Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis

Additional file 1:

Examples of reported incidences of interkingdom gene transfer between prokaryotes and fungi. One Kluyveromyces lactis gene (KLLA0D19949g) previously highlighted [22], been omitted as it is no longer recognized as an ORF. Y. lipolytica genes denoted with a * and ^ indicate possible gene duplications after HGT.

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Additional file 2:

GenBank accession numbers for PR (A) and PhzF (B) sequences used in this analysis. Species identified with an * use the accession numbers created by the Broad Institute [66] or the Wellcome Trust Sanger Institute [67].

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Additional file 3:

Gene order around Pezizomycotina proline racemase genes. Species names and identifiers are shown in each box. PR genes are labeled. Gene identifiers relate to annotations from the Broad Institute. Clade letters in parentheses correspond to those in Figure 2. There is evidence for conserved gene synteny between some species such as A. oryzae and A. flavus (clade-C). A. flavus/A. terreus and N. fischeri/A. fumigatus in the Metazoan/Pezizomycotina clade (B). The A. flavus gene denoted by a * is absent from the Broad gene set but we were able to locate it with a BlastX search.

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Additional file 4:

Correspondence analysis of codon usage. Correspondence analysis of codon usage in the C. parapsilosis (1), U. maydis (2), M. globosa (3), A. flavus (4), A. niger (5), G. zeae (6), A. oryzae (7), P. nodorum (8), and S. pombe (9) genomes. Transferred genes are highlighted. All have a codon usage similar to the rest of their genomes which is unsurprising as transferred genes have been shown to ameliorate their codon usage to their hosts [79].

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Additional file 5:

Correspondence analysis of codon usage in the proline racemase gene family analyzed in this study. Major groups are color-coded. The C. parapsilosis PR gene has a codon usage pattern distinct from other fungal species in this analysis. It is also quite distinct from the Burkholderia (β-proteobacteria) species, which were found to be its phylogenetic neighbors.

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Additional file 6:

Trees for approximately unbiased test for PhzF homologs. Tree A is the original unconstrained topology, which groups C. parapsilosis with proteobacteria. Topology B is a constrained tree that places S. pombe outside the Saccharomycotina clade. Topologies C-H are constrained and place C. parapsilosis amongst the other Saccharomycotina species. Log likelihood scores for each tree are given. To assess the likelihood that any differences in topology between the inferred trees is no more significant that that expected by chance, we performed the approximately unbiased test. The AU test shows that the unconstrained tree receives the optimal likelihood tree score. Furthermore, the differences in likelihood scores when compared to the constrained trees are significant (P < 0.05). Therefore based on these results the placement of the C. parapsilosis homolog in the proteobacterial clade to the exclusion of the Saccharomycotina and S. pombe within the Saccharomycotina clade is significant.

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Additional file 7:

PhzF spectral analysis. Analysis was performed on the Saccharomycotina and selected proteobacterial clade. Bars above the x-axis represent frequency of support for each split. Bars below the x-axis represent the sum of all corresponding conflicts. Clad grams above columns represent the corresponding splits in the data. There is no support for the placement of C. parapsilosis with the other Saccharomycotina species.

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Additional file 8:

Correspondence analysis of codon usage in the PhzF gene family analyzed in this study. Major groups are color-coded. The C. parapsilosis PhzF gene has a codon usage pattern similar to other CTG species analyzed. It is quite distinct from the proteobacterial species that were found to be its phylogenetic neighbors.

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