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

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

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

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)

Simulation

□Reasonable FP: >30% genes resolve a quartet @ 80% bootstrap support

□However, opposite to the FP, FN increase

Quartet Spectrum

□ Plurality support for all quartet

□ 685 genes (61%) have at lease one conflict

□ 30% quartet @ 80% bootstrap

Plurality supported phylogeny

□ Plurality topology

□ Prochlorococcus / marine Synechococcus group

□ Many conflict between the four genomes in this group

Intraphylum HGT

□An example of conflict

□Photosynthesis genes were involved in HGT

Hemolysin-like protein

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

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

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