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2011, Molecular ecology resources
Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.
Molecular Ecology Resources
Towards a universal barcode of oomycetes - a comparison of thecox1 andcox2 loci2015 •
Biotechnology Letters
Easy and efficient protocol for oomycete DNA extraction suitable for population genetic analysis2011 •
1998 •
Frontiers in Microbiology
DNA Metabarcoding Reveals Broad Presence of Plant Pathogenic Oomycetes in Soil From Internationally Traded Plants2021 •
Plants with roots and soil clumps transported over long distances in plant trading can harbor plant pathogenic oomycetes, facilitating disease outbreaks that threaten ecosystems, biodiversity, and food security. Tools to detect the presence of such oomycetes with a sufficiently high throughput and broad scope are currently not part of international phytosanitary testing regimes. In this work, DNA metabarcoding targeting the internal transcribed spacer (ITS) region was employed to broadly detect and identify oomycetes present in soil from internationally shipped plants. This method was compared to traditional isolation-based detection and identification after an enrichment step. DNA metabarcoding showed widespread presence of potentially plant pathogenic Phytophthora and Pythium species in internationally transported rhizospheric soil with Pythium being the overall most abundant genus observed. Baiting, a commonly employed enrichment method for Phytophthora species, led to an increas...
Phytopathology®
The Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes2010 •
Sequences of selected marker loci have been widely used for the identification of specific pathogens and the development of sequence-based diagnostic methods. Although such approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own pitfalls. These include erroneous and incomplete data in reference databases, poor or oversimplified interpretation of search results, and problems associated with defining species boundaries. In this letter, we outline the potential benefits and drawbacks of using sequence data for identification and taxonomic deductions of plant-pathogenic fungi and oomycetes, using Phytophthora as a primary example. We also discuss potential remedies for these pitfalls and address why coordinated community efforts are essential to make such remedies more efficient and robust.
Molecular Plant Pathology (BSPP) Wiley
The Top 10 oomycete pathogens in molecular plant pathologyOomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens that threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. The article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
Frontiers in Microbiology
Corrigendum: Species Richness, rRNA Gene Abundance, and Seasonal Dynamics of Airborne Plant-Pathogenic OomycetesJurnal Hama dan Penyakit Tumbuhan Tropika
Molecular identification of oomycetes related to horticultural crops in Southern Sumatera and Java, IndonesiaIndonesia is an agricultural country with more than 30 million farmers nationwide most of it with poor disease management. An identification of a pathogen is the first step to establish efficient management strategies for disease control. In this study, we survey the diversity of oomycetes in horticulture. Samples were collected from 19 sites around Lampung, Sumatera and Java Islands. The oomycetes were isolated from rhizosphere soils sample and from symptomatic plants tissues. One hundred and twelve isolates belonging to two Phytophthora spp., three Pythium spp., and one Phytophythium sp. were identified. Phytophthora nicotianae was a predominant species from pineapple but also found in cabbage, chilli, and chrysanthemum. P. colocasiae were isolated from taro in central java, Phytopythium vexans were isolated from potato in Central Java, while Pythium acanthophoron, Py. myriotylum, Py. splendens, and Py. catenulatum were isolated from soil in pineapple farms.
African Journal of Biotechnology
Technical review of molecular markers and next-generation sequencing technology to manage plant pathogenic oomycetes2018 •
Acta Crystallographica Section A Foundations of Crystallography
Residual stress distribution near HA coating interface on titanium alloy substrate2005 •
Journal de Radiologie
Le diagnostic de dissection des artères cervicales en 20062006 •
Journal of Anthropological Archaeology
Modelling mortuary populations at local and regional levels2019 •
L'Expansion Management Review
Opérateurs télécoms et équipementiers : la nouvelle donne ?2005 •
Information Bulletin on Variable Stars
Resolved photometry of the binary components of RW Aur2013 •
DEDIKASI: Jurnal Pengabdian Masyarakat
Pelatihan Pembuatan Kompos Organik Metode Keranjang Takakura sebagai Solusi Penanganan Sampah di Lingkungan Kost Mahasiswa2019 •
Suid-Afrikaanse Tydskrif vir Natuurwetenskap en Tegnologie
Fotondegradasie van Alq3-poeier2013 •
2016 •
Journal Européen des Systèmes Automatisés
Design of Neural Network Based Expert System for Automated Lime Kiln System2019 •
Forests
How Can Local and Regional Knowledge Networks Contribute to Landscape Level Action for Tree Health?2021 •
2008 •
Aeronautics and Aerospace Open Access Journal
Slip analysis of magnetohydrodynamics flow of an upper-convected Maxwell viscoelastic nanofluid in a permeable channel embedded in a porous medium2018 •
PEMODELAN ARMA UNTUK KANAL HF LINK …
Pemodelan Arma Untuk Kanal HF Link Malangsurabaya2010 •
Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Alcohol Use Disorder and Its Comorbidity With HIV Infection Disrupts Anterior Cingulate Cortex Functional Connectivity2022 •
Zeitschrift für orthomolekulare Medizin
HDL-Cholesterin aus einem anderen Blickwinkel2019 •
Cadernos De Saude Publica
Regionalização no federalismo brasileiro2019 •
Political Science Quarterly
From the “Red Juggernaut” to Iraqi WMD: Threat Inflation and How it Succeeds in the United States2007 •
2018 •