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Wang W, Liu Y, Xue Z, Li J, Wang Z, Liu X. Activity of the Novel Fungicide SYP-34773 against Plant Pathogens and Its Mode of Action on Phytophthora infestans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11794-11803. [PMID: 34605240 DOI: 10.1021/acs.jafc.1c02679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
SYP-34773 is a pyrimidinamine derivative and a novel fungicide modified from diflumetorim. This study determined the antimicrobial spectrum of SYP-34773, which showed it could strongly inhibit the growth of some important plant pathogens including fungi and oomycetes. In particular, Phytophthora infestans is an oomycete sensitive to SYP-34773, and the mycelium growth stage was found to be the most sensitive stage, with an EC50 value of 0.2030 μg/mL. At a concentration of 200 μg/mL, SYP-34773 displayed an excellent control efficacy of 69.55% and 81.48% against potato and tomato blight disease caused by P. infestans under field conditions, respectively. Mode of action investigations showed that this fungicide could cause severe ultrastructure damage to the mycelia of P. infestans, inhibit its respiration, and increase the cell membrane permeability of this pathogen. The results of this study could provide useful information for the fungicide registration and application of SYP-34773 as a novel fungicide.
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Affiliation(s)
- Weizhen Wang
- China Agricultural University, Beijing 100193, People's Republic of China
| | - Ying Liu
- China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhaolin Xue
- China Agricultural University, Beijing 100193, People's Republic of China
| | - Jingru Li
- China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhiwen Wang
- China Agricultural University, Beijing 100193, People's Republic of China
| | - Xili Liu
- China Agricultural University, Beijing 100193, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, People's Republic of China
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Niu X, Ah-Fong AMV, Lopez LA, Judelson HS. Transcriptomic and proteomic analysis reveals wall-associated and glucan-degrading proteins with potential roles in Phytophthora infestans sexual spore development. PLoS One 2018; 13:e0198186. [PMID: 29897992 PMCID: PMC5999078 DOI: 10.1371/journal.pone.0198186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/14/2018] [Indexed: 11/19/2022] Open
Abstract
Sexual reproduction remains an understudied feature of oomycete biology. To expand our knowledge of this process, we used RNA-seq and quantitative proteomics to examine matings in Phytophthora infestans. Exhibiting significant changes in mRNA abundance in three matings between different A1 and A2 strains compared to nonmating controls were 1170 genes, most being mating-induced. Rising by >10-fold in at least one cross were 455 genes, and 182 in all three crosses. Most genes had elevated expression in a self-fertile strain. Many mating-induced genes were associated with cell wall biosynthesis, which may relate to forming the thick-walled sexual spore (oospore). Several gene families were induced during mating including one encoding histidine, serine, and tyrosine-rich putative wall proteins, and another encoding prolyl hydroxylases which may strengthen the extracellular matrix. The sizes of these families vary >10-fold between Phytophthora species and one exhibits concerted evolution, highlighting two features of genome dynamics within the genus. Proteomic analyses of mature oospores and nonmating hyphae using isobaric tags for quantification identified 835 shared proteins, with 5% showing >2-fold changes in abundance between the tissues. Enriched in oospores were β-glucanases potentially involved in digesting the oospore wall during germination. Despite being dormant, oospores contained a mostly normal complement of proteins required for core cellular functions. The RNA-seq data generated here and in prior studies were used to identify new housekeeping controls for gene expression studies that are more stable than existing normalization standards. We also observed >2-fold variation in the fraction of polyA+ RNA between life stages, which should be considered when quantifying transcripts and may also be relevant to understanding translational control during development.
