ORCID Profile
0000-0003-1656-7602
Current Organisations
Oregon State University
,
USDA ARS, Agricultural Research Service
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Publisher: Springer Science and Business Media LLC
Date: 09-2009
DOI: 10.1038/NATURE08358
Abstract: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Publisher: Scientific Societies
Date: 07-2023
DOI: 10.1094/PHYTO-10-21-0430-PER
Abstract: Open research practices have been highlighted extensively during the last ten years in many fields of scientific study as essential standards needed to promote transparency and reproducibility of scientific results. Scientific claims can only be evaluated based on how protocols, materials, equipment and methods were described data were collected and prepared and analyses were conducted. Openly sharing protocols, data and computational code is central for current scholarly dissemination and communication, but in many fields, including plant pathology, adoption of these practices has been slow. We randomly selected 450 articles published from 2012 to 2021 across 21 journals representative of the plant pathology discipline and assigned them scores reflecting their openness and computational reproducibility. We found that most of the articles were not following protocols for open science and were failing to share data or code in a reproducible way. We propose that use of open-source tools facilitates computationally reproducible work and analyses benefitting not just readers, but the authors as well. Finally, we provide ideas and suggest tools to promote open, reproducible computational research practices among plant pathologists.
Publisher: Wiley
Date: 11-12-2014
DOI: 10.1111/MPP.12190
Publisher: Wiley
Date: 03-09-2021
DOI: 10.1111/MEC.16109
Abstract: Various hypotheses have been proposed regarding the origin of the plant pathogen Phytophthora cinnamomi . P . cinnamomi is a devastating, highly invasive soilborne pathogen associated with epidemics of agricultural, horticultural and forest plantations and native ecosystems worldwide. We conducted a phylogeographic analysis of populations of this pathogen s led in Asia, Australia, Europe, southern and northern Africa, South America, and North America. Based on genotyping‐by‐sequencing, we observed the highest genotypic ersity in Taiwan and Vietnam, followed by Australia and South Africa. Mating type ratios were in equal proportions in Asia as expected for a sexual population. Simulations based on the index of association suggest a partially sexual, semi‐clonal mode of reproduction for the Taiwanese and Vietnamese populations while populations outside of Asia are clonal. Ancestral area reconstruction provides new evidence supporting Taiwan as the ancestral area, given our s le, indicating that this region might be near or at the centre of origin for this pathogen as speculated previously. The Australian and South African populations appear to be a secondary centre of ersity following migration from Taiwan or Vietnam. Our work also identified two panglobal, clonal lineages PcG1‐A2 and PcG2‐A2 of A2 mating type found on all continents. Further surveys of natural forests across Southeast Asia are needed to definitively locate the actual centre of origin of this important plant pathogen.
Publisher: Wiley
Date: 30-01-2018
DOI: 10.1111/PPA.12812
Publisher: Wiley
Date: 06-04-2010
DOI: 10.1111/J.1755-0998.2010.02851.X
Abstract: This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.
