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Phytophthora kernoviae strain:P19827 WPC Genome sequencing and assembly

dataset
posted on 2024-02-06, 23:56 authored by Contact; Gloria Abad Z, USDA-APHIS-PPQ-S&T
The reference sequences derived from type specimens serve to label with the correct and most up-to-date species name. The Type is a death specimen in herbaria collection coded and described at the time of the original description and that act as reference for biological species. The Ex-type material are cultures and duplicates of the Type and deposited in additional culture collections. In order to make robust and correct molecular identification and diagnostic systems, it is crucial to have information from the Ex-type specimens for accurate comparisons. Phytophthora kernoviae is a pathogen of concern causing bleeding cankers on forest trees and foliar necrosis in nursery crops in the UK. The species has been found associated to Annona cherimolla (custard apple tree) in New Zealand and infecting Drimys winteri (winter’s bark) in Chile. For the United States, the full potential for establishment of this species is unknown. The value of U.S. forests and the nursery industry ($4.6 billion) could be at risk if P. kernoviae or any of the exotic pathogens of biosecurity concern is introduced to the country. Due to the significance of P. kernoviae as exotic species of biosecurity concern around the world there are currently 11 genome sequences for isolates of the species deposited at the NCBI, however there is no available whole genome sequence for the Ex-type. Here we report the whole-genome sequence for the Ex-type of Phytophthora kernoviae [P19827 (World Phytophthora Collection, Riverside, CA USA) = CPHST BL 91] generated using 3rd Generation (3G) ultra-long sequencing via the MinION platform from Oxford Nanopore Technology. The quality filtered 601,746 reads were assembled in to 555 contigs indicated extended genome size, total length 42 Mb. We expect this MinION assembly is highly improved as per less number of contigs and technology wise as compared to previously NCBI submissions.

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2019-08-22

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

genomics; sequence analysis; genome

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA554119

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