中央级公益性科研院所基本科研业务费专项 (HSY201902Q)；中国水产科学研究院基本科研业务费专项 (2020TD43)
Special Project for Basic Scientific Research Business Expenses of Central-level Public Welfare Research Institutes (HSY201902Q); Central Public-interest Scientific Institution Basal Research Fund, CAFS (2020TD43)
为了深入揭示我国鱼类病原菌嗜冷黄杆菌的基因组进化及其致病机制，本实验对嗜冷黄杆菌毒力菌株CH06进行全基因组测序，比较基因组分析并挖掘其毒力相关基因。基因组测序结果显示，CH06的基因组大小为2 836 981 bp，GC含量为32.56%，注释出2 437个编码基因。通过平均核苷酸一致性 (ANI) 分析结果显示，CH06与12株嗜冷黄杆菌的ANI值均高于99%，菌株CH06应属于嗜冷黄杆菌分支。基因组序列分析发现，CH06含有5个插入序列、4个基因岛和3个前噬菌体，揭示这些可移动遗传元件推动了CH06的基因组进化。系统进化树和基因组共线性分析发现，CH06与菌株CSF259-93和FPG101亲缘关系较近。分泌系统分析显示，CH06中存在Ⅰ型分泌系统(type I secretion system，T1SS)和Ⅸ型分泌系统 (T9SS)。通过蛋白结构域特征分析发现，CH06包含56个T9SS效应蛋白和29个双组分系统元件，表明嗜冷黄杆菌可能存在复杂的致病机制和调控机制。本研究对CH06的基因组进化以及毒力相关基因进行分析，为我国鱼类病原嗜冷黄杆菌的进化、多样性及致病机制研究提供参考。
Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease and rainbow trout fry syndrome, is currently an important pathogen causing great economic loss to the salmonid industry worldwide. Recently, the genomic evolution and pathogenic mechanisms of F. psychrophilum have been widely studied in many countries. However, these studies that originated from China are still rarely reported. In order to better understand the genomic evolution and pathogenesis of F. psychrophilum in China, the virulent strain CH06 was subjected to whole genome sequencing and analyzed using comparative genomics, and virulence-associated genes were predicted. The result of whole genome sequencing showed that the CH06 genome consists of a single circular chromosome of 2 836 981 base pairs (bp) harboring 2 437 protein-coding genes with an overall G+C content of 32.56%. The results of ANI analysis showed that ANI values between CH06 and 12 F. psychrophilum strains are higher than 99%, indicating that CH06 belongs to F. psychrophilum. Analysis of the genome sequence reveals that CH06 consists of 5 insertion sequences, 4 genomic islands and 3 prophage sequences, indicating that these mobile genetic elements led to the genome evolution of CH06. Collinear and phylogenetic analysis showed that CH06 is more closely related to CSF259-93 and FPG101. Secretion system analysis showed that CH06 carried type I (T1SS) and type IX (T9SS) secretion system. Among the coding proteins, 56 proteins are predicted to be secreted by the T9SS. Furthermore, CH06 was predicted to encode 11 histidine kinases (HKs) and 16 response regulators (RRs), revealing that CH06 has evolved sophisticated regulation mechanisms to export virulence factors across the bacterial cell envelope to sense and respond to environmental changes. In this study, the genomic evolution and virulence-associated genes of CH06 are analyzed, providing a basis for research on the genomic evolution and pathogenic mechanisms of this fish pathogen in China.