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Qin CF, He MH, Chen FP, Zhu W, Yang LN, Wu EJ, Guo ZL, Shang LP, Zhan J. Comparative analyses of fungicide sensitivity and SSR marker variations indicate a low risk of developing azoxystrobin resistance in Phytophthora infestans. Sci Rep 2016; 6:20483. [PMID: 26853908 PMCID: PMC4745062 DOI: 10.1038/srep20483] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/04/2016] [Indexed: 11/17/2022] Open
Abstract
Knowledge of the evolution of fungicide resistance is important in securing sustainable disease management in agricultural systems. In this study, we analyzed and compared the spatial distribution of genetic variation in azoxystrobin sensitivity and SSR markers in 140 Phytophthora infestans isolates sampled from seven geographic locations in China. Sensitivity to azoxystrobin and its genetic variation in the pathogen populations was measured by the relative growth rate (RGR) at four fungicide concentrations and determination of the effective concentration for 50% inhibition (EC50). We found that all isolates in the current study were sensitive to azoxystrobin and their EC50 was similar to that detected from a European population about 20 years ago, suggesting the risk of developing azoxystrobin resistance in P. infestans populations is low. Further analyses indicate that reduced genetic variation and high fitness cost in resistant mutations are the likely causes for the low evolutionary likelihood of developing azoxystrobin resistance in the pathogen. We also found a negative correlation between azoxystrobin tolerance in P. infestans populations and the mean annual temperature of collection sites, suggesting that global warming may increase the efficiency of using the fungicide to control the late blight.
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Affiliation(s)
- Chun-Fang Qin
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng-Han He
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Feng-Ping Chen
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen Zhu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li-Na Yang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - E-Jiao Wu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zheng-Liang Guo
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li-Ping Shang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
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Sanju S, Thakur A, Siddappa S, Sreevathsa R, Srivastava N, Shukla P, Singh BP. Pathogen virulence of Phytophthora infestans: from gene to functional genomics. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:165-77. [PMID: 24431484 PMCID: PMC3656195 DOI: 10.1007/s12298-012-0157-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The oomycete, Phytophthora infestans, is one of the most important plant pathogens worldwide. Much of the pathogenic success of P. infestans, the potato late blight agent, relies on its ability to generate large amounts of sporangia from mycelia, which release zoospores that encyst and form infection structures. Until recently, little was known about the molecular basis of oomycete pathogenicity by the avirulence molecules that are perceived by host defenses. To understand the molecular mechanisms interplay in the pathogen and host interactions, knowledge of the genome structure was most important, which is available now after genome sequencing. The mechanism of biotrophic interaction between potato and P. infestans could be determined by understanding the effector biology of the pathogen, which is until now poorly understood. The recent availability of oomycete genome will help in understanding of the signal transduction pathways followed by apoplastic and cytoplasmic effectors for translocation into host cell. Finally based on genomics, novel strategies could be developed for effective management of the crop losses due to the late blight disease.
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Affiliation(s)
- Suman Sanju
- />Central potato Research Institute, Shimla, H.P India 171001
| | - Aditi Thakur
- />Central potato Research Institute, Shimla, H.P India 171001
| | | | - Rohini Sreevathsa
- />National Research Centre for Plant Biotechnology, IARI campus, Pusa, New Delhi—12, India
| | - Nidhi Srivastava
- />Department of Biosciences and Biotechnology, Banasthali University (Rajasthan), Tonk, India 304022
| | - Pradeep Shukla
- />Department of Biological Sciences, School of Basic Sciences, SHIATS, Naini, Allahabad, India 211007
| | - B. P. Singh
- />Central potato Research Institute, Shimla, H.P India 171001
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Martens C, Van de Peer Y. The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC Genomics 2010; 11:353. [PMID: 20525264 PMCID: PMC2996974 DOI: 10.1186/1471-2164-11-353] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 06/03/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oomycetes of the genus Phytophthora are pathogens that infect a wide range of plant species. For dicot hosts such as tomato, potato and soybean, Phytophthora is even the most important pathogen. Previous analyses of Phytophthora genomes uncovered many genes, large gene families and large genome sizes that can partially be explained by significant repeat expansion patterns. RESULTS Analysis of the complete genomes of three different Phytophthora species, using a newly developed approach, unveiled a large number of small duplicated blocks, mainly consisting of two or three consecutive genes. Further analysis of these duplicated genes and comparison with the known gene and genome duplication history of ten other eukaryotes including parasites, algae, plants, fungi, vertebrates and invertebrates, suggests that the ancestor of P. infestans, P. sojae and P. ramorum most likely underwent a whole genome duplication (WGD). Genes that have survived in duplicate are mainly genes that are known to be preferentially retained following WGDs, but also genes important for pathogenicity and infection of the different hosts seem to have been retained in excess. As a result, the WGD might have contributed to the evolutionary and pathogenic success of Phytophthora. CONCLUSIONS The fact that we find many small blocks of duplicated genes indicates that the genomes of Phytophthora species have been heavily rearranged following the WGD. Most likely, the high repeat content in these genomes have played an important role in this rearrangement process. As a consequence, the paucity of retained larger duplicated blocks has greatly complicated previous attempts to detect remnants of a large-scale duplication event in Phytophthora. However, as we show here, our newly developed strategy to identify very small duplicated blocks might be a useful approach to uncover ancient polyploidy events, in particular for heavily rearranged genomes.
