Author
Michael D. Coffey
Other affiliations: University Hospitals of Cleveland, Pennsylvania State University, Case Western Reserve University
Bio: Michael D. Coffey is an academic researcher from University of California, Riverside. The author has contributed to research in topics: Phytophthora & Phytophthora capsici. The author has an hindex of 36, co-authored 74 publications receiving 4199 citations. Previous affiliations of Michael D. Coffey include University Hospitals of Cleveland & Pennsylvania State University.
Papers published on a yearly basis
Papers
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TL;DR: 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 oomy cetes.
Abstract: 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.
448 citations
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TL;DR: A genus-wide phylogeny for 82 Phytophthora species is presented using seven of the most informative loci (approximately 8700 nucleotide sites) and support the division of the genus into 10 well-supported clades.
438 citations
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TL;DR: The results showed that although the deep-sequencing profiling results are highly reproducible across technical and biological replicates, the results from deep sequencing may not always be consistent with theresults from Northern blot or miRNA quantitative RT-PCR, and discussed the procedural differences between these techniques that may cause the inconsistency.
Abstract: MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses in most eukaryotes. We globally profiled plant miRNAs in response to infection of bacterial pathogen Pseudomonas syringae pv. tomato (Pst). We sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 and 14 h post infection of non-pathogenic, virulent and avirulent strains of Pst. We identified 15, 27 and 20 miRNA families being differentially expressed upon Pst DC3000 hrcC, Pst DC3000 EV and Pst DC3000 avrRpt2 infections, respectively. In particular, a group of bacteria-regulated miRNAs targets protein-coding genes that are involved in plant hormone biosynthesis and signaling pathways, including those in auxin, abscisic acid, and jasmonic acid pathways. Our results suggest important roles of miRNAs in plant defense signaling by regulating and fine-tuning multiple plant hormone pathways. In addition, we compared the results from sequencing-based profiling of a small set of miRNAs with the results from small RNA Northern blot and that from miRNA quantitative RT-PCR. Our results showed that although the deep-sequencing profiling results are highly reproducible across technical and biological replicates, the results from deep sequencing may not always be consistent with the results from Northern blot or miRNA quantitative RT-PCR. We discussed the procedural differences between these techniques that may cause the inconsistency.
221 citations
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TL;DR: It is demonstrated that N. benthamiana NbSerk3 significantly contributes to resistance to P. infestans and regulates the immune responses triggered by the P.infestans PAMP protein INF1.
Abstract: This work was supported by the Gatsby Charitable Foundation, BBSRC, Nuffield Foundation and the German Research Foundation (DFG). SS was supported by a personal research fellowship (SCHO1347/1-1). JPR is an Australian Research Council Future Fellow (FT0992129). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
174 citations
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TL;DR: A more detailed analysis of species from clades 2 and 8 identified an additional seven phylogenetic lineages that warrant further investigation to determine if they represent distinct species.
157 citations
Cited by
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Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.
Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
4,116 citations
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TL;DR: A flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure is proposed and pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates.
Abstract: ▪ Abstract We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.
1,893 citations
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Broad Institute1, Ohio Agricultural Research and Development Center2, Sainsbury Laboratory3, Uppsala University4, Wageningen University and Research Centre5, Virginia Bioinformatics Institute6, University of California, Riverside7, University of Aberdeen8, Scottish Crop Research Institute9, University of Warwick10, Agricultural Research Service11, Royal Institute of Technology12, Cornell University13, Oregon State University14, Lafayette College15, University of Glasgow16, Harvard University17, Delaware Biotechnology Institute18, North Carolina State University19, University of Delaware20, University of Tennessee21, University of Maryland, Baltimore22, Vanderbilt University23, College of Wooster24, Bowling Green State University25, Edinburgh Cancer Research Centre26, J. Craig Venter Institute27, Tel Aviv University28, University of Wisconsin-Madison29, University of Hohenheim30, University of Dundee31
TL;DR: The sequence of the P. infestans genome is reported, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates and probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
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(1). 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(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 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 similar to 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.
1,341 citations
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TL;DR: This article examined the phylogenetic relationships among 50 Phytophthora species and between them and other oomycetes on the basis of the ITS sequences of genomic rDNA and found that they were essentially monophyletic, all but three species forming a cluster of eight clades.
1,013 citations
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TL;DR: The fungi, as thus defined, are of great importance for the following reasons: (a) They are the primary decomposers in all terrestrial ecosystems; (b) they are important symbiotic associates of vascular plants both in mutualistic and parasitic relationships.
Abstract: The fungi comprise both members of the kingdom Fungi as we now recognize it (Ascomycota, Basidiomycota, Zygomycota, and Chytridiomycota) and fungal-like protists such as the Oomycota and the cellular and acellular slime molds (Myxomycota and Acrasiomycota). Treating this admittedly polyphyletic assemblage as a group is useful because these organisms often fill rather similar roles within ecosystems, and they have traditionally been studied almost exclusively by mycologists and plant pathologists. Throughout this review, Fungi will refer to the Kingdom, fungi to the organisms studied by mycologists. The fungi, as thus defined, are of great importance for the following reasons: (a) They are the primary decomposers in all terrestrial ecosystems; (b) they are important symbiotic associates of vascular plants both in mutualistic and parasitic relationships; (c) they constitute the overwhelming majority of plant pathogens and as such have a tremendous eco-
919 citations