一株鱼源致病性嗜水气单胞菌XDMG的全基因组测序及比较基因组分析

doi:10.13560/j.cnki.biotech.bull.1985.2022-1507

摘要/Abstract

摘要：

探索致病性嗜水气单胞菌XDMG侵染鱼类的作用机制，对其基因组结构、功能和进化关系等基本特征与参考菌株进行比较分析。对嗜水气单胞菌XDMG进行全基因组测序，利用Newbler、SeqMan、Glimmer等软件对测序得到的原始数据进行组装、拼接、注释，再基于看家基因构建系统发育树分析，确定进化关系的基础上，与4株不同地区的嗜水气单胞菌进行基因组的比较分析。嗜水气单胞菌XDMG全基因组序列长4.99 Mb，GC含量为60.84%，共预测到4 935个编码基因，有明确功能的基因有4 137个，发现99个tRNA和3个rRNA；4 061个基因具有直系同源族分类，3 228个基因与基因本体论相关，与代谢通路有关的基因有2 663个；在嗜水气单胞菌XDMG基因组中预测了101个串联重复序列和14个基因岛，具有 AI-1、AI-2和AI-3 三种QS系统的相关基因。通过基因组对比分析，嗜水气单胞菌XDMG与国内嗜水气单胞菌J-1菌株和美国来源的嗜水气单胞菌AL09_71菌株具有较近的亲缘关系；在毒力基因、外膜蛋白和O-抗原基因簇的比较中与美国来源的嗜水气单胞菌AL09_71保守性更高。通过对嗜水气单胞菌XDMG基因组进行较为全面的基因组注释及基因组的比较分析，为嗜水气单胞菌功能基因组学、基因工程疫苗方面的研究提供基础数据。

关键词: 嗜水气单胞菌, 全基因组测序, 毒力基因, 外膜蛋白, O-抗原

Abstract:

The objectives of this study are to explore the mechanism of pathogenic Aeromonas hydrophila XDMG strain infecting fish, and to compare its genome structure, function and evolutionary relationship with the reference strain. The whole genome of A. hydrophila XDMG strain was sequenced, and the original data obtained by sequencing were assembled, spliced and annotated using Newbler, SeqMan, Glimmer and other software. Based on the constructing phylogenetic tree analysis from housekeeping genes and determining evolutionary relationships, the genomes of A. hydrophila were compared with those of four A. hydrophila strains in different regions. The complete genome sequence of A. hydrophila XDMG strain was 4.99 Mb in length and the GC content was 60.84%. A total of 4 935 coding genes were predicted, 4 137 genes with clear function were found, 99 tRNAs and 3 rRNAs were found; 4 061 genes had ortholog family classification, 3 228 genes were related to gene ontology, and 2 663 genes related to metabolic pathways; 101 tandem repeats and 14 gene islands were predicted in the genome of A. hydrophila XDMG strain, with genes related to three QS systems: AI 1, AI 2, and AI 3. Through genome comparative analysis, A. hydrophila XDMG was closely related to domestic A. hydrophila J-1 strain and US-derived A. hydrophila AL0971 strain; it was more conserved with US-derived A. hydrophila AL0971 in the comparison of virulence genes, outer membrane proteins, and O-antigen gene clusters. Comprehensive genome annotation and comparative analysis of the genome of A. hydrophila XDMG strain provide basic data for the study of functional genomics and genetic engineering vaccines of A. hydrophila.

Key words: Aeromonas hydrophila, whole genome sequencing, virulence gene, outer membrane protein, O-antigen

郭少华, 毛会丽, 刘征权, 付美媛, 赵平原, 马文博, 李旭东, 关建义. 一株鱼源致病性嗜水气单胞菌XDMG的全基因组测序及比较基因组分析[J]. 生物技术通报, 2023, 39(8): 291-306.

GUO Shao-hua, MAO Hui-li, LIU Zheng-quan, FU Mei-yuan, ZHAO Ping-yuan, MA Wen-bo, LI Xu-dong, GUAN Jian-yi. Whole Genome Sequencing and Comparative Genome Analysis of a Fish-derived Pathogenic Aeromonas Hydrophila Strain XDMG[J]. Biotechnology Bulletin, 2023, 39(8): 291-306.

图/表 18

参考文献 61

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序列长度范围 Sequence length range/kb	基因骨架的数量 Number of scaffolds	重叠群的数量 Number of contigs
>9	24	24
8-9	0	0
7-8	0	0
6-7	1	1
5-6	1	1
4-5	1	1
3-4	0	0
2-3	3	3
1-2	4	4
0-1	13	13

序列长度范围 Sequence length range/kb	基因骨架的数量 Number of scaffolds	重叠群的数量 Number of contigs
>9	24	24
8-9	0	0
7-8	0	0
6-7	1	1
5-6	1	1
4-5	1	1
3-4	0	0
2-3	3	3
1-2	4	4
0-1	13	13

菌株 Strain	基因长度 Gene length/Mb	GC含量 GC Content/%	编码基因 Cds	rRNA	tRNA	年份 Year	来源 Source	来源地 Source location
J-1	5.00	60.9	4 268	31	110	1989	病鲤鱼Diseased Carp	中国南京Nanjing, China
AL09_71	5.02	60.8	4 297	31	111	2009	斑点叉尾鮰Channel catfish	美国USA
AH10	4.91	61.1	4 327	33	128	2012	病草鱼Diseased Ctenopharyngodon idella	中国上海Shanghai, China
ATCC_7966	4.74	61.5	4 119	31	127	不详	牛奶Milk	美国USA
XDMG	4.99	60.8	4 935	3	99	2009	病麦穗鱼Diseased Pseudorasbora parva	中国新乡Xinxiang, China

菌株 Strain	基因长度 Gene length/Mb	GC含量 GC Content/%	编码基因 Cds	rRNA	tRNA	年份 Year	来源 Source	来源地 Source location
J-1	5.00	60.9	4 268	31	110	1989	病鲤鱼Diseased Carp	中国南京Nanjing, China
AL09_71	5.02	60.8	4 297	31	111	2009	斑点叉尾鮰Channel catfish	美国USA
AH10	4.91	61.1	4 327	33	128	2012	病草鱼Diseased Ctenopharyngodon idella	中国上海Shanghai, China
ATCC_7966	4.74	61.5	4 119	31	127	不详	牛奶Milk	美国USA
XDMG	4.99	60.8	4 935	3	99	2009	病麦穗鱼Diseased Pseudorasbora parva	中国新乡Xinxiang, China

长度 Length/kb	数量 Count
0-5	1
5-10	2
10-15	5
15-20	2
20-25	3
25-30	1