PDF(Pubmed)
Abstract：
Unlike most pathogenic oomycetes, Pythium insidiosum infects humans and animals instead of plants. P. insidiosum has three clinically relevant genotypes/clades that cause a severe disease called pythiosis. To develop strategies for infection control, it is necessary to understand the biology and pathogenesis of this pathogen. Investigating the evolutionary mechanisms behind the host-specific adaptation is vital, and comparative genomic analysis can help with this. To facilitate genomic analysis, an online bioinformatics tool called P. insidiosum (Pins) Gene Table v2.0 was developed. This tool includes genomic data from 37 genetically diverse P. insidiosum strains and four related species. The database contains 732,686 genes, grouped into 80,061 unique clusters and further divided into core and variable categories at genus, species, and genotype levels. A high-resolution phylogenomic relationship among P. insidiosum strains and other oomycetes was projected through hierarchical clustering and core gene analyses. 3156 P. insidiosum-specific genes were shared among all genotypes and may be responsible for causing disease in humans and animals. After comparing these species-specific genes to the MvirDB database, 112 had significant matches with 66 known virulence proteins, some of which might be involved in vascular occlusion, which is a pathological feature of pythiosis. The correlation of genotypes, geographic origins, and affected hosts of P. insidiosum suggests that clade-I strains are more specific to animals, while clade-II/III strains are more specific to humans. The clade-specific genes might link to host preference. In summary, Pins Gene Table v2.0 is a comprehensive genome database accessible to users with minimal bioinformatics experience for the analysis of P. insidiosum genomes.
摘要：
与大多数致病卵菌不同，里腐霉感染人类和动物而不是植物。阴间假单胞菌具有三种临床相关的基因型/进化枝,其引起称为化脓症的严重疾病。制定感染控制策略，有必要了解这种病原体的生物学和发病机理。研究宿主特异性适应背后的进化机制至关重要，和比较基因组分析可以帮助这一点。为了促进基因组分析，开发了一种名为P.insidiosum（Pins）基因表v2.0的在线生物信息学工具。该工具包括来自37种遗传多样性的阴阳假单胞菌菌株和4种相关物种的基因组数据。该数据库包含732,686个基因，分为80,061个独特的簇，并进一步分为属的核心和可变类别，物种,和基因型水平。通过分层聚类和核心基因分析，预测了泥炭菌株和其他卵菌之间的高分辨率系统基因组关系。在所有基因型中共有3156个艾氏杆菌特异性基因，可能是导致人类和动物疾病的原因。在将这些物种特异性基因与MvirDB数据库进行比较后，112与66种已知毒力蛋白有显著匹配，其中一些可能与血管闭塞有关，这是化脓症的病理特征。基因型的相关性，地理起源,和受影响的念珠菌宿主表明，进化枝I菌株对动物更有特异性，而进化枝II/III菌株对人类更有特异性。进化枝特异性基因可能与宿主偏好相关。总之,PinsGeneTablev2.0是一个全面的基因组数据库，可供具有最少生物信息学经验的用户访问，用于分析阴阳假单胞菌基因组。
