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

Whole Genome Sequencing and Comparative Genome Analysis of a Fish-derived Pathogenic Aeromonas Hydrophila Strain XDMG

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4935个编码基因,有明确功能的基因有4137个,发现99个tRNA和3个rRNA;4061个基因具有直系同源族分类,3228个基因与基因本体论相关,与代谢通路有关的基因有2663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。

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 4935 coding genes were predicted,4137 genes with clear function were found,99 tRNAs and 3 rRNAs were found;4061 genes had ortholog family classification,3228 genes were related to gene ontology,and 2663 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.