Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing
Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing
复制标题
单分子实时测序重测序多重耐药铜绿假单胞菌 PA1 的基因组分析
DOI：
10.1042/bsr20160282
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发表时间：
2016-12-01
影响因子：
4
通讯作者：
Lu, Shuguang
中科院分区：
文献类型：
--
作者：
Li, Gang;Shen, Mengyu;Lu, Shuguang
单分子实时测序(SMRT)技术作为第三代测序技术，具有较长的读数长度，非常适合于测序和从头组装。在本研究中，利用SMRT技术对铜绿假单胞菌PA1进行了鉴定和重测序。PA1还进行了基因组、比较和泛基因组分析。多药耐药株PA1的基因组为6,498,072个核苷酸，序列类型为ST-782。PA1的基因组也被可视化，结果显示了一般基因组注释、毒力因子、调节蛋白(RPS)、分泌系统蛋白、II型毒素-抗毒素(T-A)对和基因组岛的细节。全基因组比较分析表明，PA1与其他铜绿假单胞菌菌株有相似之处，但在水平基因转移(HGT)区域，如前驱体和基因组岛方面有所不同。基于16S rRNA序列的系统发育分析表明，PA1与PAO1有密切的亲缘关系，铜绿假单胞菌可分为两大类群。铜绿假单胞菌的全基因组由大约4000个基因的核心基因组和至少6600个基因的副基因组组成。本研究对PA1基因组进行了详细、直观和比较的分析，以加强我们对这种臭名昭著的病原体的了解。
As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin-antitoxin (T-A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.