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PubMed2006

Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions.

The Phytophthora Functional Genomics Database (PFGD; http://www.pfgd.org), developed by the National Center for Genome Resources in collaboration with The Ohio State University-Ohio Agricultural Research and Development Center (OSU-OARDC), is a publicly accessible information resource for Phytophthora-plant interaction research. PFGD contains transcript, genomic, gene expression and functional assay data for Phytophthora infestans, which causes late blight of potato, and Phytophthora sojae, which affects soybeans. Automated analyses are performed on all sequence data, including consensus sequences derived from clustered and assembled expressed sequence tags. The PFGD search filter interface allows intuitive navigation of transcript and genomic data organized by library and derived queries using modifiers, annotation keywords or sequence names. BLAST services are provided for libraries built from the transcript and genomic sequences. Transcript data visualization tools include Quality Screening, Multiple Sequence Alignment and Features and Annotations viewers. A genomic browser that supports comparative analysis via novel dynamic functional annotation comparisons is also provided. PFGD is integrated with the Solanaceae Genomics Database (SolGD; http://www.solgd.org) to help provide insight into the mechanisms of infection and resistance, specifically as they relate to the genus Phytophthora pathogens and their plant hosts.

Algal Proteins↗
PubMed1998

Heterologous expression of a basic elicitin from Phytophthora cryptogea in Phytophthora infestans increases its ability to cause leaf necrosis in tobacco.

The cry-b sequence, encoding a basic elicitin (cryptogein B) from Phytophthora cryptogea, was co-transformed into Phytophthora infestans. The copy number of the cry-b sequence varied in co-transformants. Nevertheless, in all cases the alien elicitin gene was transcribed, translated and the protein secreted in vitro from such transformants. Moreover, the secreted cryptogein B from P. infestans co-transformants increased their ability to cause a hypersensitive-response-like necrosis of tobacco leaves. It was thus concluded that the transfer of a single gene encoding a basic elicitin from one Phytophthora species to another can dramatically alter the phenotypic interaction of the transformed species with tobacco.

Algal Proteins↗
PubMed1997

Mating-type loci segregate aberrantly in Phytophthora infestans but normally in Phytophthora parasitica: implications for models of mating-type determination.

In the oomycete, Phytophthora infestans, mating type is determined by a locus that segregates in a non-Mendelian manner consistent with its linkage to a system of balanced lethals. The significance of this unusual phenomenon was addressed by studying the segregation patterns of DNA markers linked to mating type in the related species, P. parasitica. This was done using loci identified by either RAPD analysis of P. parasitica crosses or by cross-hybridization with RFLP markers linked to mating type in P. infestans. The resulting data revealed that, unlike P. infestans, mating type in P. parasitica was regulated by a locus displaying Mendelian segregation. An improved model for mating-type determination in Phytophthora is presented.

Chromosome Mapping↗
PubMed2005

Production of an anti-fungal substance for biological control of Phytophthora capsici causing phytophthora blight in red-peppers by Streptomyces halstedii.

The culture broth of Streptomyces halstedii AJ-7 suppressed the growth of Phytophthora capsici, which causes phytophthora blight in red-peppers, with less than 1% survival of the pathogen after 12 h of treatment. The low molecular fraction (< or = 10 kDa) of the culture broth retained anti-fungal activity against P. capsici after being held at 100 degrees C for 6 h.

Capsicum↗
PubMed1991

Genetic transformation of the plant pathogens Phytophthora capsici and Phytophthora parasitica.

Phytophthora capsici and P.parasitica were transformed to hygromycin B resistance using plasmids pCM54 and pHL1, which contain the bacterial hygromycin B phosphotransferase gene (hph) fused to promoter elements of the Ustilago maydis heat shock hsp70 gene. Enzymes Driselase and Novozyme 234 were used to generate protoplasts which were then transformed following exposure to plasmid DNA and polyethylene glycol 6000. Transformation frequencies of over 500 transformants per micrograms of DNA per 1 x 10(6) protoplasts were obtained. Plasmid pCM54 appears to be transmitted in Phytophthora spp. as an extra-chromosomal element through replication, as shown by Southern blot hybridization and by the loss of plasmid methylation. In addition, transformed strains retained their capacity of infecting Serrano pepper seedlings and Mc. Intosh apple fruits, the host plants for P.capsici and P.parasitica, respectively.

