School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland.
PLoS One. 2012;7(4):e35750. doi: 10.1371/journal.pone.0035750. Epub 2012 Apr 26.
Candida orthopsilosis is closely related to the fungal pathogen Candida parapsilosis. However, whereas C. parapsilosis is a major cause of disease in immunosuppressed individuals and in premature neonates, C. orthopsilosis is more rarely associated with infection. We sequenced the C. orthopsilosis genome to facilitate the identification of genes associated with virulence. Here, we report the de novo assembly and annotation of the genome of a Type 2 isolate of C. orthopsilosis. 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 Candida species, together with manual identification of introns. We identified 5700 protein-coding genes in C. orthopsilosis, of which 5570 have an ortholog in C. parapsilosis. The time of divergence between C. orthopsilosis and C. parapsilosis is estimated to be twice as great as that between Candida albicans and Candida dubliniensis. There has been an expansion of the Hyr/Iff family of cell wall genes and the JEN family of monocarboxylic transporters in C. parapsilosis relative to C. orthopsilosis. 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 C. orthopsilosis and C. parapsilosis. We report that TFB3, a component of the general transcription factor TFIIH, undergoes alternative splicing by intron retention in multiple Candida species. We also show that an intein in the vacuolar ATPase gene VMA1 is present in C. orthopsilosis but not C. parapsilosis, and has a patchy distribution in Candida species. Our results suggest that the difference in virulence between C. parapsilosis and C. orthopsilosis may be associated with expansion of gene families.
近平滑念珠菌与真菌病原体近平滑假丝酵母密切相关。然而，虽然 C. parapsilosis 是免疫抑制个体和早产儿中疾病的主要原因，但 C. orthopsilosis 与感染的关联更为罕见。我们对 C. orthopsilosis 基因组进行了测序，以促进鉴定与毒力相关的基因。在这里，我们报告了 C. orthopsilosis 型 2 分离株的从头组装和注释。该序列是通过将下一代测序（454 Life Sciences 和 Illumina）的数据与源自 fosmid 文库的配对末端 Sanger 读数相结合获得的。最终组装包含 8 条染色体上的 12.6 Mb。使用基于 Candida 物种基因组比较分析的自动化管道以及内含子的手动鉴定对基因组进行注释。我们在 C. orthopsilosis 中鉴定出 5700 个编码蛋白的基因，其中 5570 个在 C. parapsilosis 中有同源基因。C. orthopsilosis 和 C. parapsilosis 之间的分化时间估计是 Candida albicans 和 Candida dubliniensis 之间的两倍。与 C. orthopsilosis 相比，C. parapsilosis 中 Hyr/Iff 细胞壁基因家族和 JEN 单羧酸转运蛋白家族有所扩张。我们从一个麦芽糖/半乳糖 O-乙酰基转移酶家族中鉴定出一个基因，该基因通过水平基因转移从细菌起源于 C. orthopsilosis 和 C. parapsilosis 的共同祖先。我们报告说，一般转录因子 TFIIH 的组成部分 TFB3 通过内含子保留在多个 Candida 物种中发生选择性剪接。我们还表明，在 vacuolar ATPase 基因 VMA1 中的内含子存在于 C. orthopsilosis 中，但不存在于 C. parapsilosis 中，并且在 Candida 物种中分布不均匀。我们的结果表明，C. parapsilosis 和 C. orthopsilosis 之间毒力的差异可能与基因家族的扩张有关。
