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Chaves SC, Guayazán N, Mideros MF, Parra M, Lucca F, Restrepo S. Two Clonal Species of Phytophthora Associated to Solanaceous Crops Coexist in Central and Southern Colombia. PHYTOPATHOLOGY 2020; 110:1342-1351. [PMID: 32490753 DOI: 10.1094/phyto-05-19-0175-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In Colombia, late blight is considered one of the most limiting diseases on potato and tomato production. Recently, a new Phytophthora species, P. betacei, was described infecting tree tomato crops in the south of Colombia. However, the distribution and the host range of this new emerging pathogen in the country are unknown. The main aims of this study were to determine if this novel species is confined to the south of Colombia, to assess if P. betacei represents a genetically uniform clone across Colombia and to determine if in all regions there is a clear differentiation between the two Phytophthora species. Therefore, we characterized Phytophthora isolates obtained from tree tomato and potato crops in a central region of Colombia and compared them with the strains from the south. Initially, we evaluated the genetic differentiation among Phytophthora strains obtained from tree tomato and potato crops using simple sequence repeat markers. Results showed a strong population structure between P. infestans and P. betacei. However, we did not detect any genetic differentiation within P. infestans or P. betacei populations from different regions. Furthermore, we detected significant morphological differences among the species based on growth and sporangial morphology measurements. We also showed that strains of Phytophthora spp. are predominantly of the A1 mating type and belong to EC-1 and EC-3 clonal lineages for P. infestans and P. betacei, respectively. Our results describe the expanded geographical range of the new species of P. betacei in the central region of Colombia.
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Affiliation(s)
| | - Natalia Guayazán
- Departmento de Ingeniería Química, Universidad de los Andes, Bogotá, Colombia
| | | | - Mayra Parra
- Departmento de Ingeniería Química, Universidad de los Andes, Bogotá, Colombia
| | - Florencia Lucca
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce, República, Argentina
| | - Silvia Restrepo
- Departmento de Ingeniería Química, Universidad de los Andes, Bogotá, Colombia
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2
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Mideros MF, Mayton H, Danies G, Lagos LE, Fry WE, Restrepo S. Differential Susceptibility of Tree Tomato ( Solanum betaceum) Cultivars to Late Blight Caused by Phytophthora betacei. PLANT DISEASE 2020; 104:1113-1117. [PMID: 32040390 DOI: 10.1094/pdis-02-19-0307-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Host-pathogen interactions of a new species of Phytophthora, causal agent of late blight of tree tomato (Solanum betaceum Cav.), identified as Phytophthora betacei, were investigated with four different cultivars. Thirty-six P. betacei isolates, collected from southern Colombia between 2008 and 2009, were used to inoculate common tree tomato cultivars, Común, Híbrido, Injerto, and Holandés. Data on incubation and latent periods as well as infection efficiency, lesion development, and total sporulation were collected via detached leaf assays. Significant differences in susceptibility, based on the parameters measured, were observed. Común was the most susceptible cultivar, followed by Injerto, Híbrido, and Holandés. The mean incubation period was lowest for Común at 125.6 h post-inoculation (hpi) and highest for Híbrido at 139.4 hpi. No significant differences in latent period were observed. All 36 isolates produced necrotic lesions on Común, and 33, 24, and 21 caused infection on Injerto, Híbrido, and Holandés, respectively. Two isolates were able to cause infection only on Común, and 13 isolates were able to infect all four cultivars. Infection efficiency was significantly higher for the cultivar Común, followed by Injerto, Híbrido, and Holandés. Average lesion size was larger on Común than on any other cultivar. An inverse relationship of lesion size and total sporulation was observed. Común had significantly lower total sporulation than Híbrido and Holandés, which had the smallest average lesion sizes. These data show variation in pathogenicity of P. betacei isolates, under controlled conditions, and differential susceptibility of four distinct S. betaceum cultivars.
