Spliceosomal introns in <i>Blastocystis</i>.

<p>(A) Sequences flanking the predicted exon–intron junctions in subtype (ST) 1 were aligned separately for each intron category and visualized with WebLogo3 (<a href="http://weblogo.threeplusone.com/" target="_blank">http://weblogo.threeplusone.com/</a>). The category and number (<i>N</i>) of each spliceosomal intron type are shown on the right. (B) Distribution of intron size in 3 sequenced <i>Blastocystis</i> ST genomes. Data for this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003769#pbio.2003769.s032" target="_blank">S11 Data</a>.</p

Peroxisomal machinery genes in selected organisms.

<p>Black circles indicate the gene is present. Grey circles indicate multiple isoforms.</p

Randomized Axelerated Maximum Likelihood (RAxML) tree of kinases identified from <i>Blastocystis</i> subtypes (STs) 1, 4, and 7.

<p>Blue lines correspond to proteins from ST1, black from ST4, and red from ST7. Kinase families are indicated on the periphery.</p

Conserved polyadenylation motif sites (TGTTTGTT) in the genomes of <i>Blastocystis</i> ST1, ST4, and ST7.

<p>Conserved polyadenylation motif sites (TGTTTGTT) in the genomes of <i>Blastocystis</i> ST1, ST4, and ST7.</p

A comparison of unique genes between <i>Blastocystis</i> subtype (ST) pairs to pairs of protistan pathogens.

<p>The percentage of an organism’s protein-coding gene set, which is unique when compared to another organism’s protein-coding gene set and vice versa, is denoted by the width of the ribbon between the 2 as well as being indicated on the ribbon. For example, in a comparison between ST7 and ST1, 20% of the genes in ST7 are not represented in the ST1 set, while 10% of ST1's genes are not found in ST7. Comparisons are based on BLASTp results with an expect value (e-value) threshold of 1e-30 and >50% coverage of the query. <b>Abbreviations:</b> <i>C</i>., <i>Cryptosporidium</i>; <i>L</i>., <i>Leishmania</i>; <i>T</i>., <i>Theileria</i>. Plots were generated using Circos.</p

Maximum likelihood phylogenetic tree of Miro protein sequences.

<p>The tree was calculated using Randomized Axelerated Maximum Likelihood (RAxML). Bootstrap support values above 50% are shown at branches. For simplicity, clades comprising sequences from major monophyletic groups of eukaryotes were collapsed, displaying in detail only the clade of sequences from stramenopiles. Note the 3 Miro paralogs that have apparently emerged from <i>Blastocystis</i>-specific gene duplications before the divergence of the ST1, ST4, and ST7 lineages (gene identifiers of the <i>Blastocystis</i> Miro sequences are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003769#pbio.2003769.s025" target="_blank">S4 Data</a>).</p

Select metabolism of <i>Blastocystis</i> mitochondrion-related organelles (MROs).

<p>Proteins that were not reported in previous studies are shaded in purple. (A) Mitochondrial protein import and folding apparatus. Colored lines represent proteins destined for the outer mitochondrial membrane (blue), inner mitochondrial membrane (green and orange), and mitochondrial matrix (purple). Numbers correspond to the protein number in the complex (e.g., TOM40). Proteases are depicted with partial circles. (B) Mitochondrial carriers from solute carrier protein (SLC) family 25A and their predicted cargo. (C) Metabolic features highlighting the MRO’s role in energy generation and amino acid and lipid metabolism. Protein descriptions are outlined in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003769#pbio.2003769.s024" target="_blank">S3 Data</a>. Standard amino acid abbreviations are used: Ace, acetate; ACP, acyl carrier protein; aKG, alpha-ketoglutarate; BCD, branched chain amino acid degradation; Carn, Carnitine; CDP-DAG, cytidine diphosphate diacylglycerol; CL, cardiolipin; DHAP, dihydroxyacetone phosphate; DHOro, dihydroorotate; Fd, Ferredoxin; Fum, fumarate; Gly3P, glycerol-3-phosphate; Mal, malate; MMC, methyl-malonyl-CoA; Nd(p), NAD(P); Oaa, oxaloacetate; Oro, orotate; PA, phosphatidic acid; PE phosphatidylethanolamine; Pep, phosphoenol pyruvate; PI, phosphatidylinositol; Prop, propionate; PS, phosphatidylserine; Q^O/R, quinone/quinol, oxidized or reduced; RQ, rhodoquinone; SAHC, S-adenosylhomocysteine; SAM, S-adenosylmethionine; Suc, succinate; THF, tetrahydrafolate; ThiMP, thiamine monophosphate; ThiPP, thiamine pyrophosphate; UQ, ubiquinone. Data for this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003769#pbio.2003769.s024" target="_blank">S3 Data</a>.</p

Genome statistics for <i>Blastocystis</i> ST1, ST4, and ST7.

<p>Genome statistics for <i>Blastocystis</i> ST1, ST4, and ST7.</p

Proteases by type in <i>Blastocystis</i> subtype (ST) 1, ST4, and ST7.

<p><b>Abbreviations:</b> Asp, aspartic; Cys, cysteine; Metal., metallo; Ser, serine; Thr, threonine. Data for this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003769#pbio.2003769.s023" target="_blank">S2 Data</a>.</p

Eukaryotic orthologous groups (KOG) classification of putative <i>Blastocystis</i> subtype (ST) 1 secreted proteins.

<p>Eighty-nine proteins were predicted as secreted based on predicted signal peptide, extracellular localization prediction, and the absence of transmembrane regions. KOG categories were assigned using the Conserved Domain Database online tool. Percentage of secretome proteins of higher-order (inner circle) and lower-order (outer circle) KOG categories are shown. Single letter code(s) for each category are shown in square brackets. Data for this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003769#pbio.2003769.s022" target="_blank">S1 Data</a>.</p