Abstract
Newly discovered Phytophthora species include invasive pathogens that threaten trees and shrubs. We present draft genome assemblies for three isolates of Phytophthora kernoviae and one isolate of the EU2 lineage of Phytophthora ramorum, collected from outbreak sites in Scotland.
| Specifications | |
| Organism/cell line/tissue | Phytophthora ramorum and Phytophthora kernoviae |
| Sex | Not applicable |
| Sequencer or array type | Illumina HiSeq |
| Data format | Analyzed; i.e. raw data filtered and assembled. |
| Experimental factors | Genomic sequence of pure microbial cultures |
| Experimental features | Genomic sequence of pure microbial cultures |
| Consent | Not applicable. Data are available without restriction. |
| Sample source location | Scotland, United Kingdom |
1. Direct links to deposited data
http://www.ncbi.nlm.nih.gov/bioproject?LinkName=assembly_bioproject&from_uid=529658.
http://www.ncbi.nlm.nih.gov/bioproject?LinkName=assembly_bioproject&from_uid=529668.
http://www.ncbi.nlm.nih.gov/bioproject?LinkName=assembly_bioproject&from_uid=529678.
http://www.ncbi.nlm.nih.gov/bioproject?LinkName=assembly_bioproject&from_uid=534508.
2. Experimental design, materials and methods
Newly discovered Phytophthora species are increasingly reported as invasive pathogens, threatening trees and shrubs in the natural environment as well as in public and heritage gardens. For example, Phytophthora kernoviae is a recently described species first isolated in the south west of England [1] from bleeding stem lesions on mature beech trees (Fagus sylvatica) and foliar and stem necroses on Rhododendron ponticum. It also infects a range of other woodland and ornamental trees and shrubs such as Quercus robur, Quercus ilex, Magnolia spp., Pieris spp. and heathland plants (e.g. Vaccinium myrtillus).
In the USA, Phytophthora ramorum is the causative agent of sudden oak death, killing millions of trees along the Pacific West Coast since the mid 1990s [2]. In Europe P. ramorum was initially associated with Rhododendron and Viburnum within the ornamental nursery trade but the known host range has now expanded to well over 100 species of trees, shrubs and herbaceous plants. In the UK, initial findings were quickly followed by spread into landscaped and wider environments driven mainly by Rhododendron ponticum and again affecting Vaccinium myrtillus in heathland. Few trees were infected in the UK until 2009, when P. ramorum began to rapidly spread through Japanese larch (Larix kaempferi) and to a lesser extend to other larch plantations, necessitating the premature felling of large numbers of trees [3]. Four distinct genetic lineages of P. ramorum are known: The NA1 and NA2 lineages are present in North America; in Europe are the EU1 lineage and the recently discovered EU2 lineage, which is currently restricted to Northern Ireland and the south-west of Scotland [4], [5]. Only the NA1 lineage has a previously published genome sequence [6]. We used the Illumina HiSeq to sequence genomic DNA of three isolates of P. kernoviae and one isolate of the EU2 lineage of P. ramorum, all isolated from different outbreak sites in Scotland (Table 1). Paired 100-bp reads were assembled de novo and scaffolded using Velvet v. 1.2.03 [7]. The availability of the first genome sequences for P. kernoviae and its comparison with other Phytophthora will facilitate insights into the infection biology of this invasive pathogen and identification of core sets of genes shared across the genus. Availability of the first genome sequence from the EU2 lineage will be a useful resource for investigating the relationships among the four lineages as well as developing assays for detection and monitoring.
Table 1.
Sequenced isolates.
| Isolate | Accession numbers: GenBank1 (and SRA) | Scaffold assembly size (bp) | Number of scaffolds | Scaffold N50 (bp) | Host | Date of isolation |
|---|---|---|---|---|---|---|
| P. kernoviae 00238/432 | AOFI00000000 (SRX212407) | 43,208,681 | 1805 | 72,999 | Rhododendron ponticum | August 2010 |
| P. kernoviae 00629/1 | AOFJ00000000 (SRX212404) | 43,295,191 | 2542 | 58,074 | Rhododendron ponticum | May 2011 |
| Phytophthora kernoviae 00844/4 | AOFK00000000 (SRX212403) | 42,716,609 | 2538 | 58,795 | Rhododendron ponticum | October 2011 |
| P. ramorum EU2 996/3 | AOBL00000000 (SRX212402) | 49,703,133 | 3450 | 51,489 | Magnolia stellata | November 2011 |
Data have been deposited at GenBank under these accession numbers, and the version described in this paper is version XXXX01000000.
Sequence data are available via the accession numbers listed in Table 1 and annotation of the genome assemblies is available via Ensembl Protists [8].
Acknowledgements
Work in the laboratory of DJS is supported by the BBSRC (BB/L012499/1 and Nornex). Sequencing was performed by the Exeter Sequencing Service at the University of Exeter, which is supported by Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1).
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