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.

Affiliation

USDA, 1097, PPQ, APHIS, S&T Beltsville Laboratory, Beltsville, Maryland, United States; [Email]

Abstract

Phytophthora ramorum, P. kernoviae and P. melonis are each species of current regulatory concern in United States, 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 Whole Genome Sequence (WGS) for the Ex-type material of P. ramorum, P. kernoviae and P. melonis generated using High Throughput Sequencing (HTS) via the MinION third generation (3G-HTS) platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of P. ramorum, P. kernoviae and P. melonis (1322, 545 and 2091 contigs respectively). The Ab initio prediction of genes from these species reveals that there are 16,838, 12,793 and 34,580 genes in P. ramorum, P. kernoviae and P. melonis, respectively. Of the 34,580 P. melonis genes, 10,164 genes were conserved among all three of these Phytophthora species which may include pathogenicity genes. We compared the ex-type of P. ramorum EU1 lineage assembly with another selected isolate of EU1 available at NCBI and found 251,859 SNPs genome-wide; the comparison with EU2 lineage genome isolate revealed 441,859 SNPs genome wide. This genome resource of the ex-types of P. ramorum, and P. kernoviae is a significant contribution as these species are among the most important pathogens of regulatory concern at different regions of the world.

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