Journal of Fisheries Research ›› 2023, Vol. 45 ›› Issue (5): 415-426.DOI: 10.14012/j.cnki.fjsc.2023.05.001
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LI Chenrui(), XU Rongliang, ZHANG Xiaoxu, CHEN Dongping, QIU Yuyang, CHEN Weiqin, QIN Yingxue*()
Received:
2023-03-08
Online:
2023-10-25
Published:
2023-10-07
李辰睿(), 徐荣亮, 张小旭, 陈东萍, 邱于洋, 陈伟琴, 覃映雪*()
通讯作者:
覃映雪(1976—),女,教授,硕士生导师,研究方向为水生动物病原微生物。E-mail:作者简介:
李辰睿(2001—),女,本科,研究方向为水生动物医学。E-mail:1091222815@qq.com
基金资助:
CLC Number:
LI Chenrui, XU Rongliang, ZHANG Xiaoxu, CHEN Dongping, QIU Yuyang, CHEN Weiqin, QIN Yingxue. Genome analysis of pathogenic Vibrio harveyi strain TS-628[J]. Journal of Fisheries Research, 2023, 45(5): 415-426.
李辰睿, 徐荣亮, 张小旭, 陈东萍, 邱于洋, 陈伟琴, 覃映雪. 病原哈维氏弧菌(Vibrio harveyi)TS-628菌株基因组分析[J]. 渔业研究, 2023, 45(5): 415-426.
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URL: http://www.hyyysci.com/EN/10.14012/j.cnki.fjsc.2023.05.001
Fig.1 GC% and sequencing depth profiles of strains TS-628 Notes:The abscissa of the scatter chart is the GC content,and the ordinate is the read coverage depth;the histogram at right and up sides shows the frequency distribution of sliding window of GC content and sequencing depth,respectively.
样品名称 Sample name | 染色体数量 Chromosome no. | 质粒数量 Plasmid no. | 基因长度/bp Genome size | GC含量/% GC content |
---|---|---|---|---|
哈维氏弧菌 V.harveyi | 2 | 2 | 6 151 198 | 44.68 |
Tab.1 The genome assembly results of strains TS-628
样品名称 Sample name | 染色体数量 Chromosome no. | 质粒数量 Plasmid no. | 基因长度/bp Genome size | GC含量/% GC content |
---|---|---|---|---|
哈维氏弧菌 V.harveyi | 2 | 2 | 6 151 198 | 44.68 |
程序集 Assembly ID | 序列号 Sequence ID | 样品名称 Sample name | 长度/bp Length | GC含量/% GC content | 组成信息 Bases statistics | 序列类型 Sequence type |
---|---|---|---|---|---|---|
染色体1 Chromosome 1 | Scaffold 1 | V.harveyi | 3 574 667 | 44.95 | A:980761;T:986964; G:80357;C:803371 | Chromosome |
染色体2 Chromosome 2 | Scaffold 2 | V.harveyi | 2 292 642 | 44.76 | A:633107;T:633402; G:514578;C:511555 | Chromosome |
质粒A Plasmid A | Scaffold 3 | V.harveyi | 217 554 | 39.41 | A:61456;T:70356; G:43418;C:42324 | Known-Plasmid |
质粒B Plasmid B | Scaffold 4 | V.harveyi | 66 335 | 44.56 | A:17821;T:18954; G:15310;C:14250 | New-Plasmid |
Tab.2 The genome assembly details of strains TS-628
程序集 Assembly ID | 序列号 Sequence ID | 样品名称 Sample name | 长度/bp Length | GC含量/% GC content | 组成信息 Bases statistics | 序列类型 Sequence type |
---|---|---|---|---|---|---|
染色体1 Chromosome 1 | Scaffold 1 | V.harveyi | 3 574 667 | 44.95 | A:980761;T:986964; G:80357;C:803371 | Chromosome |
染色体2 Chromosome 2 | Scaffold 2 | V.harveyi | 2 292 642 | 44.76 | A:633107;T:633402; G:514578;C:511555 | Chromosome |
质粒A Plasmid A | Scaffold 3 | V.harveyi | 217 554 | 39.41 | A:61456;T:70356; G:43418;C:42324 | Known-Plasmid |
质粒B Plasmid B | Scaffold 4 | V.harveyi | 66 335 | 44.56 | A:17821;T:18954; G:15310;C:14250 | New-Plasmid |
Fig.2 The CGView map of genome Notes:Figture 2A is chromosome 1;Figture 2B is chromosome 2;Figture 2C is plasmid A;Figture 2D is plasmid B.From the inner circle to the outer circle,the first circle represents the total length of the genome;the second circle represents the GC skeleton,where green represents G-C>0,while purple represents the opposite,the intersection of green and purple represents the start point and end point of replication,respectively;the black in the third circle indicates the GC content,and the protruding part of the peak indicates that the GC content in this region is higher than the average GC content of the whole genome,while the opposite is true inward;the fourth and fifth circles respectively represent genes on the positive and negative chains,including tRNA,rRNA,CDS and other genes.