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Affiliation(s)
- Xiaofan Niu
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
| | - Audrey M. V. Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
| | - Lilianna A. Lopez
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
| | - Howard S. Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
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Grenville-Briggs LJ, Horner NR, Phillips AJ, Beakes GW, van West P. A family of small tyrosine rich proteins is essential for oogonial and oospore cell wall development of the mycoparasitic oomycete Pythium oligandrum. Fungal Biol 2013; 117:163-72. [PMID: 23537873 DOI: 10.1016/j.funbio.2013.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 12/31/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
The mycoparasitic oomycete Pythium oligandrum is homothallic, producing an abundance of thick-walled spiny oospores in culture. After mining a cDNA sequence dataset, we identified a family of genes that code for small tyrosine rich (Pythium oligandrumsmall tyrosine rich (PoStr)) proteins. Sequence analysis identified similarity between the PoStr proteins and putative glycine-rich cell wall proteins from the related plant pathogenic oomycete Pythium ultimum, and mating-induced genes from the oomycete Phytophthora infestans. Expression analysis showed that PoStr transcripts accumulate during oospore production in culture and immunolocalisation indicates the presence of these proteins in oogonial and oospore cell walls. PoStr protein abundance correlated positively with production of oogonia as determined by antibiotic-mediated oogonia suppression. To further characterise the role of PoStr proteins in P. oligandrum oospore production, we silenced this gene family using homology-dependent gene silencing. This represents the first characterisation of genes using gene silencing in a Pythium species. Oospores from silenced strains displayed major ultrastructural changes and were sensitive to degradative enzyme treatment. Oogonia of silenced strains either appeared to be arrested at the mature oosphere stage of development or in around 40 % of the structures, showed a complete suppression of oospore formation. Suppressed oogonia were highly vacuolated and the oogonium wall was thickened by a new inner wall layer. Our data suggest PoStr proteins are probably integral structural components of the normal oospore cell wall and play a key role in oospore formation.
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Affiliation(s)
- Laura J Grenville-Briggs
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm SE-106 91, Sweden
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Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1350-60. [PMID: 22712506 PMCID: PMC3551261 DOI: 10.1094/mpmi-02-12-0028-r] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.
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Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution. EUKARYOTIC CELL 2012; 11:1304-12. [PMID: 22923046 DOI: 10.1128/ec.00155-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.
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Llaurens V, McMullan M, van Oosterhout C. Cryptic MHC Polymorphism Revealed but Not Explained by Selection on the Class IIB Peptide-Binding Region. Mol Biol Evol 2012; 29:1631-44. [DOI: 10.1093/molbev/mss012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Horner NR, Grenville-Briggs LJ, van West P. The oomycete Pythium oligandrum expresses putative effectors during mycoparasitism of Phytophthora infestans and is amenable to transformation. Fungal Biol 2011; 116:24-41. [PMID: 22208599 DOI: 10.1016/j.funbio.2011.09.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 09/16/2011] [Accepted: 09/20/2011] [Indexed: 01/22/2023]
Abstract
The oomycete Pythium oligandrum is a mycoparasitic biocontrol agent that is able to antagonise several plant pathogens, and can promote plant growth. In order to test the potential usefulness of P. oligandrum as a biocontrol agent against late blight disease caused by the oomycete Phytophthora infestans, we investigated the interaction between P. oligandrum and Ph. infestans using the green fluorescent protein (GFP) as a reporter gene. A CaCl(2) and polyethylene-glycol-based DNA transformation protocol was developed for P. oligandrum and transformants constitutively expressing GFP were produced. Up to 56 % of P. oligandrum transformants showed both antibiotic resistance and fluorescence. Mycoparasitic interactions, including coiling of P. oligandrum hyphae around Ph. infestans hyphae, were observed with fluorescent microscopy. To gain further insights into the nature of P. oligandrum mycoparasitism, we sequenced 2376 clones from cDNA libraries of P. oligandrum mycelium grown in vitro, or on heat-killed Ph. infestans mycelium as the sole nutrient source. 1219 consensus sequences were obtained including transcripts encoding glucanases, proteases, protease inhibitors, putative effectors and elicitors, which may play a role in mycoparasitism. This represents the first published expressed sequence tag (EST) resource for P. oligandrum and provides a platform for further molecular studies and comparative analysis in the Pythiales.
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Affiliation(s)
- Neil R Horner
- Aberdeen Oomycete Laboratory, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, UK
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Raffaele S, Win J, Cano LM, Kamoun S. Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics 2010; 11:637. [PMID: 21080964 PMCID: PMC3091767 DOI: 10.1186/1471-2164-11-637] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 11/16/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation. RESULTS We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors. CONCLUSIONS This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.
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Affiliation(s)
- Sylvain Raffaele
- The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK
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Abstract
Phytophthora infestans remains a problem to production agriculture. Historically there have been many controversies concerning its biology and pathogenicity, some of which remain today. Advances in molecular biology and genomics promise to reveal fascinating insight into its pathogenicity and biology. However, the plasticity of its genome as revealed in population diversity and in the abundance of putative effectors means that this oomycete remains a formidable foe.
