Michael D. Coffey
University of California, Riverside
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Molecular Ecology Resources | 2011
Gregg P. Robideau; Arthur W.A.M. de Cock; Michael D. Coffey; Hermann Voglmayr; H. Brouwer; Kanak Bala; David W. Chitty; Nicole L. Désaulniers; Quinn A. Eggertson; Claire M. M. Gachon; Chia-Hui Hu; Frithjof C. Küpper; Tara L. Rintoul; Ehab Sarhan; Els C. P. Verstappen; Yonghong Zhang; P.J.M. Bonants; Jean Beagle Ristaino; C. André Lévesque
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.
Mycologia | 1990
Helga Förster; Michael D. Coffey; Hille J. Elwood; Mitchell L. Sogin
ABSTRACTThe small-subunit ribosomal RNA gene sequences of the chytridiomycete Blastocladiella emersomi and the oomycetes Lagenidium giganteum and Phytophthora megasperma f. sp. glycinea were determ...
Fungal Biology | 1991
Peter Oudemans; Michael D. Coffey
One hundred and sixty-two isolates representing worldwide sources of Phytophthora cambivora, P. cinnamomi and P. cactorum were compared using 18 isozyme loci separated by starch-gel electrophoresis. Based on isozyme analysis, the three species were clearly separated and each was further subdivided into electrophoretic types (ETs). No evidence suggests a close relationship between P. cambivora and P. cinnamomi. P. cambivora separated into eight ETs. One ET was the most common worldwide; there were four unique ETs from Australia, one from Japan and two from the U.S.A. No distinguishing morphological features were associated with the different ETs. P. cinnamomi also divided into eight ETs. The two ETs, which represented all the A2 isolates used in the study, could be distinguished from the majority of the A1 isolates based on the migration pattern of isocitrate dehydrogenase. Only one exception to this was seen in an isolate which was reported to have switched mating types from A2 to A1. P. cactorum was divided into two ETs, one common and the other represented by two isolates from strawberry from New York. These two isolates also differed in their sporangial dimensions and oospore pigmentation. The potential of cellulose acetate electrophoresis was evaluated as a rapid diagnostic method. Three enzymes — phosphoglucose isomerase, malate dehydrogenase and lactate dehydrogenase — were found to be diagnostic, thus allowing clear differentiation of the three species.
Experimental Mycology | 1990
Helga Fo¨rster; Peter Oudemans; Michael D. Coffey
Abstract The extent of intraspecific mitochondrial DNA (mtDNA) diversity was investigated in isolates of Phytophthora capsici , P. citricola, P. citrophthora, P. megakarya, P. palmivora , and P. parasitica that represented a wide range of host plants and geographic origins. Phenograms were constructed following the analysis of restriction fragment patterns that were generated by several endonucleases. The six species showed different degrees of mtDNA diversity. Restriction fragment patterns in P. palmivora and P. parasitica were very uniform. Distinct subgroups could be distinguished in P. megakarya and P. citrophthora that correlated with the geographic origin or the host plant, respectively. These subgroups did not seem to be closely related to each other. High degrees of diversity were also evident in P. citricola and P. capsici . Although some isolates of P. capsici had identical mtDNA patterns, no distinct subgroups were found that could be correlated with either a specific host plant or geographic origin. In P. capsici and P. parasitica variation in nuclear DNA was much more pronounced as compared to mtDNA. In P. capsici both types of analysis correlated well. Because of very limited variation of mtDNA in P. parasitica a comparison between the two phenograms was difficult.