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Affiliation(s)
- Maria F Mideros
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hilary Mayton
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Giovanna Danies
- Department of Design, Universidad de los Andes, Bogotá, Colombia
| | - Luz E Lagos
- Department of Biology, Universidad de Nariño, Pasto, Colombia
| | - William E Fry
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Ratti MF, Farrer RA, Cano LM, Faedda R, Goss EM. Evaluation of High-Resolution Melting for Rapid Differentiation of Phytophthora Hybrids and Their Parental Species. PLANT DISEASE 2019; 103:2295-2304. [PMID: 31355734 DOI: 10.1094/pdis-12-18-2291-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Phytophthora species hybrids have been repeatedly reported as causing damaging diseases to cultivated and wild plants. Two known hybrids, P. andina and P. × pelgrandis, are pathogens of Solanaceae and ornamentals, respectively, although the extent of their host ranges are unknown. P. andina emerged from hybridization of P. infestans and an unidentified related species, whereas P. × pelgrandis emerged from P. nicotianae and P. cactorum. Considering that hybrids and parental species can coexist in the same regions and to distinguish them usually requires cloning or whole genome sequencing, we aimed to develop a rapid tool to distinguish them. Specifically, we used high-resolution melting (HRM) assays to differentiate genotypes based on their amplicon melting profiles. We designed primers for P. × pelgrandis and parental species based on available sequences of P. nicotianae and P. cactorum nuclear genes containing polymorphisms between species. For P. andina, heterozygous sites from Illumina short reads were used for the same purpose. We identified multiple amplicons exhibiting differences in melting curves between parental species and hybrids. We propose HRM as a rapid method for differentiation of P. andina and P. × pelgrandis hybrids from parental species that could be employed to advance research on these pathogens.
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Affiliation(s)
- Maria F Ratti
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 U.S.A
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo, Km 30.5 Vía Perimetral. P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Rhys A Farrer
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Liliana M Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Roberto Faedda
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 U.S.A
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Chaves SC, Rodríguez MC, Mideros MF, Lucca F, Ñústez CE, Restrepo S. Determining Whether Geographic Origin and Potato Genotypes Shape the Population Structure of Phytophthora infestans in the Central Region of Colombia. PHYTOPATHOLOGY 2019; 109:145-154. [PMID: 30474515 DOI: 10.1094/phyto-05-18-0157-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pathogen variation plays an important role in the dynamics of infectious diseases. In this study, the genetic variation of 279 Phytophthora infestans isolates was assessed using a combination of 12 microsatellite simple-sequence repeat markers. Isolates were collected from 11 different potato cultivars in 11 different geographic localities of the central region of Colombia. The objective of this study was to determine whether populations were differentiated by host genotype or geographic origin. Within a single clonal lineage, EC-1, 76 genotypes were detected. An analysis of molecular variance attributed most of the variation to differences within host genotypes rather than among the host genotypes, suggesting that host cultivars do not structure the populations of the pathogen. Furthermore, the lack of a genetic population structure according to the host cultivar was confirmed by all of the analyses, including the Bayesian clustering analysis and the minimum spanning network that used the Bruvo genetic distance, which suggested that there are no significant barriers to gene flow for P. infestans among potato cultivars. According to the geographic origin, the populations of P. infestans were also not structured, and most of the variation among the isolates was attributed to differences within localities. Only some but not all localities in the north and west of the central region of Colombia showed some genetic differentiation from the other regions. The absence of sexual reproduction of this pathogen in Colombia was also demonstrated. Important insights are discussed regarding the genetic population dynamics of the P. infestans populations of the central region of Colombia that were provided by the results. In Colombia, there is a high genetic variation within the EC-1 clonal lineage with closely related genotypes, none dominant, that coexist in a wide geographic area and on several potato cultivars.