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Affiliation(s)
- William Fry
- Cornell University, Department of Plant Pathology, Ithaca, NY 14853, USA.
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Blair JE, Coffey MD, Park SY, Geiser DM, Kang S. A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet Biol 2008; 45:266-77. [DOI: 10.1016/j.fgb.2007.10.010] [Citation(s) in RCA: 359] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 09/17/2007] [Accepted: 10/15/2007] [Indexed: 11/30/2022]
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Sipos B, Somogyi K, Andó I, Pénzes Z. T2prhd: a tool to study the patterns of repeat evolution. BMC Bioinformatics 2008; 9:27. [PMID: 18205906 PMCID: PMC2267704 DOI: 10.1186/1471-2105-9-27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 01/18/2008] [Indexed: 11/18/2022] Open
Abstract
Background The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Phylogenetic reconstruction is the method of choice to study the evolution of gene families and also sequence repeats in the light of these models. The characterization of the gene family evolution in view of the evolutionary models is done by the evaluation of the clustering of the sequences with the originating loci in mind. As the locus represents positional information, it is straightforward that in the case of the repeats the exact position in the sequence should be used, as the simple numbering according to repeat order can be misleading. Results We have developed a novel rapid visual approach to study repeat evolution, that takes into account the exact repeat position in a sequence. The "pairwise repeat homology diagram" visualizes sequence repeats detected by a profile HMM in a pair of sequences and highlights their homology relations inferred by a phylogenetic tree. The method is implemented in a Perl script (t2prhd) available for downloading at and is also accessible as an online tool at . The power of the method is demonstrated on the EGF-like and fibronectin-III-like (Fn-III) domain repeats of three selected mammalian Tenascin sequences. Conclusion Although pairwise repeat homology diagrams do not carry all the information provided by the phylogenetic tree, they allow a rapid and intuitive assessment of repeat evolution. We believe, that t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families), as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of scripts.
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Affiliation(s)
- Botond Sipos
- Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, P.O. Box 521, H-6701 Szeged, Hungary.
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Intraspecific concerted evolution of the rDNA ITS1 in Anopheles farauti sensu stricto (Diptera: Culicidae) reveals recent patterns of population structure. J Mol Evol 2008; 67:397-411. [PMID: 18818859 PMCID: PMC9931795 DOI: 10.1007/s00239-008-9161-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 06/18/2008] [Accepted: 08/28/2008] [Indexed: 10/21/2022]
Abstract
We examined the intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) of Anopheles farauti to determine the level of divergence among populations for this important malarial vector. We isolated 187 clones from 70 individuals and found regional variation among four internal tandem repeats. The data were partitioned prior to analysis given the presence of a paralogous ITS2 sequence, called the 5'-subrepeat, inserted in the ITS1 of most clones. A high level of homogenization and population differentiation was observed for this repeat, which indicates a higher rate of turnover relative to the adjacent 'core' region. Bayesian analysis was performed using several substitutional models on both a combined and a partitioned data set. On the whole, the ITS1 phylogeny and geographic origin of the samples appear to be congruent. Some interesting exceptions indicate the spread of variant repeats between populations and the retention of ancestral polymorphism. Our data clearly demonstrate concerted evolution at the intraspecific level despite intraindividual variation and a complex internal repeat structure from a species that occupies a continuous coastal distribution. A high rate of genomic turnover in combination with a high level of sequence divergence appears to be a major factor leading to its concerted evolution within these populations.
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Prakob W, Judelson HS. Gene expression during oosporogenesis in heterothallic and homothallic Phytophthora. Fungal Genet Biol 2007; 44:726-39. [PMID: 17215149 DOI: 10.1016/j.fgb.2006.11.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 11/21/2006] [Accepted: 11/28/2006] [Indexed: 11/24/2022]
Abstract
A large-scale screen for genes induced during sexual development was performed in the heterothallic oomycete Phytophthora infestans, the potato blight agent. Of 15,644 unigenes on an Affymetrix chip, 87 were induced >10-fold during mating, with 28 induced >100-fold. This was validated in independent matings using RNA blots and RT-PCR. Only 44 genes resembled sequences in GenBank. These encoded regulators such as protein kinases, protein phosphatases, and transcription factors, plus enzymes with metabolic, transport, or cell-cycle activities. Several genes were induced during both mating and asexual sporogenesis, suggesting crosstalk between those pathways. In the homothallic species P. phaseoli, 20% of the 87 genes were expressed at higher levels during conditions conducive to oosporogenesis than non-conducive conditions, while the rest were at similar levels. Many of the latter exhibited higher mRNA concentrations in P. phaseoli than in any non-mating culture of P. infestans, suggesting that part of the sexual pathway is active constitutively in homothallics.