Publisher: Cold Spring Harbor Laboratory
Date: 22-09-2021
DOI: 10.1101/2021.09.22.460084
Abstract: Oomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed for rapid and accurate characterization of oomycete communities using DNA metabarcoding. We have identified the mitochondrial 40S ribosomal protein S10 gene ( rps10 ) as a locus useful for oomycete metabarcoding and provide primers predicted to lify all oomycetes based on available reference sequences from a wide range of taxa. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental s les and a mock community using Illumina MiSeq. Amplified sequence variants (ASVs) and operational taxonomic units (OTUs) were identified per community. Both the sequence and predicted taxonomy of ASVs and OTUs were compared to the known composition of the mock community. Both rps10 and ITS yielded ASVs with sequences matching 21 of the 24 species in the mock community and matching all 24 when allowing for a 1 bp difference. Taxonomic classifications of ASVs included 23 members of the mock community for rps10 and 17 for ITS1. Sequencing results for the environmental s les suggest the proposed rps10 locus results in substantially less lification of non-target organisms than the ITS1 method. The lified rps10 region also has higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchable rps10 reference database for species identification and all protocols needed for oomycete metabarcoding. The rps10 barcode and methods described herein provide an effective tool for metabarcoding oomycetes using short-read sequencing. Oomycetes are a group of eukaryotes related to brown algae and diatoms, many of which cause diseases in plants and animals. Improved methods are needed to rapidly characterize the ersity of oomycete species found in environmental s les. We have identified the mitochondrial 40S ribosomal protein S10 gene ( rps10 ) as being useful for oomycete community sequencing. We evaluated its utility relative to a popular barcode, the internal transcribed spacer 1 (ITS1), by sequencing environmental s les and a community we synthesized in the laboratory. The lified rps10 region is predicted to have a higher taxonomic resolution than ITS1, allowing for greater discrimination of closely related species. We present a new website with a searchable rps10 reference database for species identification and all protocols needed for oomycete community sequencing. The rps10 barcode and methods described herein provide an effective tool for characterizing oomycetes using environmental DNA sequencing.
Publisher: Naturalis Biodiversity Center
Date: 31-12-2013
Publisher: Scientific Societies
Date: 11-2019
DOI: 10.1094/PHYTO-04-19-0146-R
Abstract: Downy mildew of grape caused by Plasmopara viticola is a global pathogen of economic importance to commercial viticulture. In contrast to populations in the northern hemisphere, few studies have investigated the population biology, genetic ersity, and origin of the pathogen in Australian production systems. DNA was extracted from 381 P. viticola s les from Vitis vinifera and alternate hosts collected via fresh and herbarium leaves from populations within Australia and Whatman FTA cards from North America, Brazil, and Uruguay. A total of 32 DNA s les were provided from a French population. The populations were genotyped using 16 polymorphic microsatellite markers. Representative s les from within Australia, Brazil, and Uruguay were also genotyped to determine which of the cryptic species (clades) within the P. viticola species complex were present. Our findings suggest the Australian and South American populations of P. viticola are more closely related to the European population than the North American population, the reported source of origin of the pathogen. The Western Australian population had similarities to the South Australian population, and the tight clustering of s les suggests a single introduction into Western Australia. P. viticola clade aestivalis was the only clade detected in Australian and South American populations. Analysis of the Western Australian population suggests that it is reproducing clonally, but additional research is required to determine the mechanism as to how this is occurring.
Publisher: Scientific Societies
Date: 12-2013
DOI: 10.1094/PHYTO-01-13-0023-R
Abstract: The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the ersity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for ≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD's future direction.
Publisher: Scientific Societies
Date: 2021
DOI: 10.1094/PHYTO-06-20-0232-FI
Abstract: Phytophthora pluvialis is an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir−tanoak forests of the U.S. Pacific Northwest (PNW). It was then identified as the causal agent of red needle cast of radiata pine (Pinus radiata) in New Zealand (NZ). Genotyping-by-sequencing was used to obtain 1,543 single nucleotide polymorphisms across 145 P. pluvialis isolates to characterize the population structure in the PNW and NZ. We tested the hypothesis that P. pluvialis was introduced to NZ from the PNW using genetic distance measurements and population structure analyses among locations between countries. The low genetic distance, population heterozygosity, and lack of geographic structure in NZ suggest a single colonization event from the United States followed by clonal expansion in NZ. The PNW Coast Range was proposed as a presumptive center of origin of the currently known distribution of P. pluvialis based on its geographic range and position as the central cluster in a minimum spanning network. The Coastal cluster of isolates were located at the root of every U.S. cluster and emerged earlier than all NZ clusters. The Coastal cluster had the highest degree of heterozygosity (Hs = 0.254) and median pairwise genetic distance (0.093) relative to any other cluster. Finally, the rapid host ersification between closely related isolates of P. pluvialis in NZ indicate that this pathogen has the potential to infect a broader range of hosts than is currently recognized.
Location: United States of America
Location: United States of America
No related grants have been discovered for Niklaus Grünwald.