Phytophthora ramorum strain:Ex-type CPHST BL 55G Genome sequencing and assembly

Plant Pathogens draft genome sequences (WGS) are vital for understanding pathogen mechanism as well as for various diagnostics and taxonomic purposes. Type material is the taxonomic important support for formal names to the specimens submitted to museums or herbaria that serve as exemplars for the species. Ex-type material are cultures and duplicates of the Type deposited in culture collections from which sequences including WGS are generated. It is crucial to have a right organism’s sequences especially for identification and diagnostic purposes. The Phytophthora ramorum is one of the most important species of biosecurity concern for agriculture at the United States, United Kingdom and other areas of the world. Here we report whole genome sequences for first Ex-type material for Phytophthora ramorum using Oxford Nanopore Technology (ONT) for various applications. At the present there are more than 20 whole genome sequences of specimens of Phytophthora ramorum submitted to the NCBI but none of them correspond to the Ex-type. This is the first Ex-type material of Phytophthora ramorum using MinION Oxford Nanopore Technology (ONT) long-read sequencing also for the assembly of a whole genome sequence of Phytophthora species using the Third Generation Sequencing MinION long-read sequencing portable device.

植物病原体全基因组测序草图（WGS，Whole Genome Sequencing）对于解析病原体致病机制、开展各类诊断检测及分类学研究均具有至关重要的价值。模式材料（Type material）是指提交至博物馆或标本馆、作为物种类群标准参照的标本，其为物种正式学名的命名提供了分类学层面的核心支撑。副模式材料（Ex-type material）则是保藏于菌种保藏中心的模式材料的培养物及副本，可从中获取包括全基因组测序（WGS）在内的各类序列数据。获取精准的生物体序列信息，尤其是用于物种鉴定与诊断的序列，具有关键意义。栎树猝死病菌（Phytophthora ramorum）是美国、英国及全球其他地区农业领域最受关注的生物安全关切物种之一。本研究利用牛津纳米孔测序技术（Oxford Nanopore Technology, ONT），首次完成了栎树猝死病菌副模式材料的全基因组测序，可应用于多类研究场景。目前，提交至美国国家生物技术信息中心（NCBI）的栎树猝死病菌标本全基因组序列已超过20条，但均未对应副模式材料。本研究不仅首次利用MinION牛津纳米孔长读长测序技术完成了栎树猝死病菌副模式材料的全基因组测序，同时也是首次借助第三代测序技术（Third Generation Sequencing）的便携式MinION长读长测序设备，完成疫霉属物种的全基因组序列组装。