USDA-APHIS-PPQ, Science and Technology Beltsville Laboratory, Beltsville, MD 20705, U.S.A.
Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A.
Mol Plant Microbe Interact. 2020 Jun;33(6):794-797. doi: 10.1094/MPMI-12-19-0342-A. Epub 2020 Apr 16.
, , and are each species of current regulatory concern in the United States, the United Kingdom, and other areas of the world. Ex-type material are cultures and duplicates of the type that was used to describe each species and that are deposited in additional culture collections. Using these type specimens as references is essential to designing correct molecular identification and diagnostic systems. Here, we report a whole genome sequence for the Ex-type material of , , and generated using high-throughput sequencing via the MinION third generation platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of , , and (1,322, 545, and 2,091 contigs, respectively). The prediction of genes from these species reveals that there are 16,838, 12,793, and 34,580 genes in , , and , respectively. Of the 34,580 P. genes, 10,164 genes were conserved among all three of these species which may include pathogenicity genes. We compared the ex-type of EU1 lineage assembly with another selected isolate of EU1 available at the National Center for Biotechnology Information and found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; the comparison with the EU2 lineage genome isolate revealed 441,859 SNPs genome-wide. This genome resource of the ex-types of , and is a significant contribution as these species are among the most important pathogens of regulatory concern in different regions of the world.
，，和 都是目前在美国、英国和世界其他地区受到监管关注的物种。Ex-type 材料是指用于描述每个物种的模式标本的培养物和复制品，这些材料被保存在其他培养物收藏中。使用这些模式标本作为参考对于设计正确的分子鉴定和诊断系统至关重要。在这里，我们报告了使用牛津纳米孔技术的 MinION 第三代平台通过高通量测序生成的 Ex-type 材料的全基因组序列。我们将质量过滤后的读取组装成每个物种的连续 contigs。我们分别组装了,, 和 的连续 contigs（分别为 1,322、545 和 2,091 个 contigs）。这些物种的基因预测表明， 中分别有 16,838、12,793 和 34,580 个基因， 中分别有 12,793、34,580 和 20,910 个基因， 中分别有 16,838、34,580 和 20,910 个基因。在这 34,580 个 P. 基因中，有 10,164 个基因在这三个 物种中是保守的，这些基因可能包括致病性基因。我们比较了 EU1 谱系的 Ex-type 组装与国家生物技术信息中心（National Center for Biotechnology Information）可获得的另一个 EU1 选定分离株，发现全基因组有 251,859 个单核苷酸多态性（SNP）；与 EU2 谱系基因组分离株的比较显示全基因组有 441,859 个 SNP。这些 Ex-type 的基因组资源是一个重要的贡献，因为这些物种是世界不同地区最重要的监管关注病原体之一。