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Affiliation(s)
- Sandra Catalina Chaves
- First, second, third, and sixth authors: Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia; fourth author: Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce, República Argentina; and fifth author: Departmento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - María Camila Rodríguez
- First, second, third, and sixth authors: Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia; fourth author: Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce, República Argentina; and fifth author: Departmento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - María Fernanda Mideros
- First, second, third, and sixth authors: Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia; fourth author: Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce, República Argentina; and fifth author: Departmento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Florencia Lucca
- First, second, third, and sixth authors: Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia; fourth author: Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce, República Argentina; and fifth author: Departmento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos E Ñústez
- First, second, third, and sixth authors: Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia; fourth author: Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce, República Argentina; and fifth author: Departmento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Silvia Restrepo
- First, second, third, and sixth authors: Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia; fourth author: Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce, República Argentina; and fifth author: Departmento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
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5
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Mideros M, Turissini D, Guayazán N, Ibarra-Avila H, Danies G, Cárdenas M, Myers K, Tabima J, Goss E, Bernal A, Lagos L, Grajales A, Gonzalez L, Cooke D, Fry W, Grünwald N, Matute D, Restrepo S. Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia. PERSOONIA 2018; 41:39-55. [PMID: 30728598 PMCID: PMC6344807 DOI: 10.3767/persoonia.2018.41.03] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/12/2017] [Indexed: 11/25/2022]
Abstract
Over the past few years, symptoms akin to late blight disease have been reported on a variety of crop plants in South America. Despite the economic importance of these crops, the causal agents of the diseases belonging to the genus Phytophthora have not been completely characterized. In this study, a new Phytophthora species was described in Colombia from tree tomato (Solanum betaceum), a semi-domesticated fruit grown in northern South America. Comprehensive phylogenetic, morphological, population genetic analyses, and infection assays to characterize this new species, were conducted. All data support the description of the new species, Phytophthora betacei sp. nov. Phylogenetic analyses suggest that this new species belongs to clade 1c of the genus Phytophthora and is a close relative of the potato late blight pathogen, P. infestans. Furthermore, it appeared as the sister group of the P. andina strains collected from wild Solanaceae (clonal lineage EC-2). Analyses of morphological and physiological characters as well as host specificity showed high support for the differentiation of these species. Based on these results, a complete description of the new species is provided and the species boundaries within Phytophthora clade 1c in northern South America are discussed.
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Affiliation(s)
- M.F. Mideros
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - D.A. Turissini
- Biology Department, University of North Carolina, Chapel Hill, USA
| | - N. Guayazán
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - H. Ibarra-Avila
- Head of Microscopy Core (MCUA), Vice-Presidency of Research, Universidad de Los Andes, Bogotá, Colombia
| | - G. Danies
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
- Biology Department, Universidad de Nariño, Pasto, Colombia
| | - M. Cárdenas
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - K. Myers
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, USA
| | - J. Tabima
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, USA
| | - E.M. Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - A. Bernal
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - L.E. Lagos
- Biology Department, Universidad de Nariño, Pasto, Colombia
| | - A. Grajales
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - L.N. Gonzalez
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - D.E.L. Cooke
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - W.E. Fry
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, USA
| | - N. Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, USA
| | - D.R. Matute
- Biology Department, University of North Carolina, Chapel Hill, USA
| | - S. Restrepo
- Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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6
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Shimelash D, Hussien T, Fininsa C, Forbes G, Yuen J. Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity. Curr Genet 2016; 62:657-67. [PMID: 26873223 DOI: 10.1007/s00294-016-0572-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA (mtDNA) haplotypes were determined using restriction fragment length polymorphism (RFLP) for P. infestans sampled from 513 foliar lesions of late blight found on potato and tomato in different regions of Ethiopia. Among the four reported mitochondrial haplotypes of Phytophthora infestans, Ia, Ib and IIb were detected in 93 % of the samples analyzed but the vast majority of these were Ia. The remaining 7 % represented a previously unreported haplotype. DNA sequencing of this new haplotype also confirmed a single base nucleotide substitution that resulted in loss of EcoRI restriction site and gain of two additional MspI sites in cox1 and atp1 genes, respectively. There were 28 polymorphic sites among all nucleotide sequences including five reference isolates. Sites with alignment gaps were observed in P4 with one nucleotide deletion in 11 Ethiopian isolates. None of the reference sequence produced frame-shifts, with the exception of the 3-nucleotide deletion in the P4 region by Phytophthora andina, a feature that can be used to distinguish the new Ethiopian isolates from P. andina. While a distinguishing molecular data presented here clearly separated them from P. infestans, 7 % of the isolates that share this feature formed an important component of the late blight pathogen causing disease on Solanum tuberosum in Ethiopia. Thus, these Ethiopian isolates could represent a novel Phytophthora species reported for the first time here.
