Draft Genome Resource for the Ex-types of Phytophthora ramorum, P. kernoviae, and P. melonis, Species of Regulatory Concern, Using Ultra–Long Read MinION Nanopore Sequencing

• DOI: 10.1094/mpmi-12-19-0342-a
• Publication Date: 2020-03-04T16:02:13Z
• Authors: Subodh K. Srivastava; Z. Gloria Abad; Leandra M. Knight; Kurt Zeller; Vessela Mavrodieva; Mark Nakhla
• Keywords: Phytophthora ramorum; Minion; Lineage (genetic)

Phytophthora ramorum, P. kernoviae, and melonis are each species of current regulatory concern in the United States, Kingdom, other areas world. Ex-type material cultures duplicates type that was used to describe deposited additional culture collections. Using these specimens as references is essential designing correct molecular identification diagnostic systems. Here, we report a whole genome sequence for generated using high-throughput sequencing via MinION third generation platform from Oxford Nanopore Technology. We assembled quality filtered reads into contigs species. continuous (1,322, 545, 2,091 contigs, respectively). The ab initio prediction genes reveals there 16,838, 12,793, 34,580 melonis, respectively. Of genes, 10,164 were conserved among all three which may include pathogenicity genes. compared ex-type ramorum EU1 lineage assembly with another selected isolate available at National Center Biotechnology Information found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; comparison EU2 revealed 441,859 SNPs genome-wide. This resource ex-types kernoviae significant contribution most important pathogens different regions