Sequence and Analysis of the Genome of the Pathogenic Yeast Candida orthopsilosis

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.类近平滑念珠菌（Candida orthopsilosis）与真菌致病菌近平滑念珠菌（Candida parapsilosis）亲缘关系密切。然而，近平滑念珠菌是免疫功能低下人群及早产儿感染的主要致病菌，而类近平滑念珠菌的致病检出率则相对较低。为助力与毒力相关的基因鉴定研究，本研究对类近平滑念珠菌的基因组进行了测序。本研究报道一株类近平滑念珠菌2型分离株的从头组装（de novo assembly）及基因组注释结果。该基因组序列通过结合下一代测序（next generation sequencing，涵盖454生命科学公司与Illumina平台数据）及黏粒文库（fosmid library）的双末端桑格（Sanger）测序读段获取。最终组装结果显示，该菌株基因组包含8条染色体，总长度为12.6 Mb。基因组注释流程基于念珠菌属物种的基因组比较分析构建自动化注释管线，并辅以内含子的人工鉴定步骤。本研究在类近平滑念珠菌中共鉴定出5700个蛋白编码基因，其中5570个基因在近平滑念珠菌中存在直向同源基因（ortholog）。类近平滑念珠菌与近平滑念珠菌的分化时间估算值约为白念珠菌（Candida albicans）与都柏林念珠菌（Candida dubliniensis）分化时间的两倍。相较于类近平滑念珠菌，近平滑念珠菌的细胞壁基因Hyr/Iff家族以及单羧酸转运蛋白JEN家族均发生了基因扩张。本研究还鉴定出一个属于麦芽糖/半乳糖苷O-乙酰转移酶家族的基因，该基因通过水平基因转移（horizontal gene transfer）从细菌进入类近平滑念珠菌与近平滑念珠菌的共同祖先基因组。本研究发现，通用转录因子TFIIH的组成亚基TFB3在多种念珠菌属物种中均存在通过内含子保留方式发生的可变剪接（alternative splicing）现象。本研究同时证实，液泡ATP酶基因VMA1中的内含肽（intein）仅存在于类近平滑念珠菌中，而近平滑念珠菌并无该序列；且该内含肽在念珠菌属物种中呈现散在分布的特征。本研究结果表明，近平滑念珠菌与类近平滑念珠菌之间的毒力差异，可能与基因家族扩张事件存在关联。