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基于长片段PCR扩增的牡蛎疱疹病毒基因组高通量测序
引用本文:史杰,白昌明,李晨,蔡生力,王崇明.基于长片段PCR扩增的牡蛎疱疹病毒基因组高通量测序[J].水产学报,2018,42(2):216-225.
作者姓名:史杰  白昌明  李晨  蔡生力  王崇明
作者单位:上海海洋大学水产与生命学院,中国水产科学研究院黄海水产研究所,中国水产科学研究院黄海水产研究所,上海海洋大学水产与生命学院,中国水产科学研究院黄海水产研究所
基金项目: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)
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。

关 键 词:栉孔扇贝  高通量测序  长片段PCR  牡蛎疱疹病毒
收稿时间:2016/12/30 0:00:00
修稿时间:2017/5/9 0:00:00

Long-range PCR and next generation sequencing of Ostreid herpesvirus genome
SHI Jie,BAI Changming,LI Chen,CAI Shengli and WANG Chongming.Long-range PCR and next generation sequencing of Ostreid herpesvirus genome[J].Journal of Fisheries of China,2018,42(2):216-225.
Authors:SHI Jie  BAI Changming  LI Chen  CAI Shengli and WANG Chongming
Institution:College of Fisheries and Life Science, Shanghai Ocean University,,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,,Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
Abstract:To obtain the genome sequence of Ostreid herpesvirus 1 (OsHV-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 were 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 were more closely related to OsHV-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 OsHV-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 OsHV-1 variants will be the necessary for further study of the genetic variation, evolution and phylogenetic analysis of the virus.
Keywords:Chlamys farreri  Next-generation  sequencing  Long-range  PCR  Ostreid  herpesvirus 1
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