Blotting, Southern↗
PubMed2006

The repertoire of transfer RNA genes is tuned to codon usage bias in the genomes of Phytophthora sojae and Phytophthora ramorum.

In all, 238 and 155 transfer (t)RNA genes were predicted from the genomes of Phytophthora sojae and P. ramorum, respectively. After omitting pseudogenes and undetermined types of tRNA genes, there remained 208 P. sojae tRNA genes and 140 P. ramorum tRNA genes. There were 45 types of tRNA genes, with distinct anticodons, in each species. Fourteen common anticodon types of tRNAs are missing altogether from the genome in the two species; however, these appear to be compensated by wobbling of other tRNA anticodons in a manner which is tied to the codon bias in Phytophthora genes. The most abundant tRNA class was arginine in both P. sojae and P. ramorum. A codon usage table was generated for these two organisms from a total of 9,803,525 codons in P. sojae and 7,496,598 codons in P. ramorum. The most abundant codon type detected from the codon usage tables was GAG (encoding glutamic acid), whereas the most numerous tRNA gene had a methionine anticodon (CAT). The correlation between the frequencies of tRNA genes and the codon frequencies in protein-coding genes was very low (0.12 in P. sojae and 0.19 in P. ramorum); however, the correlation between amino acid tRNA gene frequency and the corresponding amino acid codon frequency in P. sojae and P. ramorum was substantially higher (0.53 in P. sojae and 0.77 in P. ramorum). The codon usage frequencies of P. sojae and P ramorum were very strongly correlated (0.99), as were tRNA gene frequencies (0.77). Approximately 60% of orthologous tRNA gene pairs in P sojae and P. ramorum are located in regions that have conserved synteny in the two species.

Anticodon↗
PubMed1998

Identification of ceramide-phosphorylethanolamine in oomycete plant pathogens: Pythium ultimum, Phytophthora infestans, and Phytophthora capsici.

Cellular lipids were extracted from three species of Oomycete plant pathogens (Pythium ultimum, Phytophthora infestans, and Ph. capsici) and analyzed via normal-phase high-performance liquid chromatography with flame-ionization detection. The most abundant polar lipids in each of the three species were the polar membrane lipids, phosphatidylethanolamine (PE), phosphatidylcholine, and a phosphosphingolipid that eluted soon after PE. Structural analysis via mass spectrometry and nuclear magnetic resonance spectrometry revealed that the phosphosphingolipid was ceramide phosphorylethanolamine (Cer-PE). The most abundant molecular species of Cer-PE in P. ultimum had a molecular weight of 670.5, contained an unusual 19-carbon branched triunsaturated sphingoid (C19-delta 4, 8, 10, 9-methyl long-chain base) and palmitic acid as the amide-linked fatty acid. The most abundant molecular species of Cer-PE in Ph. infestans had a molecular weight of 714.5, contained a common 16-carbon 1,3 di-OH sphingoid, and erucic (cis 13-docosenoic, C22-delta 13) acid as the amide-linked fatty acid. The Cer-PE in Ph. capsici comprised a mixture of each of the two molecular species found in P. ultimum and Ph. infestans.

Ceramides↗
PubMed2005

Characterisation of European and North American Phytophthora ramorum isolates due to their morphology and mating behaviour in vitro with heterothallic Phytophthora species.

