Evidence of a chimeric genome in the cyanobacterial ancestor of plastids

Additional file 1:

Phylogeny of MenC. This figure indicates that the MenC module of PHYLLO and the individual plastidencoded MenC proteins of Cyanidiales are related to homologs of Chlorobi and Gammaproteobacteria. This is a Bayesian majority rule consensus tree using 58 taxa. Posterior probability support values are only indicated (as percentages) for external nodes of the major clades. Analysis parameters: mcmc ngen = 500,000; startingtree = PHYML; samplefreq = 100; aamodel = mixed; rates = invgamma; burnin = 1,250.

Format: PDF Size: 1.8MB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 2:

Phylogeny of MenB. The tree is juxtaposed to a partial alignment of the corresponding amino acid positions 69 – 116 in the E. coli MenB homolog (GenBank accession number, NP_416765.1). Two deletions are correlated with the tree topology. Note that deletion 2 is shared by all Group 1 taxa in Fig. 1b, including photosynthetic eukaryotes, Chlorobi, and Gammaproteobacteria. This is a Bayesian majority rule consensus tree using MrBayes and the following parameters: mcmc ngen = 500,000; startingtree = PHYML; samplefreq = 100; aamodel = mixed; rates = invgamma; burnin = 1,250. Posterior probability support values are only indicated (as percentages) for external nodes of the major clades.

Format: PDF Size: 306KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 3:

Phylogeny of MenE. The plastid-encoded menE of Cyanidiales has its origin in the same gene cluster that was transferred to the plastid ancestor from a Chlorobi/Gammaproteobacteria source. The MenE proteins in the nuclear genome of the remaining algae and plants have a different phylogenetic provenance and are most likely derived by HGT, presumably directly into the host nucleus. This is a Bayesian majority rule consensus tree using 66 taxa. Posterior probability support values are only indicated (as percentages) for external nodes of the major clades. Analysis parameters are: mcmc ngen = 500,000; startingtree = PhyML generated tree; samplefreq = 100; aamodel = mixed; rates = invgamma; burnin = 1,250.

Format: PDF Size: 258KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 4:

Phylogeny of MenG/UbiE. MenG proteins are responsible for the methylation step of the MQ/PhQ pathway (Lohmann et al. 2006). In eubacteria the same enzymes also catalyse the methylation required for biosynthesis of ubiquinone (Meganathan 2001). In this case MenG homologs are referred to as UbiE. In photosynthetic eukaryotes UbiE functions in mitochondria and MenG is plastid targeted for the synthesis of PhQ. In accordance with its organellar distribution, UbiEs are related to homologs in Alphaproteobacteria, whereas MenG in the nuclear genomes of plants and green algae is derived from the cyanobacterial endosymbiont. MenG encoded in the nuclear genome of Cyanidiales and diatoms are related to Deltaproteobacteria and presumably originated via HGT. This is Bayesian majority rule consensus tree using 81 taxa. Posterior probability support values are only indicated (as percentages) for external nodes of the major clades. Analysis parameters: ngen = 1,100,000; startingtree = PHYML generated tree; samplefreq = 100; aamodel = mixed; rates = gamma; burnin = 2,750.

Format: PDF Size: 1.5MB Download file

This file can be viewed with: Adobe Acrobat Reader