1. 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 Journal Club 10-10-06 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. Investigating HGT □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