Sequence and Analysis of the Genome of the Pathogenic Yeast <em>Candida orthopsilosis</em>

<div><p><em>Candida orthopsilosis</em> is closely related to the fungal pathogen <em>Candida parapsilosis.</em> However, whereas <em>C. parapsilosis</em> is a major cause of disease in immunosuppressed individuals and in premature neonates, <em>C. orthopsilosis</em> is more rarely associated with infection. We sequenced the <em>C. orthopsilosis</em> genome to facilitate the identification of genes associated with virulence. Here, we report the <em>de novo</em> assembly and annotation of the genome of a Type 2 isolate of <em>C. orthopsilosis</em>. The sequence was obtained by combining data from next generation sequencing (454 Life Sciences and Illumina) with paired-end Sanger reads from a fosmid library. The final assembly contains 12.6 Mb on 8 chromosomes. The genome was annotated using an automated pipeline based on comparative analysis of genomes of <em>Candida</em> species, together with manual identification of introns. We identified 5700 protein-coding genes in <em>C. orthopsilosis</em>, of which 5570 have an ortholog in <em>C. parapsilosis.</em> The time of divergence between <em>C. orthopsilosis</em> and <em>C. parapsilosis</em> is estimated to be twice as great as that between <em>Candida albicans</em> and <em>Candida dubliniensis</em>. There has been an expansion of the Hyr/Iff family of cell wall genes and the JEN family of monocarboxylic transporters in <em>C. parapsilosis</em> relative to <em>C. orthopsilosis</em>. We identified one gene from a Maltose/Galactoside O-acetyltransferase family that originated by horizontal gene transfer from a bacterium to the common ancestor of <em>C. orthopsilosis</em> and <em>C. parapsilosis</em>. We report that <em>TFB3</em>, a component of the general transcription factor TFIIH, undergoes alternative splicing by intron retention in multiple <em>Candida</em> species. We also show that an intein in the vacuolar ATPase gene <em>VMA1</em> is present in <em>C. orthopsilosis</em> but not <em>C. parapsilosis</em>, and has a patchy distribution in <em>Candida</em> species. Our results suggest that the difference in virulence between <em>C. parapsilosis</em> and <em>C. orthopsilosis</em> may be associated with expansion of gene families.</p>