Vegetative growth rate, and size of sporangia, chlamydospores and oospores from 94 P. ramorum isolates were measured and the isolates were paired in vitro with four different heterothallic Phytophthora species isolated from infected nursery plants in Germany. P. ramorum isolates originated from different European countries and from Canada and the USA. 66 of the 67 European isolates were determined as mating type A1; only one isolate was of mating type A2. Of the 27 North American isolates tested, seven (all from nurseries) were determined to be the A1 mating type and 17 to be the A2 mating type. Three isolates did not produce gametangia during the incubation period. Discriminant analysis of all data allowed a grouping based on the vegetative growth rate. The two groups corresponded with the mating type no matter whether the isolates originated from Europe or North America. The A1 isolates were much more homogeneous in their morphology than the A2 isolates. They grew faster, had larger chlamydospores and did not produce gametangia with P. cambivora. Within the A2 group, the single European isolate of mating type A2 (BBA 16/02) and three US isolates showed intermediate characters and were classified with the discriminant function into that of the opposite mating type. The morphological characters and the mating behaviour of the isolates will be discussed.

Crosses, Genetic↗
PubMed2006

Extensive variation in nuclear mitochondrial DNA content between the genomes of Phytophthora sojae and Phytophthora ramorum.

Fragments of mitochondrial DNA (mtDNA) transferred to the nuclear genome are called nuclear mitochondrial DNAs (NUMTs). We report here a comparison of NUMT content between genomes from two species of the same genus. Analysis of the genomes of Phytophthora sojae and P. ramorum revealed large differences in the NUMT content of the two genomes: 16.27 x 10(-3) and 2.28 x 10(-3)% of each genome, respectively. Substantial differences also exist between the two species in the sizes of the NUMTs found in each genome, with ranges of 20 to 405 bp for P. sojae and 19 to 137 bp for P. ramorum. Furthermore, in P. sojae, fragments from the mitochondrial genes rns, rnl, coxl, and nad (various subunits) are found most frequently, whereas P. ramorum NUMTs most often originate from the cox3, rpsl4, nad4, and nad5 genes. The large differences in the presumptive mtDNA insertions suggest that the insertions occurred subsequent to the divergence of the two species, and this is supported by sequence comparisons among the NUMTs and the mtDNA sequences of the two species. P. sojae mtDNA sequences inserted in the nuclear genome appear to have been altered as a result of insertions, deletions, inversions, and translocations and provide insights into active mechanisms of sequence divergence in this plant pathogen. No clear examples were found of NUMTs forming functional nuclear genes or of NUMTs inserted into exons or introns of any nuclear gene.

Cell Nucleus↗
PubMed2003

Single-strand-conformation polymorphism of ribosomal DNA for rapid species differentiation in genus Phytophthora.

Single-strand-conformation polymorphism (SSCP) of ribosomal DNA of 29 species (282 isolates) of Phytophthora was characterized in this study. Phytophthora boehmeriae, Phytophthora botryosa, Phytophthora cactorum, Phytophthora cambivora, Phytophthora capsici, Phytophthora cinnamomi, Phytophthora colocasiae, Phytophthora fragariae, Phytophthora heveae, Phytophthora hibernalis, Phytophthora ilicis, Phytophthora infestans, Phytophthora katsurae, Phytophthora lateralis, Phytophthora meadii, Phytophthora medicaginis, Phytophthora megakarya, Phytophthora nicotianae, Phytophthora palmivora, Phytophthora phaseoli, Phytophthora pseudotsugae, Phytophthora sojae, Phytophthora syringae, and Phytophthora tropicalis each showed a unique SSCP pattern. Phytophthora citricola, Phytophthora citrophthora, Phytophthora cryptogea, Phytophthora drechsleri, and Phytophthora megasperma each had more than one distinct pattern. A single-stranded DNA ladder also was developed, which facilitates comparison of SSCP patterns within and between gels. With a single DNA fingerprint, 277 isolates of Phytophthora recovered from irrigation water and plant tissues in Virginia were all correctly identified into eight species at substantially reduced time, labor, and cost. The SSCP analysis presented in this work will aid in studies on taxonomy, genetics, and ecology of the genus Phytophthora.

DNA, Fungal↗
PubMedDate not supplied

Examination of some morphologically unusual cultures of Phytophthora species using a mitochondrial DNA miniprep technique and a standardised sporangium caducity assessment.

