摘要
为获取2001年低温冻存栉孔扇贝感染牡蛎疱疹病毒(Os HV-1)变异株(ZK2001)基因组序列,并分析ZK2001与其他Os HV-1变异株的序列差异和系统发育关系,利用基于长片段PCR的基因组DNA的扩增和富集技术,获取2001年栉孔扇贝感染Os HV-1变异株的基因组DNA;再使用Illumina Hiseq 2500 PE250高通量测序平台对其测序。最后分析ZK2001与Os HV-1其他变异株基因组的序列差异和系统发育关系。测序数据组装后获得8个Scaffold。基因组变异分析结果显示,ZK2001与参考基因组相比存在328个SNP位点,SNP和序列插入/缺失变异是导致Os HV-1基因组序列变异的主要变异类型。系统发育分析结果显示,ZK2001变异株与分离自我国的Os HV-1变异株亲缘关系最近,与分离自欧洲的Os HV-1μvar及其相关变异株的亲缘关系最远,说明中国和欧洲分布Os HV-1间存在因地理隔离导致的遗传分化。研究表明,基于长片段PCR的DNA富集技术,可以有效地扩增和富集冷冻样本中Os HV-1基因组DNA,并应用于高通量测序。Os HV-1不同变异株基因组序列数据的获取和积累,将为其基因组尺度的基因变异、株系演化和系统发育关系等研究提供重要基础。
To obtain the genome sequence of Ostreid herpesvirus 1（Os HV-1） infected Zhikong scallop（Chlamys farreri） in 2001（ZK2001）, and its phylogenetic relationship with the other reported variants, the genome DNA of the ZK2001 variant was firstly enriched through long-range PCR, and sequenced with Illumina Hiseq 2500 PE250 platform. Then the variation and phylogenetic relationship between ZK2001 and the other reported variants were analyzed. 8 scaffolds were obtained after assembly. Genome variation analysis indicated that there were 328 SNPs between ZK2001 and the reference genome. SNPs and insert/deletion were the main cause of genome differentiation. Phylogenetic inference indicated that ZK2001 variant was more closely related to Os HV-1 variants isolated from China than those from Europe. These results indicated that genetic differentiation had occurred as a result of geographic isolation. This study indicated genomic DNA of Os HV-1, which had been frozen for a long time, could be enriched with long-range PCR and used for high-throughput sequencing. The genomic data of different Os HV-1 variants will be necessary for further study of the genetic variation, evolution and phylogenetic analysis of the virus.
出处
《水产学报》
CAS
CSCD
北大核心
2018年第2期216-225,共10页
Journal of Fisheries of China
基金
国家自然科学基金(31502208,31302233)
现代农业产业技术体系建设专项(CARS-48)
青岛海洋科学与技术国家实验室鳌山科技创新计划(2015ASKJ02)
关键词
栉孔扇贝
高通量测序
长片段PCR
牡蛎疱疹病毒
Chlamysfarreri
next-generation sequencing
long-range PCR
Ostreid herpesvirus 1
作者简介
通信作者：王崇明，E-mail：wangcm@ysfri．ac．cn
