1
|
Turner J, O'Neill P, Grant M, Mumford RA, Thwaites R, Studholme DJ. Genome sequences of 12 isolates of the EU1 lineage of Phytophthora ramorum, a fungus-like pathogen that causes extensive damage and mortality to a wide range of trees and other plants. GENOMICS DATA 2017; 12:17-21. [PMID: 28243575 PMCID: PMC5320048 DOI: 10.1016/j.gdata.2017.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/05/2017] [Indexed: 11/24/2022]
Abstract
Here we present genome sequences for twelve isolates of the invasive pathogen Phytophthora ramorum EU1. The assembled genome sequences and raw sequence data are available via BioProject accession number PRJNA177509. These data will be useful in developing molecular tools for specific detection and identification of this pathogen.
Collapse
Affiliation(s)
- Judith Turner
- Fera Science Ltd (Fera), National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Paul O'Neill
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Murray Grant
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Rick A. Mumford
- Fera Science Ltd (Fera), National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Richard Thwaites
- Fera Science Ltd (Fera), National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, United Kingdom
| | - David J. Studholme
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| |
Collapse
|
2
|
Gagnon MC, Feau N, Dale AL, Dhillon B, Hamelin RC, Brasier CM, Grünwald NJ, Brière SC, Bilodeau GJ. Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data. PLANT DISEASE 2017; 101:666-673. [PMID: 30678572 DOI: 10.1094/pdis-11-16-1586-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.
Collapse
Affiliation(s)
| | - Nicolas Feau
- Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Angela L Dale
- Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Braham Dhillon
- UBC and Department of Plant Pathology, University of Arkansas, Fayetteville
| | - Richard C Hamelin
- UBC and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | | | | | | | | |
Collapse
|
3
|
Derevnina L, Petre B, Kellner R, Dagdas YF, Sarowar MN, Giannakopoulou A, De la Concepcion JC, Chaparro-Garcia A, Pennington HG, van West P, Kamoun S. Emerging oomycete threats to plants and animals. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150459. [PMID: 28080985 PMCID: PMC5095538 DOI: 10.1098/rstb.2015.0459] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2016] [Indexed: 12/31/2022] Open
Abstract
Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans, Phytophthora palmivora, Phytophthora ramorum, Plasmopara obducens, and the animal pathogens Aphanomyces invadans, Saprolegnia parasitica and Halioticida noduliformans For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
Collapse
Affiliation(s)
- Lida Derevnina
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Yasin F Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mohammad Nasif Sarowar
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | | | | | | | | | - Pieter van West
- International Centre for Aquaculture Research and Development, Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| |
Collapse
|
4
|
Feau N, Taylor G, Dale AL, Dhillon B, Bilodeau GJ, Birol I, Jones SJ, Hamelin RC. Genome sequences of six Phytophthora species threatening forest ecosystems. GENOMICS DATA 2016; 10:85-88. [PMID: 27752469 PMCID: PMC5061060 DOI: 10.1016/j.gdata.2016.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 01/25/2023]
Abstract
The Phytophthora genus comprises of some of the most destructive plant pathogens and attack a wide range of hosts including economically valuable tree species, both angiosperm and gymnosperm. Many known species of Phytophthora are invasive and have been introduced through nursery and agricultural trade. As part of a larger project aimed at utilizing genomic data for forest disease diagnostics, pathogen detection and monitoring (The TAIGA project: Tree Aggressors Identification using Genomic Approaches; http://taigaforesthealth.com/), we sequenced the genomes of six important Phytophthora species that are important invasive pathogens of trees and a serious threat to the international trade of forest products. This genomic data was used to develop highly sensitive and specific detection assays and for genome comparisons and to make evolutionary inferences and will be useful to the broader plant and tree health community. These WGS data have been deposited in the International Nucleotide Sequence Database Collaboration (DDBJ/ENA/GenBank) under the accession numbers AUPN01000000, AUVH01000000, AUWJ02000000, AUUF02000000, AWVV02000000 and AWVW02000000.
Collapse
Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Greg Taylor
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- FPInnovations, Vancouver, British Columbia, Canada
| | - Braham Dhillon
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Inanç Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J.M. Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative des Systèmes, Université Laval, Québec, Canada
| |
Collapse
|