Using the mitochondrial DNA miniprep technique, the identity of sixteen morphologically unusual cultures allocated to Phytophthora nicotianae, Phytophthora mexicana or Phytophthora porri was determined by comparison with a library of mtDNA band patterns obtained from reference cultures. Seven cultures were identified as Phytophthora nicotianae (including those assigned to Phytophthora mexicana and Phytophthora porri), six as strains of Phytophthora palmivora with small, ovoid, weakly caducous sporangia, and one as Phytophthora citrophthora. Some cultures of P. nicotianae had a low percentage of caducous sporangia. Percentage sporangium caducity, but not sporangium L:B ratio, is considered a useful taxonomic criterion for separating species morphologically similar to Phytophthora nicotianae. One culture from tobacco in New Zealand had a highly unusual morphology and a unique DNA band pattern, but was not identifiable. One culture from Acacia mearnsii in South Africa had a unique DNA band pattern which was identical to that of an isolate from Annona squamosa from Australia previously identified as Phytophthora palmivora, the precise identity of which is still unclear. The identity of most isolates from diseased durian was found to be Phytophthora palmivora, confirming its role as the main pathogen, but P. nicotianae was also identified from this host.

Journal Article↗
PubMed2005

Ancient origin of elicitin gene clusters in Phytophthora genomes.

The genus Phytophthora belongs to the oomycetes in the eukaryotic stramenopile lineage and is comprised of over 65 species that are all destructive plant pathogens on a wide range of dicotyledons. Phytophthora produces elicitins (ELIs), a group of extracellular elicitor proteins that cause a hypersensitive response in tobacco. Database mining revealed several new classes of elicitin-like (ELL) sequences with diverse elicitin domains in Phytophthora infestans, Phytophthora sojae, Phytophthora brassicae, and Phytophthora ramorum. ELIs and ELLs were shown to be unique to Phytophthora and Pythium species. They are ubiquitous among Phytophthora species and belong to one of the most highly conserved and complex protein families in the Phytophthora genus. Phylogeny construction with elicitin domains derived from 156 ELIs and ELLs showed that most of the diversified family members existed prior to divergence of Phytophthora species from a common ancestor. Analysis to discriminate diversifying and purifying selection showed that all 17 ELI and ELL clades are under purifying selection. Within highly similar ELI groups there was no evidence for positively selected amino acids suggesting that purifying selection contributes to the continued existence of this diverse protein family. Characteristic cysteine spacing patterns were found for each phylogenetic clade. Except for the canonical clade ELI-1, ELIs and ELLs possess C-terminal domains of variable length, many of which have a high threonine, serine, or proline content suggesting an association with the cell wall. In addition, some ELIs and ELLs have a predicted glycosylphosphatidylinositol site suggesting anchoring of the C-terminal domain to the cell membrane. The eli and ell genes belonging to different clades are clustered in the genomes. Overall, eli and ell genes are expressed at different levels and in different life cycle stages but those sharing the same phylogenetic clade appear to have similar expression patterns.

Algal Proteins↗
PubMed1976

Specificity of cytoplasmic and cell-wall antigens from four species of Phytophthora.

Cytoplasmic and cell-wall antigens and antisera were prepared from four Phytophthora species, and cell-wall antigens were prepared from two Pythium species. Immunodiffusion of the Pythium and Phytophthora cell-wall antigens showed that the two Pythium species did not cross-react with the Phytophthora cell-wall antisera. Immunodiffusion analysis of both cell-wall and cytoplasmic antigens of Phytophthora revealed some degree of specificity between species but not between A1 and A2 mating types in Phytophthora cinnamomi. Species specificity was improved by using indirect fluorescent antibody techniques and by the use of cross-absorbed sera. Agglutination and quantitative precipitation techniques did not significantly improve specificity. It was possible to distinguish serologically between Phytophthora cinnamomi and Phytophthora cambivora and the Phytophthora cryptogea-Phytophthora drechsleri group. The absence of consistent serological variation between P. cryptogea and P dreschsleri is consistent with the suggestion (Bumbieris, 1974) that P. cryptogea and P. drechsleri should be considered as one species.