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Affiliation(s)
- Daniel Shimelash
- School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia.
| | - Temam Hussien
- School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia
| | - Chemeda Fininsa
- School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia
| | - Greg Forbes
- CIP-China Center for Asia Pacific, Pan Pacific Plaza A12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Jonathan Yuen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07, Uppsala, Sweden
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7
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Lassiter ES, Russ C, Nusbaum C, Zeng Q, Saville AC, Olarte RA, Carbone I, Hu CH, Seguin-Orlando A, Samaniego JA, Thorne JL, Ristaino JB. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species. Curr Genet 2015; 61:567-77. [PMID: 25754775 PMCID: PMC4659649 DOI: 10.1007/s00294-015-0480-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 01/24/2023]
Abstract
Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.
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Affiliation(s)
- Erica S Lassiter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | | | | | - Amanda C Saville
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rodrigo A Olarte
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Chia-Hui Hu
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jose A Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey L Thorne
- Department of Biological Sciences and Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
| | - Jean B Ristaino
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
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8
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Restrepo S, Tabima JF, Mideros MF, Grünwald NJ, Matute DR. Speciation in fungal and oomycete plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:289-316. [PMID: 24906125 DOI: 10.1146/annurev-phyto-102313-050056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The process of speciation, by definition, involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed that speciation in pathogens is heavily influenced by host-pathogen dynamics and that traits that mediate such interactions (e.g., host mobility, reproductive mode of the pathogen, complexity of the life cycle, and host specificity) must lead to reproductive isolation and ultimately affect speciation rates. In this review, we summarize the main evolutionary processes that lead to speciation of fungal and oomycete plant pathogens and provide an outline of how speciation can be studied rigorously, including novel genetic/genomic developments.
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Affiliation(s)
- Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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9
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Yang ZH, Qi MX, Qin YX, Zhu JH, Gui XM, Tao B, Xu XH, Zhang FG. Mitochondrial DNA polymorphisms in Phytophthora infestans: new haplotypes are identified and re-defined by PCR. J Microbiol Methods 2013; 95:117-21. [PMID: 23954478 DOI: 10.1016/j.mimet.2013.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/02/2013] [Accepted: 08/03/2013] [Indexed: 10/26/2022]
Abstract
Polymorphisms of mitochondrial DNA (mt-DNA) are particularly useful for monitoring specific pathogen populations like Phytophthora infestans. Basically type I and II of P. infestans mt-DNA were categorized by means of polymorphism lengths caused by an ~2 kb insertion, which can be detected via restriction enzyme digestion. In addition genome sequencing of haplotype Ib has been used as a simple Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method to indirectly identify type I and II alterations through EcoR I restriction enzyme DNA fragment patterns of the genomic P4 area. However, with the common method, wrong mt-DNA typing occurs due to an EcoR I recognition site mutation in the P4 genomic area. Genome sequencing of the four haplotypes (Ia, Ib, IIa, and IIb) allowed us to thoroughly examine mt-DNA polymorphisms and we indentified two hypervariable regions (HVRs) named HVRi and HVRii. The HVRi length polymorphism caused by a 2 kb insertion/deletion was utilized to identify mt-DNA types I and II, while another length polymorphism in the HVRii region is caused by a variable number of tandem repeats (n = 1, 2, or 3) of a 36 bp sized DNA stretch and was further used to determine mt-DNA sub-types, which were described as R(n = 1, 2, or 3). Finally, the P. infestans mt-DNA haplotypes were re-defined as IR(1) or IIR(2) according to PCR derived HVRi and HVRii length polymorphisms. Twenty-three isolates were chosen to verify the feasibility of our new approach for identifying mt-DNA haplotypes and a total of five haplotypes (IR(1), IR(2), IR(3), IIR(2) and IIR(3)) were identified. Additionally, we found that six isolates determined as type I by our method were mistakenly identified as type II by the PCR-RFLP technique. In conclusion, we propose a simple and rapid PCR method for identification of mt-DNA haplotypes based on sequence analyses of the mitochondrial P. infestans genome.