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Affiliation(s)
- Waraporn Prakob
- Department of Plant Pathology, University of California, Riverside, CA 92521, USA
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Judelson HS. Genomics of the plant pathogenic oomycete Phytophthora: insights into biology and evolution. ADVANCES IN GENETICS 2007; 57:97-141. [PMID: 17352903 DOI: 10.1016/s0065-2660(06)57003-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The genus Phytophthora includes many destructive pathogens of plants. Although having "fungus-like" appearances, Phytophthora species reside in a eukaryotic kingdom separate from that of true fungi. Distinct strategies are therefore required to study and defend against Phytophthora. Large sequence databases have recently been developed for several species, and tools for functional genomics have been enhanced. This chapter will review current progress in understanding the genome and transcriptome of Phytophthora, and provide examples of how genomics resources are advancing molecular studies of pathogenesis, development, transcription, and evolution. A better understanding of these remarkable pathogens should lead to new approaches for managing their diseases.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
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Qutob D, Tedman-Jones J, Gijzen M. Effector-triggered immunity by the plant pathogen Phytophthora. Trends Microbiol 2006; 14:470-3. [PMID: 16996740 DOI: 10.1016/j.tim.2006.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 09/07/2006] [Accepted: 09/12/2006] [Indexed: 11/25/2022]
Abstract
A new genetic locus mediating avirulence in the potato late blight pathogen Phytophthora infestans has been discovered. The Avr3b-Avr10-Avr11 locus is recognized by three different potato resistance genes, and is different from other Avr loci that have been identified thus far. This locus encodes a large protein with a WD40 domain and sequence similarities to transcription factors. Multiple, truncated copies of this gene have arisen by gene amplification and are characteristic of avirulent strains of P. infestans. Here, we describe the new avirulence locus and discuss the importance of this finding.
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Affiliation(s)
- Dinah Qutob
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada.
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Jiang RHY, Weide R, van de Vondervoort PJI, Govers F. Amplification generates modular diversity at an avirulence locus in the pathogen Phytophthora. Genome Res 2006; 16:827-40. [PMID: 16818726 DOI: 10.1101/gr.5193806] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The destructive late blight pathogen Phytophthora infestans is notorious for its rapid adaptation to circumvent detection mediated by plant resistance (R) genes. We performed comparative genomic hybridization on microarrays (array-CGH) in a near genome-wide survey to identify genome rearrangements related to changes in virulence. Six loci with copy number variation were found, one of which involves an amplification colocalizing with a previously identified locus that confers avirulence in combination with either R gene R3b, R10, or R11. Besides array-CGH, we used three independent approaches to find candidate genes at the Avr3b-Avr10-Avr11 locus: positional cloning, cDNA-AFLP analysis, and Affymetrix array expression profiling. This resulted in one candidate, pi3.4, that encodes a protein of 1956 amino acids with regulatory domains characteristic for transcription factors. Amplification is restricted to the 3' end of the full-length gene but the amplified copies still contain the hallmarks of a regulatory protein. Sequence comparison showed that the amplification may generate modular diversity and assist in the assembly of novel full-length genes via unequal crossing-over. Analyses of P. infestans field isolates revealed that the pi3.4 amplification correlates with avirulence; isolates virulent on R3b, R10, and R11 plants lack the amplified gene cluster. The ancestral state of 3.4 in the Phytophthora lineage is a full-length, single-copy gene. In P. infestans, however, pi3.4 is a dynamic gene that is amplified and has moved to other locations. Modular diversity could be a novel mechanism for pathogens to quickly adapt to changes in the environment.
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Affiliation(s)
- Rays H Y Jiang
- Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, NL-5-6709 PD Wageningen and Graduate School Experimental Plant Sciences, The Netherlands
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