Fungal Biology | 1991
Peter Oudemans; Michael D. Coffey
Isozyme analysis was used to examine intraspecific diversity and interspecific relatedness of P. cactorum (group I) and twelve papillate species of Phytophthora within group II of Waterhouses (1963) taxonomic scheme. Isolates of six species, specifically P. botryosa, P. heveae, P. katsurae, P. meadii, P. palmivora and P. parasitica (P. nicotianae) , contained low levels of genetic diversity and were judged to be valid species. Based upon isozyme analysis, all isolates of P. arecae were found to be identical with some isolates of P. palmivora . Thus, it is proposed that these two species are synonymous. For P. parasitica , differences in oospore size or host plant were contrasted with the isozyme data using single locus coefficients and no evidence was found to support the existence of distinct varieties. In contrast, several other species, particularly P. capsici, P. citrophthora and P. megakarya , demonstrated much higher levels of variation in isozyme pattern and subgroups were readily identified. Isolates of P. capsici , including those previously identified as P. palmivora ‘MF4’ separated into three subgroups CAP1, CAP2 and CAP3. Those in CAP1 were from widely distributed geographical locations on a range of hosts including Capsicum sp., tomato, cucurbits, as well as cacao and black pepper and it contained the greatest amount of intraspecific diversity. A single representative of P. mexicana also clustered with this subgroup and as such is considered conspecific to P. capsici . CAP2 isolates were found primarily on black pepper and from Hawaii on Macadamia integrifolia as well as other hosts. In some instances, specifically with isolates from India and Indonesia on black pepper both CAP1 and CAP2 were found. However, the evidence from isozymes suggests that the two groups are genetically isolated from one another. All representatives of CAP3 were derived from diseased cacao in Brazil and this subgroup was monomorphic for all loci examined. P. citrophthora was divided into two subgroups. Isolates of CTR1 were derived from a large range of hosts including citrus and kiwi fruit. CTR2 was composed of only Brazilian isolates from cacao. P. megakarya , which has only been reported on cacao from West Africa, was also divided into two subgroups which were separated geographically. Isolates of MGK1 originated from either Nigeria or Guinea and isolates of MGK2 were from Cameroon. P. boehmeriae was the most genetically diverse species examined with four isozymically diverse ETs representing only 11 isolates. Interspecific comparisons revealed relationships which would not have been predicted based on morphological comparisons alone. For example, P. meadii and P. botryosa clustered together indicating a very close genetic relatedness. P. katsurae and P. heveae also formed a single cluster. However, comparison of oospores of these two species showed that the oogonial stalk length of P. katsurae was consistently much longer. Unexpectedly, P. capsici and P. citrophthora also formed a cluster indicating that they were genetically related. Finally, the results of this isozyme analysis suggest that the papillate species of Group II of Waterhouses (1963) scheme may form at least six distinct evolutionary lines.
PLOS ONE | 2011
Angela Chaparro-Garcia; Rachael C. Wilkinson; Selena Gimenez-Ibanez; Kim Findlay; Michael D. Coffey; Cyril Zipfel; John P. Rathjen; Sophien Kamoun; Sebastian Schornack
Background The filamentous oomycete plant pathogen Phytophthora infestans causes late blight, an economically important disease, on members of the nightshade family (Solanaceae), such as the crop plants potato and tomato. The related plant Nicotiana benthamiana is a model system to study plant-pathogen interactions, and the susceptibility of N. benthamiana to Phytophthora species varies from susceptible to resistant. Little is known about the extent to which plant basal immunity, mediated by membrane receptors that recognise conserved pathogen-associated molecular patterns (PAMPs), contributes to P. infestans resistance. Principal Findings We found that different species of Phytophthora have varying degrees of virulence on N. benthamiana ranging from avirulence (incompatible interaction) to moderate virulence through to full aggressiveness. The leucine-rich repeat receptor-like kinase (LRR-RLK) BAK1/SERK3 is a major modulator of PAMP-triggered immunity (PTI) in Arabidopsis thaliana and N. benthamiana. We cloned two NbSerk3 homologs, NbSerk3A and NbSerk3B, from N. benthamiana based on sequence similarity to the A. thaliana gene. N. benthamiana plants silenced for NbSerk3 showed markedly enhanced susceptibility to P. infestans infection but were not altered in resistance to Phytophthora mirabilis, a sister species of P. infestans that specializes on a different host plant. Furthermore, silencing of NbSerk3 reduced the cell death response triggered by the INF1, a secreted P. infestans protein with features of PAMPs. Conclusions/Significance We 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. In the future, the identification of novel surface receptors that associate with NbSERK3A and/or NbSERK3B should lead to the identification of new receptors that mediate recognition of oomycete PAMPs, such as INF1.