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Affiliation(s)
- Zhi-Hui Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding 071001, China
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10
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Blair JE, Coffey MD, Martin FN. Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives. PLoS One 2012; 7:e37003. [PMID: 22615869 PMCID: PMC3355167 DOI: 10.1371/journal.pone.0037003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/11/2012] [Indexed: 01/13/2023] Open
Abstract
To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.
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Affiliation(s)
- Jaime E Blair
- Department of Biology, Franklin & Marshall College, Lancaster, Pennsylvania, United States of America.
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11
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Goss EM, Cardenas ME, Myers K, Forbes GA, Fry WE, Restrepo S, Grünwald NJ. The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish potato famine pathogen, P. infestans. PLoS One 2011; 6:e24543. [PMID: 21949727 PMCID: PMC3174952 DOI: 10.1371/journal.pone.0024543] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 08/12/2011] [Indexed: 11/19/2022] Open
Abstract
Emerging plant pathogens have largely been a consequence of the movement of pathogens to new geographic regions. Another documented mechanism for the emergence of plant pathogens is hybridization between individuals of different species or subspecies, which may allow rapid evolution and adaptation to new hosts or environments. Hybrid plant pathogens have traditionally been difficult to detect or confirm, but the increasing ease of cloning and sequencing PCR products now makes the identification of species that consistently have genes or alleles with phylogenetically divergent origins relatively straightforward. We investigated the genetic origin of Phytophthora andina, an increasingly common pathogen of Andean crops Solanum betaceum, S. muricatum, S. quitoense, and several wild Solanum spp. It has been hypothesized that P. andina is a hybrid between the potato late blight pathogen P. infestans and another Phytophthora species. We tested this hypothesis by cloning four nuclear loci to obtain haplotypes and using these loci to infer the phylogenetic relationships of P. andina to P. infestans and other related species. Sequencing of cloned PCR products in every case revealed two distinct haplotypes for each locus in P. andina, such that each isolate had one allele derived from a P. infestans parent and a second divergent allele derived from an unknown species that is closely related but distinct from P. infestans, P. mirabilis, and P. ipomoeae. To the best of our knowledge, the unknown parent has not yet been collected. We also observed sequence polymorphism among P. andina isolates at three of the four loci, many of which segregate between previously described P. andina clonal lineages. These results provide strong support that P. andina emerged via hybridization between P. infestans and another unknown Phytophthora species also belonging to Phytophthora clade 1c.
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Affiliation(s)
- Erica M. Goss
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, Oregon, United States of America
| | - Martha E. Cardenas
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Kevin Myers
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | | | - William E. Fry
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, Oregon, United States of America
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Cárdenas M, Grajales A, Sierra R, Rojas A, González-Almario A, Vargas A, Marín M, Fermín G, Lagos LE, Grünwald NJ, Bernal A, Salazar C, Restrepo S. Genetic diversity of Phytophthora infestans in the Northern Andean region. BMC Genet 2011; 12:23. [PMID: 21303555 PMCID: PMC3046917 DOI: 10.1186/1471-2156-12-23] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 02/09/2011] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, β-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. RESULTS Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. CONCLUSIONS The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.
