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Olga Zhaxybayeva, J. Peter Gogarten, Robert L. Charlebois, W. Ford Doolittle and R. Thane Papke

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  1. Journal Club 10-10-06 Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events Olga Zhaxybayeva, J. Peter Gogarten, Robert L. Charlebois, W. Ford Doolittle and R. Thane Papke Genome Res. 2006 16: 1099-1108 Presented by Song Yang

  2. Cyanobacteria • Also called blue-green bacteria • Gram-negative • Aquatic and photosynthetic • Among the oldest known organism, 3.8 bya • Photosynthesis • Nitrogen fixation • Form chloroplast by endosymbiosis Anabaena sphaerica

  3. InvestigatingHGT • Previous Methods • Unusual evolutionary patterns in gene phylogenies • Patchy phylogenetic distribution • Atypical nucleotide composition • Previous beliefs of HGT • Coherence of phyla: monophyly • HGT is a weak force in the long run

  4. Data Set and Method • 11 complete genomes • Select orthologous genes • Reciprocal top-scoring BLAST hit (10-4) • Relaxed core: 9 of 11 genomes • 1128 genes (3804 at least 4 of 11) • Embedded quartet decomposition • All possible four-taxon trees • Tolerant to missing data • Short internal branch (27) • Long branch attraction (798)

  5. Simulation • Reasonable FP: >30% genes resolve a quartet @ 80% bootstrap support • However, opposite to the FP, FN increase

  6. Quartet Spectrum • Plurality support for all quartet • 685 genes (61%) have at lease one conflict • 30% quartet @ 80% bootstrap

  7. Plurality supported phylogeny • Plurality topology • Prochlorococcus / marine Synechococcus group • Many conflict between the four genomes in this group

  8. Intraphylum HGT • An example of conflict • Photosynthesis genes were involved in HGT Hemolysin-like protein

  9. Transfer with other Phyla • 168 Bacteria and Archaea genomes • Among 1128 data set • 879 detectable homologs • 249 cyanobacteria specific • 700 has 80% bootstrap • 540 support coherent cyanobacteria phyla (77%) • 294 conflict with plurality consensus (54%) • 160 suggest transfer (23%) Threonyl tRNA synthetase

  10. Functional Categories of HGT genes • Across short phylogenetic distance • all types of genes appears to be equally affected by transfer • Across long phylogenetic distance • genes encoding metabolic functions are more frequently transferred, • genes in transcription and translation are transferred less frequent

  11. Conclusion • In previous studies, the number of HGT events are underestimated, based on an assumption that most of genes have a single history • In quartet decomposition, no such assumption is enforced, and conflict does been found • 23% does not support coherence • 61% conflict within phyla • HGT plays an important role in the evolution of cyanobacteria, both within the phylum and with other phyla

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