嗜水气单胞菌AH10(CCTCC AB2014155)的全基因组测序及比较分析

Whole-genome sequencing and comparative analysis of Aeromonas hydrophila AH10 (CCTCC AB2014155)

为了解嗜水气单胞菌全基因组信息的结构和功能,对嗜水气单胞菌(Aeromonas hydrophila)AH10(CCTCC保藏号:AB2014155)进行了全基因组测序。将提取的AH10全基因组DNA进行片段化、构建文库后上机测序;将基因组组装后进行注释和比较分析。结果显示:AH10全基因组序列总长度为4.91 Mb,GC含量为61.1%,共预测到4570个基因,3351个基因具有明确的生物学功能。共找到2592个基因具有直系同源族(cluster of orthologous groups,COG)分类,1281个与代谢通路有关的基因,基因组岛31个。比较基因组学研究发现:AH10比对到SNP位点102481个,与Aeromonas hydrophila YL17基因结构共线性最好,与美国来源的嗜水气单胞菌标准菌株Aeromonas hydrophila ATCC 7966具有较近的亲缘关系,AH10的致病性与溶血素基因hly(hemolysin gene)、气溶素基因aer(aerolysin gene)、黏附素基因ahal(major adhesion gene)、丝氨酸蛋白酶基因ahp(serine protease gene)、细胞兴奋性肠毒素基因alt(cytotonic enterotoxin gene)密切相关。这些基因在嗜水气单胞菌中同源性较高。存在自体诱导物信号分子-2(autoinducer-2)与合成信号分子酶基因(signal molecule synthetase gene,ahy Ⅰ)和转录调节蛋白基因(transcriptional regular gene,Ahy R)群体感应(quorum sensing,QS)系统,不存在Ⅲ型分泌系统(type Ⅲ secretion system,TTSS)。通过对AH10全基因组序列进行较为全面的注释和比较统计分析,为嗜水气单胞菌的分子生物学研究提供理论支持。

Aeromonas hydrophila exists widely in aquatic environments throughout the world. It is highly pathogenic and infection with this bacterium entails extremely high mortality. To facilitate the prevention and treatment of the diseases caused by A. hydrophila, we sequenced the whole genome of A. hydrophila AH10 （CCTCC AB2014155）, to fully understand its information structure and functions and to provide a basis for future molecular pathology research. Genomic DNA was extracted from strain AH10, and a library was constructed and sequenced. The raw data were filtered and their quality was assessed, the sequence was assembled, and the genome was annotated and analyzed comparatively. The full-length genome of strain AH10 is 4.91 Mb, with a G＋C content of 61.1%, and encodes 4570 predicted genes, including 3351 genes with a clear biological function, 2592 genes found in the Clusters of Orthologous Groups （COG） database, 1281 genes related to metabolic pathways, and 31 genomic islands. The study of comparative genomics showed that AH10 has 102481 single-nucleotide polymorphisms （SNPs）, 402 insertions/deletions, and a linear genomic organization most similar to A. hydrophila YL17. AH10 is closely related to A. hydrophila ATCC7966, the standard strain in the USA. The pathogenicity of AH 10 is closely associated with the hemolysin gene （hly）, aerolysin gene （aer）, major adhesion gene （ahal）, serine protease gene （ahp）, and cytotonic enterotoxin gene （alt）. These genes are highly homologous in different strains. Autoinducer-2 （AI-2） quorum sensing （QS） and AhyI/AhyR QS are found in AH10, but there is no type III secretion system （TTSS）. With a comparative analysis, we demonstrate the specificity of the A10 genomic structure, its SNPs, and the pathogenic system differences in different strain. Our analysis not only provides a guide to distinguishing the specificities of different species, but also a reference for the analysis of the genomic information of A. hydrophila. Research into the A. hydrophila genome has accelerated related studies of its pathogenicity. Identify- ing the causes of disease requires that the accuracy of their clinical diagnosis be effectively improved. This, in turn, will offer clues to their pathogenic mechanisms in humans. The study ofAeromonas hydrophila genome also provides the foundation to the research of proteomics. According to the specific functional areas of protein conservative sequences, setting up a corresponding protein database can help to quickly find the protein function area. In this way, we can not only study the cell wall composition and the functions of the membrane proteins and secreted proteins ofA. hydrophila, but can also predict the functions of related proteins based on genomic information. This research provides unlimited opportunities for the development of new drugs that not only effectively avoid the generation of drug resistance, but also circumvent the abuse of antibiotics, thus providing people with a healthy environment. Studies of the A. hydrophila genome should also promote vaccine research. With the comparison of homologous sequences, effective antigen can be rapidly identified and vaccines prepared, efficiently reducing the incidence of disease. Genomic information has potentially wide applications, and its use in the prevention and treatment of the diseases caused by A. hydrophila will continue to increase.