Investigated strains of vampire amoebae and corresponding data.

<p>CCAC = Culture Collection of Algae at the University of Cologne.</p><p>NA = not available (deceased).</p><p>nt = nucleotides.</p

Trophozoites and digestive cysts of <i>Vampyrella pendula</i>.

<p><b>3A & B.</b> Advancing trophozoites. Brightfield. <b>3C.</b> Trophozoite and digestive cyst on a filament of <i>Oedogonium</i>. Brightfield. <b>3D.</b> Trophozoite with clear pseudopodia lacking membranosomes. DIC. <b>3E & F.</b> Trophozoite producing claviform pseudopodia (arrows). DIC. <b>3G.</b> Early digestive cyst stage. DIC. <b>3H.</b> Mature digestive cyst. DIC. <b>3I.</b> Remaining digestive cyst envelopes with food remnant. DIC. Asterisk = very faint outer sheath, hollow arrows = outer cyst envelope, hollow arrowheads = delicate strands between outer and intermediate cyst envelope, arrowheads = central stand running from innermost cyst envelope through stalk. <b>Scale bars:</b> 10 µm.</p

Life history stages and morphological traits of <i>Vampyrella lateritia</i>.

<p><b>2A.</b> Advancing trophozoite. DIC. <b>2B.</b> Large trophozoite likely a result from cell fusions. DIC. <b>2C.</b> membranosomes moving along the pseudopodia. DIC. <b>2D.</b> ‘pin-like’ pseudopodia, arrowheads: membranosomes. DIC. <b>2E.</b> Numerous vacuoles in the cell periphery. <b>2F.</b> Large, bulky plasmodium. DIC. <b>2G.</b> Attached <i>Vampyrella</i> cell ingesting algal cell content. Brightfield. <b>2H.</b> Ingestion pseudopodium (arrow) emptying an algal cell. DIC. <b>2I.</b> Immobile <i>Vampyrella</i> cell with retracted pseudopodia and spiny surface turning into digestive cyst. DIC. <b>2J.</b> Green motile cell after food uptake. Brightfield. <b>2K.</b> Early digestive cyst stage with greenish contents. Brightfield. <b>2L.</b> Mature digestive cyst with delicate outer cyst envelope (arrowhead). Brightfield. <b>2M.</b> Digestive cyst with progeny after cell divisions in characteristic arrangement, arrowhead: outer cyst envelope. Brightfield. <b>2N.</b> Digestive cysts at various stages in different colours. Dark field. <b>2O.</b> Resting cyst with four envelopes (arrowheads). DIC. <b>Scale bars:</b> 2A, B, H, I, O = 10 µm; 2C–E = 5 µm; 2F = 50 µm; 2G, J–M = 20 µm.</p

Reconstructed phylogeny of the Vampyrellida in a cercozoan context based on SSU rDNA sequence comparisons.

<p>Shown is the best maximum likelihood tree obtained by RAxML analyses of 81 sequences using 1640 aligned characters. The order Vampyrellida as well as the families Vampyrellidae and Leptophryidae are shaded in yellow/red colours, the remaining two deep-branching endomyxan clades in grey. The branch containing ‘Novel Clades’ 10–12 and some members of the ‘core Filosa’ are defined as outgroup. For previously published sequences taxonomic names and accession numbers are given. Sequences without taxonomic designations are environmental sequences and newly obtained sequences are combined with the strain designation only and are in bold (for accession numbers see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031165#pone-0031165-t001" target="_blank">Table 1</a>). The support values of all methods applied are shown on the respective branches in the following order: ML/NJ/MP/BI. Support values less than 50% or 0.5 are not shown (−), whereas bold branches were maximally supported by all methods (100/100/100/1.00). Interrupted branches (//) show 50% of their original length. NC = ‘Novel Clade’ according to Bass & Cavalier-Smith (2004) and Bass et al. (2008) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031165#pone.0031165-Bass1" target="_blank">[11]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031165#pone.0031165-Bass2" target="_blank">[38]</a>.</p

Venn diagram showing the number of chlamydial proteins shared by different photoautotrophic eukaryotes

<p><b>Copyright information:</b></p><p>Taken from "Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes"</p><p>http://www.biomedcentral.com/1471-2148/8/203</p><p>BMC Evolutionary Biology 2008;8():203-203.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2490706.</p><p></p

Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes-3

Els of all data sets: WAG+I+Γ, except for Fig. 1E: RtREV+I+Γ ([]. Support values: maximum likelihood bootstrap/posterior probability; branches in bold: ML bootstrap > 95% and posterior probability of 1.0. Scale bars = substitutions per site. For enlarged trees with taxon names, see Additional File . (A) Glycerol-3-phosphate acyltransferase (EC 2.3.1.15; 21 taxa, 281 amino acid positions). (B) tRNA delta(2)-isopentenylpyrophosphate transferase (EC 2.5.2.8; 38 taxa, 240 positions). (C) 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (D; EC 2.7.7.60; 38 taxa, 198 positions). Rhodoplantae, Bacillariophyta and Viridiplantae group with the Chlamydiae. (D) Putative ribosome release/recycling factor (COG0233; 30 taxa, 171 positions). (E) Ribosomal large subunit pseudouridine synthase (EC 4.2.1.70; 38 taxa, 262 positions). (F) Folylpolyglutamate synthase (EC 6.3.2.17; 26 taxa, 208 positions).<p><b>Copyright information:</b></p><p>Taken from "Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes"</p><p>http://www.biomedcentral.com/1471-2148/8/203</p><p>BMC Evolutionary Biology 2008;8():203-203.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2490706.</p><p></p

Plasmodia and digestive cysts of <i>Leptophrys vorax</i>.

<p><b>5A.</b> Large extended Plasmodia. Phase contrast. <b>5B.</b> Plasmodium showing several anastomoses (arrowheads) and a normal sized trophozoite for comparison of the sizes. Phase contrast. <b>5C.</b> Small elliptical cyst. Brightfield. <b>5D.</b> Roundish cyst. Brightfield. <b>5E.</b> Irregular lobed cyst. Brightfield. <b>5F.</b> Dumbbell-shaped cyst. Brightfield. <b>5G.</b> Numerous digestive cysts in growing culture with <i>Closterium</i> sp. sometimes banana-shaped. Oblique illumination. <b>5H.</b> Slender cyst containing <i>Synedra</i> sp. Brightfield. <b>5I.</b> Moving trophozoite tightly packed with <i>Closterium</i> cells. Brightfield. <b>5J.</b> Early digestive cyst stage with greenish food inclusions. Brightfield. <b>5K.</b> Later digestive cyst stage with brownish food inclusions indicating the proceeding digestion. Brightfield. <b>5L.</b> Digestive cysts after hatching of the trophozoites just containing brown food remnants. Brightfield. <b>Scale bars:</b> 5A, B = 100 µm; 5C–F, H–L = 20 µm; 5G = 200 µm.</p

Trophozoites of <i>Leptophrys vorax</i> and their variability.

<p><b>4A & B.</b> Small, compact trophozoites. DIC. <b>4C.</b> Advancing cell with fan-like outline. DIC. <b>4D.</b> Branched cell. DIC. <b>4E.</b> Elongated cell with several attachment sites. DIC. <b>4F.</b> Cell drawn out into thin cytoplasmic strand due to extending cell ends. DIC. <b>4G.</b> Advancing trophozoite showing clear pseudopodia emerging from a hyaline fringe, a tail-like posterior projection and dendritic pseudopodial structures (arrowheads). DIC <b>4H.</b> Vesicular nuclei in the cytoplasm of a dying individual (arrowheads). DIC. <b>4I.</b> Isodiametric floating form with radiating pseudopodia. DIC. <b>Scale bars:</b> 4A–E, 4G, I = 20 µm; 4F = 100 µm; 4H = 10 µm.</p

Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes-2

maximum likelihood bootstrap/posterior probability. Scale bars = substitutions per site. () Concatenated data set of seven proteins showing relationship of diatoms to rhodoplants (12 taxa; 2675 amino acid positions). () Concatenated data set of five proteins showing a relationship of viridiplant and diatom genes (same 12 taxa as in Fig. 3A; 1736 amino acid positions). For a complete list of genes used in the two concatenated analyses see Additional File .<p><b>Copyright information:</b></p><p>Taken from "Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes"</p><p>http://www.biomedcentral.com/1471-2148/8/203</p><p>BMC Evolutionary Biology 2008;8():203-203.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2490706.</p><p></p

Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes-0

Els of all data sets: WAG+I+Γ, except for Fig. 1E: RtREV+I+Γ ([]. Support values: maximum likelihood bootstrap/posterior probability; branches in bold: ML bootstrap > 95% and posterior probability of 1.0. Scale bars = substitutions per site. For enlarged trees with taxon names, see Additional File . (A) Glycerol-3-phosphate acyltransferase (EC 2.3.1.15; 21 taxa, 281 amino acid positions). (B) tRNA delta(2)-isopentenylpyrophosphate transferase (EC 2.5.2.8; 38 taxa, 240 positions). (C) 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (D; EC 2.7.7.60; 38 taxa, 198 positions). Rhodoplantae, Bacillariophyta and Viridiplantae group with the Chlamydiae. (D) Putative ribosome release/recycling factor (COG0233; 30 taxa, 171 positions). (E) Ribosomal large subunit pseudouridine synthase (EC 4.2.1.70; 38 taxa, 262 positions). (F) Folylpolyglutamate synthase (EC 6.3.2.17; 26 taxa, 208 positions).<p><b>Copyright information:</b></p><p>Taken from "Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes"</p><p>http://www.biomedcentral.com/1471-2148/8/203</p><p>BMC Evolutionary Biology 2008;8():203-203.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2490706.</p><p></p