Agglutination Tests↗
PubMed2003

Identification of QTLs related to cocoa resistance to three species of Phytophthora.

This study aimed to compare the genetic control of cacao resistance to three species of Phytophthora: Phytophthora palmivora, Phytophthora megakarya and Phytophthora capsici. The study was conducted on 151 hybrid progenies created in Côte d'Ivoire and grown in a green-house in Montpellier. Phytophthora resistance was screened by leaf-test inoculation with two different strains per species. Selection of the best individuals for resistance to P. palmivora at a 10% selection rate, would lead to a genetic progress of 47% in the disease evaluation for this species and a genetic progress of 42% and 21% for the two other species. A genetic map with a total length of 682 cM was built with 213 markers, 190 AFLPs and 23 microsatellites. QTLs were identified using composite interval mapping. QTLs were found located in six genomic regions. One of these was detected with five strains belonging to the three Phytophthora species. Two other regions were detected with two or three strains of two different species. Three additional QTLs were detected for only one species of Phytophthora. Each QTL explained between 8 to 12% of the phenotypic variation. For each strain, between 11.5% to 27.5% of the total phenotypic variation could be explained by the QTLs identified. The identification of multiple QTLs involved in resistance to Phytophthora offers the possibility to improve durability of resistance in cocoa by a possible cumulation of many different resistance genes located in different chromosome regions using marker-aided selection.

Cacao↗
PubMed2005

A transmembrane phospholipase D in Phytophthora; a novel PLD subfamily.

Phospholipase D (PLD) is a ubiquitous enzyme in eukaryotes that participates in various cellular processes. Its catalytic domain is characterized by two HKD motifs in the C-terminal part. Until now, two subfamilies were recognized based on their N-terminal domain structure. The first has a PX domain in combination with a PH domain and is designated as PXPH-PLD. Members of the second subfamily, named C2-PLD, have a C2 domain and have, so far, only been found in plants. Here we describe a novel PLD subfamily that we identified in Phytophthora, a genus belonging to the class oomycetes and comprising many important plant pathogens. We cloned Pipld1 from Phytophthora infestans and retrieved full-length sequences of its homologues from Phytophthora sojae and Phytophthora ramorum genome databases. Their promoters contain two putative regulatory elements, one of which is highly conserved in all three genes. The three Phytophthora pld1 genes encode nearly identical proteins of around 1807 amino acids, with the two characteristic HKD motifs in the C-terminal part. Homology of the predicted proteins with known PLDs however is restricted to the two catalytic HKD motifs and adjacent domains. In the N-terminal part Phytophthora PLD1 has a PX-like domain, but it lacks a PH domain. Instead the N-terminal region contains five putative membrane spanning domains suggesting that Phytophthora PLD1 is a transmembrane protein. Since Phytophthora PLD1 cannot be categorized in one of the two existing subfamilies we propose to create a novel subfamily named PXTM-PLD.

Algal Proteins↗
PubMed2000

A molecular phylogeny of Phytophthora and related oomycetes.

Phylogenetic relationships among 50 Phytophthora species and between Phytophthora and other oomycetes were examined on the basis of the ITS sequences of genomic rDNA. Phytophthora grouped with Pythium, Peronospora, and Halophytophthora, distant from genera in the Saprolegniales. Albugo was intermediate between these two groups. Unlike Pythium, Phytophthora was essentially monophyletic, all but three species forming a cluster of eight clades. Two clades contained only species with nonpapillate sporangia. The other six clades included either papillate and semipapillate, or semipapillate and nonpapillate types, transcending traditional morphological groupings, which are evidently not natural assemblages. Peronospora was related to P. megakarya and P. palmivora and appears to be derived from a Phytophthora that has both lost the ability to produce zoospores and become an obligate biotroph. Three other Phytophthoras located some distance from the main Phytophthora-Peronospora cluster probably represent one or more additional genera.

DNA, Fungal↗
PubMed2006

Nonneutral GC3 and retroelement codon mimicry in Phytophthora.

Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.

Base Composition↗