LGTs with large variations in codon bias among their orthologs.

<p>(A) CAI scores of orthologues to LmjF.15.0740, and the fate of the LGT in genus <i>Leishmania</i>. The average CAI score of LmjL.15.0740 and LtrX.15.0740 is significantly lower than the average CAI score of the other orthologs to LmjF.15.0740 (p<0,001). Frame shift indels and stop codons in LmjL.15.0740 and LtrX.15.0740, as well as major in-frame indels in subgenus <i>Viannia</i> and <i>mexicana-</i>complex are indicated in the phylogenetic tree. (B) CAI scores of orthologues to LmjF.23.0260, and the fate of the LGT in genus <i>Leishmania</i>. The average CAI scores of orthologs to LmjF.23.0260 in subgenus <i>Viannia</i> is significantly lower than the average CAI scores of the other orthologs to LmjF.23.0260 (p<0,001). Major in-frame indels, frame shift indels and stop codons in all orthologs of subgenus <i>Viannia</i>, as well as stop codon in <i>L</i>. <i>tarentolae</i> are indicated in the phylogenetic tree. (C) CAI scores of orthologues to LmjF.36.0260, and the fate of the LGT in genus <i>Leishmania</i>. The average CAI scores of orthologs to LmjF.36.0260 in subgenus <i>Viannia</i> is significantly lower than the average CAI scores of the other orthologs to LmjF.23.0260 (p<0,001). LamH.36.0260 displays the lowest CAI score among orthologs of subgenus <i>Leishmania</i>. Major in-frame indels contributing to divergence of orthologs of subgenus <i>Viannia</i>, frame shift indels and stop codons in LamH.36.0260 and gene loss in <i>L</i>. <i>tropica</i> are indicated in the phylogenetic tree. Significance in panel A-C was calculated with a pooled two-sample t-test.</p

Average K_a/K_s ratios between the LGTs.

<p>The average K_a/K_s ratios for each of the LGTs and reference genes between strains. The numbers under the bars in represent the LGTs as listed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004326#pntd.0004326.g001" target="_blank">Fig 1A</a>. The boxes under the bars shows the fate of the corresponding LGT in genus <i>Leishmania</i>–classified as gene acquisition, degradation, acquirement of stop codons and indels respectively. Four LGTs (LmjF.03.0390, LmjF.15.0740, LmjF.23.0260 and LmjF.36.0260) have K_a/K_s ratios ≥1, and these LGTs have frame shift- and major in-frame indels, and contain stop codons.</p

Consensus trees with orthologues to LGTs.

<p><b>(A)</b> Phylogenetic tree (congruent with the systematics proposed by Fraga and co-workers from 2010) showing the presence of LGT orthologs in five sequenced genomes of <i>Leishmania</i> and the sequenced genomes of <i>Trypanosoma cruzi</i> and <i>Trypanosoma bruceii</i>. The number of acquired genes (green boxes) and lost genes (red boxes) are presented numerically. (Red boxes*) refers to gene loss of orthologs to universal trypanosomatid LGTs. <b>(B)</b> Consensus tree summarizing the agreement between the phylogenetic trees for the twenty-three LGTs, investigated in detail in this study. Genus <i>Leishmania</i> is divided into the three subgenera <i>Viannia</i>, <i>Sauroleishamania</i> (here represented by only one species and one strain–<i>L</i>. <i>tarentolae</i>) and <i>Leishmania</i>. Subgenera <i>Viannia</i> and <i>Leishmania</i> are further divided into several complexes, and the topology of the consensus tree is completely congruent with the systematics proposed by Fraga and co-workers (2010). The fate of each LGT is illustrated with coloured boxes. “Gene acquisition” (green boxes) and “Gene loss” (red boxes) are based on presence of orthologs in published genomes or amplification of orthologs with PCR. Insertions/deletions (indels) (blue and orange boxes) and presence of stop codons (brown boxes) have been determined by manual inspections of alignments of obtained sequences and are relative to the gene sequence in <i>L</i>. <i>major</i> F. “In-frame Indels” (blue boxes) are insertions or deletions of more than 50 nucleotides not causing any frame-shift. “Frame-shift Indels” (orange boxes) are insertions or deletions that causes frame-shifts. Remnants (black boxes) of orthologs have been identified with synteny analyses (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004326#sec005" target="_blank">Material and Methods</a>).</p

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原著和名: [記載なし]科名: マメ科 = Leguminosae採集地: タイ チャンタブリ付近山地 (タイ国 チャンタブリ付近山地)採集日: 1984/11/2採集者: 萩庭丈壽整理番号: JH049857国立科学博物館整理番号: TNS-VS-99478

Additional file 3: of Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes

Distribution of base variation for the ten C. parvum single cell genomes relative the IowaII reference genome. Each line represents a single cell genome and % reads denote the fraction of the reads with bases that differ from the reference. Positions that, in the SNP analysis, were detected in all cells were excluded from the plot. (PDF 29 kb