29 research outputs found
Phylogenetic relationships among <i>Eimeria</i> species and <i>C</i>. <i>cayetanensis</i> based on mitochondrial genome sequences.
<p>NCBI accession numbers are included. The evolutionary relationship between the <i>Eimeria</i> (13), <i>Cyclospora(1)</i> and <i>P</i>.<i>falciparum</i> (1) mitochondrial genomes was inferred using the Maximum Likelihood method with 500 replications for bootstrap analysis. The confidence value for clustering is given as percentage above the branches. The scale bar points to the number of substitutions per site. After analysis, the outgroup branch was removed for clarity. Default parameters in MEGA6 were retained for phylogenetic analysis and tree building.</p
Confirmation of the <i>C</i>. <i>Cayetanensis</i> mt genome sequence.
<p>A) Overlapping PCR fragments used to confirm the <i>C</i>. <i>cayetanenesis</i> mt genome sequence and concatemeric structure. PCR fragments are shown with dotted lines. Forward sequence reads are shown in blue or orange and reverse reads are shown in red or light blue. Terminal grey bands indicate identical sequence regions. B) A 659 bp contig constructed using overlapping junction PCR fragment sequences (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128645#pone.0128645.t002" target="_blank">Table 2</a>) is represented in gray. Diagonal red bars represent portions of the junction PCR product mapping to the ends of the complete <i>C</i>. <i>cayetanensis</i> mt genome. C) WGS reads spanning the junction region in the initial mt assembly. The vertical red lines mark the tail:head junction.</p
Gene arrangement of the <i>C</i>. <i>cayetanensis</i> mt genome.
<p>Predicted genes on the <i>Cyclospora</i> mitochondrial genomes were derived based on ClustalW alignment with the Eimeria gallopavonis (KJ608417). Orange indicates coding genes, blue indicates fragments of LSU rRNA, and yellow indicates fragments of SSU rRNA. Transcriptional direction is indicated by arrowed end.</p
Molecular mechanisms underlying RyR2 (Ca2+ release channel) dysfunction in stress-induced VT
34,146Â bp apicoplast reference genome and consensus sequences from 11 geographical strains used in the multiple alignment to identify genomic changes and clustering analysis. KP866208 was not used in the clustering analysis. Indonesia-1 apicoplast is 34,148 long with a missing base (filled in as N) in 14,602 and a âGGAâ insertion in 7780 base positions. Virginia-1 consensus sequence is 33,625 bases long reflecting coverage gaps. Rhodeisland-1 sequence is 34,132 bases long with gaps at 12,579-80 and 15,372-383. All gaps were filled with N for multiple-alignment and clustering analysis. The base positions are for the Reference Genome. (TIF 105 kb
