Additional file 1 of Circlator: automated circularization of genome assemblies using long sequencing reads

Supplementary text and figures supporting the main text. (PDF 803 kb

Additional file 2 of Circlator: automated circularization of genome assemblies using long sequencing reads

An Excel spreadsheet containing Tables S1–5 and S7. Table S1. NCTC project IDs and accession numbers for the PacBio bacterial samples Table S2. A complete breakdown of results on the PacBio bacterial samples (an expanded version of Table 1) Table S3. QUAST results on the PacBio bacterial samples Table S4. Results of testing user-defined parameters for all NCTC data sets Table S5. Results of testing user-defined parameters for the MinION data set Table S7. Run time and memory usage for all data sets (excluding those in Tables S4 and S5). (XLS 305 kb

Additional file 3 of Circlator: automated circularization of genome assemblies using long sequencing reads

A gzipped archive containing all scripts, corrected reads, assemblies, and other data necessary to reproduce the results. (gzipped archive 11GB

Additional file 8:Figure S6. of Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

RAxML Phylogenetic trees reconstructed with parsimony for the five homologous sequences contained in the mgp operon and the MgPar regions of Mycoplasma genitalium genomes. Numbers over the scale line represent SNPs. Clustering of sequencing by sample or genomic location has been emphasized by displacing rectangles within the metadata columns. (PDF 539 kb

Additional file 3: Figure S1. of Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

Dendogram output bipartitions tangled trees representing changes on topology before (left) and after (right) running Gubbins. (PDF 124 kb

Additional file 7: Figure S5. of Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

RAxML Phylogenetic trees reconstructed with parsimony for the five homologous repeat sequences contained in the mgp operon and the MgPar regions for isolates of the same patient. Sequences were coloured when they were not the same in the three isolates. Numbers over the scale line represent SNPs. For the EF sequences, as an example, all SNPs with respect to the G37T EF sequence at the mgp operon location are plotted after reconstruction on the right. As identical samples contain identical SNPs profiles, it is easy to spot blocks of sequence replacements due to recombination. One reciprocal recombination is marked with a cross for the two locations where it happened within the same sample. Other blocks do not have reciprocal counterparts, a sign of multiple recombination steps or a unique non-reciprocal recombination event. (PDF 195 kb

Additional file 4: Figure S2. of Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

Bootstrapping values for the M. genitalum phylogenetic tree represented in Fig. 1. (PDF 852 kb

Additional file 6: Figure S4. of Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

Sequence homology representation of the mgpB and mgpC genes repeats positions and their homologous sequences in MgPar regions. Homologue repeat positions in each of the different structured MgPar region are highlighted in the same colours. All based on the M. genitalium G37T genome. Dotted vertical lines represent restriction fragments and hatched boxes represents intervening sequences that are unusually A-T rich and contain stop codons [15]. (PDF 114 kb

Knockdown analysis of <i>CPIJ005623</i> in <i>C. quinquefasciatus</i> Pel females.

<p><b>A</b>. Diagram representing experimental design of knockdown (KD) experiments, d-day post pupal eclosion, BF-Blood feed, T-time point. <b>B</b>. KD assessment of i<i>CPIJ005623</i> in Pel ovaries. Reduction of <i>CPIJ005623</i> mRNA levels similar to uninfected ovaries was observed in infected ovaries when CI developmental progression was seen. <b>C</b>. Increased early embryo (stageI) developmental arrest is detected after i<i>CPIJ005623</i> in compatible Pel male cross.</p

Knockdown analysis of <i>CPIJ005623</i> in <i>C. molestus</i> Italy females.

<p><b>A</b>. Diagram representing experimental design of knockdown (KD) experiments, d-day post pupal eclosion, T-time point. <b>B</b>. KD assessment of i<i>CPIJ005623</i> in Italy ovaries. Reduction of <i>CPIJ005623</i> mRNA levels similar to uninfected ovaries was observed in infected ovaries when CI developmental progression was seen. <b>C</b>. Picture examples of developmental progression in <i>Culex</i> embryos undergoing CI, Stage I: early arrest, Stage II and III: late arrest. <b>D</b>. Increased percentage of unhatched embryos mimic a reduced rescue function. Also increased early embryo (stageI) developmental arrest is detected after i<i>CPIJ005623</i> in compatible Italy male cross.</p