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Affiliation(s)
- Cindy Martens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Technologiepark 927, Ghent University, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium
- Bioinformatics and Evolutionary Genomics, Department of Molecular Genetics, Technologiepark 927, Ghent University, B-9052 Ghent, Belgium
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Wang J, Du Y, Wang S, Brown SJ, Park Y. Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 38:490-8. [PMID: 18342253 PMCID: PMC3206788 DOI: 10.1016/j.ibmb.2007.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 04/04/2007] [Accepted: 04/25/2007] [Indexed: 05/12/2023]
Abstract
The piggyBac transposable element (TE), originally discovered in the cabbage looper, Trichoplusia ni, has been widely used in insect transgenesis including the red flour beetle Tribolium castaneum. We surveyed piggyBac-like (PLE) sequences in the genome of T. castaneum by homology searches using as queries the diverse PLE sequences that have been described previously. The search yielded a total of 32 piggyBac-like elements (TcPLEs) which were classified into 14 distinct groups. Most of the TcPLEs contain defective functional motifs in that they are lacking inverted terminal repeats (ITRs) or have disrupted open reading frames. Only one single copy of TcPLE1 appears to be intact with imperfect 16bp ITRs flanking an open reading frame encoding a transposase of 571 amino acid residues. Many copies of TcPLEs were found to be inserted into or close to other transposon-like sequences. This large diversity of TcPLEs with generally low copy numbers suggests multiple invasions of the TcPLEs over a long evolutionary time without extensive multiplications or occurrence of rapid loss of TcPLEs copies.
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Affiliation(s)
- Jianjun Wang
- Department of Plant Protection, Yangzhou University, Yangzhou, China.
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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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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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Govers F, Gijzen M. Phytophthora genomics: the plant destroyers' genome decoded. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2006; 19:1295-301. [PMID: 17153913 DOI: 10.1094/mpmi-19-1295] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The year 2004 was an exciting one for the Phytophthora research community. The United States Department of Energy Joint Genome Institute (JGI) completed the draft genome sequence of two Phytophthora species, Phytophthora sojae and Phytophthora ramorum. In August of that year over 50 people gathered at JGI in Walnut Creek, California, for an annotation jamboree and searched for the secrets and surprises that the two genomes have in petto. This culminated in a paper in Science in September of this year describing the highlights of the sequencing project and emphasizing the power of having the genome sequences of two closely related organisms. This MPMI Focus issue on Phytophthora genomics contains a number of more specialized manuscripts centered on gene annotation and genome organization, and complemented with manuscripts that rely on genomics resources.
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Affiliation(s)
- Francine Govers
- Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, Binnenhaven 5, NL-6709 PD Wageningen, The Netherlands.
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Jiang RHY, Govers F. Nonneutral GC3 and retroelement codon mimicry in Phytophthora. J Mol Evol 2006; 63:458-72. [PMID: 16955239 DOI: 10.1007/s00239-005-0211-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Accepted: 05/20/2006] [Indexed: 10/24/2022]
Abstract
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.
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Affiliation(s)
- Rays H Y Jiang
- Laboratory of Phytopathology, Plant Sciences Group, and Graduate School of Experimental Plant Sciences, Wageningen University, Binnenhaven 5, NL-6709 PD, Wageningen, The Netherlands
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Randall TA, Dwyer RA, Huitema E, Beyer K, Cvitanich C, Kelkar H, Fong AMVA, Gates K, Roberts S, Yatzkan E, Gaffney T, Law M, Testa A, Torto-Alalibo T, Zhang M, Zheng L, Mueller E, Windass J, Binder A, Birch PRJ, Gisi U, Govers F, Gow NA, Mauch F, van West P, Waugh ME, Yu J, Boller T, Kamoun S, Lam ST, Judelson HS. Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:229-243. [PMID: 15782637 DOI: 10.1094/mpmi-18-0229] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coveragethe P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.
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Affiliation(s)
- Thomas A Randall
- Syngenta Biotechnology, Inc., Research Triangle Park, NC 27709, USA
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Jiang RHY, Dawe AL, Weide R, van Staveren M, Peters S, Nuss DL, Govers F. Elicitin genes in Phytophthora infestans are clustered and interspersed with various transposon-like elements. Mol Genet Genomics 2005; 273:20-32. [PMID: 15702346 DOI: 10.1007/s00438-005-1114-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 12/21/2004] [Indexed: 10/25/2022]
Abstract
Sequencing and annotation of a contiguous stretch of genomic DNA (112.3 kb) from the oomycete plant pathogen Phytophthora infestans revealed the order, spacing and genomic context of four members of the elicitin (inf) gene family. Analysis of the GC content at the third codon position (GC3) of six genes encoded in the region, and a set of randomly selected coding regions as well as random genomic regions, showed that a high GC3 value is a general feature of Phytophthora genes that can be exploited to optimize gene prediction programs for Phytophthora species. At least one-third of the annotated 112.3-kb P. infestans sequence consisted of transposons or transposon-like elements. The most prominent were four Tc3/gypsy and Tc1/copia type retrotransposons and three DNA transposons that belong to the Tc1/mariner, Pogo and PiggyBac groups, respectively. Comparative analysis of other available genomic sequences suggests that transposable elements are highly heterogeneous and ubiquitous in the P. infestans genome.
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Affiliation(s)
- Rays H Y Jiang
- Plant Sciences Group, Laboratory of Phytopathology, Graduate School of Experimental Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD, Wageningen, The Netherlands
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Abstract
Members of the genus Phytophthora are among the most serious threats to agriculture and food production, causing devastating diseases in hundreds of plant hosts. These fungus-like eukaryotes, which are taxonomically classified as oomycetes, generate asexual and sexual spores with characteristics that greatly contribute to their pathogenic success. The spores include survival and dispersal structures, and potent infectious propagules capable of actively locating hosts. Genetic tools and genomic resources developed over the past decade are now allowing detailed analysis of these important stages in the Phytophthora life cycle.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Center for Plant Cell Biology, University of California, Riverside, California 92521, USA.
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