样品名称 Sample name | 类别1 Level 1 | 类别2 Level 2 | 基因数量 Gene no. | 类别1 Level 1 | 类别2 Level 2 | 基因数量 Gene no. | |
---|---|---|---|---|---|---|---|
防御性毒力因子 | 应激蛋白 | 13 | 攻击性毒力因子 | 入侵类 | 13 | ||
哈维氏弧菌 V.harveyi | 非特异性毒力因子 | 铁吸收系统 | 130 | 防御性毒力因子 | 相位变异 | 9 | |
防御性毒力因子 | 抗吞噬类 | 36 | 防御性毒力因子 | 抗血清 | 11 | ||
毒力调控相关基因 | 调控相关 | 35 | 非特异性毒力因子 | 镁吸收系统 | 4 | ||
攻击性毒力因子 | 分泌系统 | 107 | 防御性毒力因子 | 补体蛋白酶 | 2 | ||
攻击性毒力因子 | 附着类 | 132 | 攻击性毒力因子 | 毒素 | 30 |
Tab.3 The prediction and classification of virulence genes
样品名称 Sample name | 类别1 Level 1 | 类别2 Level 2 | 基因数量 Gene no. | 类别1 Level 1 | 类别2 Level 2 | 基因数量 Gene no. | |
---|---|---|---|---|---|---|---|
防御性毒力因子 | 应激蛋白 | 13 | 攻击性毒力因子 | 入侵类 | 13 | ||
哈维氏弧菌 V.harveyi | 非特异性毒力因子 | 铁吸收系统 | 130 | 防御性毒力因子 | 相位变异 | 9 | |
防御性毒力因子 | 抗吞噬类 | 36 | 防御性毒力因子 | 抗血清 | 11 | ||
毒力调控相关基因 | 调控相关 | 35 | 非特异性毒力因子 | 镁吸收系统 | 4 | ||
攻击性毒力因子 | 分泌系统 | 107 | 防御性毒力因子 | 补体蛋白酶 | 2 | ||
攻击性毒力因子 | 附着类 | 132 | 攻击性毒力因子 | 毒素 | 30 |
样品名称 Sample name | 类型1 Type Ⅰ | 类型2 Type Ⅱ | 类型3 Type Ⅲ | 类型4 Type Ⅳ | 类型5 Type Ⅴ | 类型6 Type Ⅵ | Sec-SRP型 Sec-SRP | Tat型 Tat | 基因总数 Total gene no. |
---|---|---|---|---|---|---|---|---|---|
V.harveyi | 1 | 12 | 17 | 1 | 0 | 7 | 13 | 3 | 54 |
Tab.4 The classification and statistics of secretory system
样品名称 Sample name | 类型1 Type Ⅰ | 类型2 Type Ⅱ | 类型3 Type Ⅲ | 类型4 Type Ⅳ | 类型5 Type Ⅴ | 类型6 Type Ⅵ | Sec-SRP型 Sec-SRP | Tat型 Tat | 基因总数 Total gene no. |
---|---|---|---|---|---|---|---|---|---|
V.harveyi | 1 | 12 | 17 | 1 | 0 | 7 | 13 | 3 | 54 |
Fig.5 The secretory pathway Notes:The secretory system pathway diagram is a graphical representation of all secretory systems in each sample.The red box marks the genes related to the secretion system predicted in the sample.
样品名称 Sample name | 调控基因数量 Gene no.of regulator | 传感基因数量 Gene no.of sensor | 混合基因数量 Gene no.of hybrid |
---|---|---|---|
V.harveyi | 149 | 63 | 30 |
Tab.5 The statistics of two-component regulation classification
样品名称 Sample name | 调控基因数量 Gene no.of regulator | 传感基因数量 Gene no.of sensor | 混合基因数量 Gene no.of hybrid |
---|---|---|---|
V.harveyi | 149 | 63 | 30 |
菌株 Strains | 菌株来源 Source | 基因 长度/bp Genome length | GC 含量/% GC content | 染色体 数量 Chromosome no. | 质粒 数量 Plasmid no. | 主要毒力基因种类 Major virulence gene species |
---|---|---|---|---|---|---|
TS-628(PRJNA874896) | 青石斑鱼 | 6 151 198 | 44.68 | 2 | 2 | 附着类、铁摄取、分泌类 |
QT-520(PRJNA340970) | 卵形鲳鲹 | 6 070 846 | 45.05 | 2 | 3 | 附着类、抗吞噬类、毒素 |
345(PRJNA418027) | 龙胆石斑 | 6 185 822 | 44.76 | 2 | 2 | 附着类、铁摄取、运动性、分泌类 |
Tab.6 Comparative analysis table of the main virulence factors of 3 strains of V.harveyi
菌株 Strains | 菌株来源 Source | 基因 长度/bp Genome length | GC 含量/% GC content | 染色体 数量 Chromosome no. | 质粒 数量 Plasmid no. | 主要毒力基因种类 Major virulence gene species |
---|---|---|---|---|---|---|
TS-628(PRJNA874896) | 青石斑鱼 | 6 151 198 | 44.68 | 2 | 2 | 附着类、铁摄取、分泌类 |
QT-520(PRJNA340970) | 卵形鲳鲹 | 6 070 846 | 45.05 | 2 | 3 | 附着类、抗吞噬类、毒素 |
345(PRJNA418027) | 龙胆石斑 | 6 185 822 | 44.76 | 2 | 2 | 附着类、铁摄取、运动性、分泌类 |
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