Fungal Biology | 2000
Helga Förster; Michael P. Cummings; Michael D. Coffey
Phylogenetic relationships among Phytophthora species were investigated by sequence analysis of the internal transcribed spacer region I of the ribosomal DNA repeat unit. The extensive collection of isolates included taxa from all six morphological groups recognized by Waterhouse (1963) including molecular groups previously identified using isozymes and mtDNA restriction fragment length polymorphisms. Similar to previous studies, the inferred relationships indicated that molecular groups of P. cryptogea}drechslerilike and P. megasperma-like taxa are polyphyletic. Morphological groups V and VI, which are dierentiated by the presence of amphigynous or paragynous antheridia, are not monophyletic: species of the two groups are interspersed in the tree. Species with papillate and semi-papillate sporangia (groups I‐IV) clustered together and this cluster was distinct from those of species with nonpapillate sporangia. There was no congruence between the mode of antheridial attachment, sporangial caducity, or homo- or heterothallic habit and the molecular grouping of the species. Our study provides evidence that the antheridial position together with homo- or heterothallic habit does not reflect phylogenetic relationships within Phytophthora. Consequently, confirming studies done previously (Cooke & Duncan 1997), this study provides evidence that the morphological characters used in Phytophthora taxonomy are of limited value for deducing phylogenetic relationships, because they exhibit convergent evolution.
Fungal Biology | 1991
Scott D. Mills; Helga Förster; Michael D. Coffey
Intra- and interspecific isozyme variation was evaluated for 123 isolates assigned to either Phytophthora cryptogea or P. drechsleri , and compared with that of 15 isolates of P. erythroseptica and 11 isolates of P. lateralis . Isolates of P. cryptogea and P. drechsleri were from worldwide sources and displayed a high degree of variability. The majority of these isolates were subsequently divided into ten distinct groups based on numerical analysis of 24 putative enzyme loci. None of the enzyme loci were monomorphic for all ten groups. Analysis of mitochondrial (mt) DNA restriction fragment length polymorphisms of selected isolates from each isozyme group supported the isozyme data. Differences in morphological features of the ten isozyme groups of P. cryptogea and P. drechsleri were not sufficiently distinct to readily distinguish between them. Isozyme analysis of P. erythroseptica revealed that it is a uniform and distinct taxon. The isolates of P. lateralis also formed a homogeneous and discrete group. An interspecific comparison revealed that the variation among the ten isozyme groups of P. cryptogea and P. drechsleri was as great as that observed among P. cinnamomi, P. cambivora, P. lateralis, P. erythroseptica and P. richardiae . The combined results of isozyme and mtDNA analysis indicate that there are at least seven distinct molecular species represented by the 123 isolates of P. cryptogea and P. drechsleri evaluated in this study.
Fungal Genetics and Biology | 2014
Frank N. Martin; Jaime E. Blair; Michael D. Coffey
The most recent phylogenetic analysis of the genus Phytophthora was completed in 2008 (Blair et al., 2008) and utilized 8.1 kb of sequence data from seven nuclear loci. Given the large number of species that have recently been described, this study was undertaken to broaden the available information on the phylogeny of the genus. A total of 166 isolates representing 92 recognized species and 17 provisional species were analyzed, including many of the same isolates used in the nuclear multilocus study of Blair et al. (2008). Four mitochondrial genes (cox2, nad9, rps10 and secY) were sequenced with a total of 2373 bp used in the analysis; the species relationships recovered with mitochondrial data were largely consistent with those observed previously in the nuclear analysis. Combining the new mitochondrial data with the nuclear data from Blair et al. (2008) generated a dataset of 10,828 bp representing 11 loci, however resolution of basal clade relationships was still low. We therefore implemented a modified multispecies coalescent approach with a subset of the data, and recovered increased resolution and moderate to high support for clade relationships. 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. As has been reported in other phylogenetic studies of the genus, there was no consistent correlation between phylogenetic relatedness and morphological features or ecology.
Phytopathology | 2010
Seogchan Kang; Michele A. Mansfield; Bongsoo Park; David M. Geiser; Kelly Ivors; Michael D. Coffey; Niklaus J. Grünwald; Frank N. Martin; C. André Lévesque; Jaime E. Blair
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 deduction 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.