Transcript Phylogenetic analyses of cyanobacterial genomes: Quantification of

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
□ 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