RQUA tree datasets

File - Description ## Within MLanalysis ## *iqtree.log logfile from IQTREE analysis *IQtreefile.nex IQTREE output tree *seqs.fasta sequences unaligned *mafft.fasta sequences aligned with mafft *mafft.bmge_masked.fasta BMGE masked alignment ## Within TopologyTests ## *.log IQTREE logfile from site likelihood inference *.sitelh site likelihood file from IQTREE *_ContrainTrees_BootstrapTrees.tre ML cosntrain trees *_consel.catpv output from CONSEL ## FILES ## RQUA_full_datasets/MLanalysis rqua.iqtree.log rqua.IQtreefile.nex rqua.mafft.bmge_masked.fasta rqua.mafft.fasta rqua.seqs.fasta RQUA_full_datasets/TopologyTests RQUA_fulldataset_consel.catpv RQUA_fulldataset_ContrainTress_BootstrapTrees.tre RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.log RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.sitelh RQUA_GroupA_datasets/MLanalysis rqua.GroupA.IQtree.log rqua.GroupA.IQtree.treefile rqua.GroupA.mafft.bmge_masked.fasta rqua.GroupA.mafft.fasta rqua.GroupA.seqs.fasta RQUA_GroupA_datasets/TopologyTests RQUA_GroupA_consel.catpv RQUA_GroupA_ConstrainTrees.tre RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.log RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.sitelh RQUA_GroupB_datasets/MLanalysis rqua.GroupB.IQtree.log rqua.GroupB.IQtree.treefile rqua.GroupB.mafft.bmge_masked.fasta rqua.GroupB.mafft.fasta rqua.GroupB.seqs.fasta RQUA_GroupB_datasets/TopologyTests RQUA_GroupB_consel.catpv RQUA_GroupB_ConstrainTrees.tre RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.log RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.sitel

alphaprotebacteria_datasets

Alignment file and raw tree file for alphaproteobacteria phylogeny. See Figure 2 - figure supplement 2

Data Sources

Fasta files with assembled transcriptomes of Carpediemonas-like organism

Protein alignments

Alignments of organellar protein

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

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

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