Figure 1.
Bayesian consensus phylogeny of small subunit rRNA sequences from alveolates representing the available diversity of colpodellids, chromerids, and related environmental sequences.
Support for nodes is indicated by % bootstrap support (out of 1000) in the ML analysis (RAxML GTRΓ)/Bayesian posterior probability (Phylobayes GTRCAT) where greater than 55 or 0.9. The subject of this study, Voromonas pontica, is indicated by white text on a black background. The photosynthetic chromerids Chromera velia and Vitrella brassicaformis are indicated by bold text. A question mark after accession AF372772 indicates a possible misidentification or chimeric sequence; this study also sampled a lake.
Table 1.
Presence/absence of plastid-associated biosynthetic pathway enzymes sought in the V. pontica transcriptome.
Table 2.
Predicted plastid targeting signal and transit peptide characteristics.
Figure 2.
Maximum likelihood phylogeny of plastidic phosphate transporters.
Support for nodes is indicated by % bootstrap support (out of 1000) in the ML analysis and by posterior probabilities from two Bayesian analyses, one employing the LG model of amino acids substitution, and the other using the CAT model (RAxML LG+Γ+F/Phylobayes LG+Γ/Phylobayes CAT+Γ), where greater than 50% bootstrap support or 0.9 posterior probability. Black dots on branches indicate full support from all three analyses for the adjacent node, i.e. 100/1.0/1.0. The subject of this study, Voromonas pontica, is indicated by white text on a black background. Experimentally apicoplast-localized proteins are indicated by bold text. Hatch marks indicate a branch whose length has been reduced by half. Aside from the primary plastid pPTs enclosed by the lower shaded box, all sequences belong to secondary, rhodophyte-derived plastids.
Figure 3.
Maximum likelihood phylogeny of SufB amino acids sequences.
Support for nodes is indicated by % bootstrap support (out of 1000) in the ML analysis and by posterior probabilities from two Bayesian analyses, one employing the LG model of amino acids substitution, and the other using the CAT model (RAxML LG+Γ+F/Phylobayes LG+Γ/Phylobayes CAT+Γ), where greater than 50% bootstrap support or 0.9 posterior probability. The subject of this study, Voromonas pontica, is indicated by white text on a black background. Hatch marks indicate branches whose lengths have been reduced by half.