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Affiliation(s)
| | | | | | | | | | | | | | - Gustavo Fermín
- Universidad de Los Andes, La Hechicera, Mérida, Venezuela
| | - Luz E Lagos
- Universidad de Nariño, Pasto, Nariño, Colombia
| | | | | | - Camilo Salazar
- Smithsonian Tropical Research Institute. Apartado 0843-03092, Panamá, República de Panamá
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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Vargas AM, Quesada Ocampo LM, Céspedes MC, Carreño N, González A, Rojas A, Zuluaga AP, Myers K, Fry WE, Jiménez P, Bernal AJ, Restrepo S. Characterization of Phytophthora infestans populations in Colombia: first report of the A2 mating type. PHYTOPATHOLOGY 2009; 99:82-8. [PMID: 19055438 DOI: 10.1094/phyto-99-1-0082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Phytophthora infestans, the causal agent of late blight in crops of the Solanaceae family, is one of the most important plant pathogens in Colombia. Not only are Solanum lycopersicum, and S. tuberosum at risk, but also several other solanaceous hosts (Physalis peruviana, S. betaceum, S. phureja, and S. quitoense) that have recently gained importance as new crops in Colombia may be at risk. Because little is known about the population structure of Phytophthora infestans in Colombia, we report here the phenotypic and molecular characterization of 97 isolates collected from these six different solanaceous plants in Colombia. All the isolates were analyzed for mating type, mitochondrial haplotypes, genotype for several microsatellites, and sequence of the internal transcribed spacer (ITS) region. This characterization identified a single individual of A2 mating type (from Physalis peruviana) for the first time in Colombia. All isolates had an ITS sequence that was at least 97% identical to the consensus sequence. Of the 97 isolates, 96 were mitochondrial haplotype IIa, with the single A2 isolate being Ia. All isolates were invariant for the microsatellites. Additionally, isolates collected from S. tuberosum and P. peruviana (64 isolates) were tested for: aggressiveness on both hosts, genotype for the isozymes (glucose-6-phosphate isomerase and peptidase), and restriction fragment length polymorphism fingerprint pattern as detected by RG57. Isolates from S. tuberosum were preferentially pathogenic on S. tuberosum, and isolates from P. peruviana were preferentially pathogenic on P. peruviana. The population from these two hosts was dominated by a single clonal lineage (59 of 64 individuals assayed), previously identified from Ecuador and Peru as EC-1. This lineage was mating type A1, IIa for mitochondrial DNA, invariant for two microsatellites, and invariant for both isozymes. The remaining four A1 isolates were in lineages very closely related to EC-1 (named EC-1.1, CO-1, and CO-2). The remaining lineage (the A2 mating type) had characteristics of the US-8 lineage (previously identified in Mexico, the United States, and Canada). These results have important epidemiological implications for the production of these two crops in Colombia.
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Affiliation(s)
- Angela M Vargas
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
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Gómez-Alpizar L, Hu CH, Oliva R, Forbes G, Ristaino JB. Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans. Mycologia 2008; 100:590-602. [PMID: 18833752 DOI: 10.3852/07-074r1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phylogenetic relationships of Phytophthora infestans sensu lato in the Andean highlands of South America were examined. Three clonal lineages (US-1, EC-1, EC-3) and one heterogeneous lineage (EC-2) were found in association with different host species in genus Solanum. The EC-2 lineage includes two mitochondrial (mtDNA) haplotypes, Ia and Ic. Isolates of P. infestans sensu lato EC-2 fit the morphological description of P. infestans but are different from any genotypes of P. infestans described to date. All isolates of P. infestans sensu lato from Ecuador were amplified by a P. infestans specific primer (PINF), and restriction fragment length patterns were identical in isolates amplified with ITS primers 4 and 5. The EC-1 clonal lineage of P. infestans sensu lato from S. andreanum, S. columbianum, S. paucijugum, S. phureja, S. regularifolium, S. tuberosum and S. tuquerense was confirmed to be P. infestans based on sequences of the cytochrome oxidase I (cox I) gene and intron 1 of ras gene. The EC-2 isolates with the Ic haplotype formed a distinct branch in the same clade with P. infestans and P. mirabilis, P. phaseoli and P. ipomoeae for both cox I and ras intron 1 phylogenies and were identified as the newly described species P. andina. Ras intron 1 sequence data suggests that P. andina might have arisen via hybridization between P. infestans and P. mirabilis.
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Affiliation(s)
- Luis Gómez-Alpizar
- Agronomic Research Center, Box 2060, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
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Abstract
Three common systemic human fungal pathogens--Cryptococcus neoformans, Candida albicans and Aspergillus fumigatus--have retained all the machinery to engage in sexual reproduction, and yet their populations are often clonal with limited evidence for recombination. Striking parallels have emerged with four protozoan parasites that infect humans: Toxoplasma gondii, Trypanosoma brucei, Trypanosoma cruzi and Plasmodium falciparum. Limiting sexual reproduction appears to be a common virulence strategy, enabling generation of clonal populations well adapted to host and environmental niches, yet retaining the ability to engage in sexual or parasexual reproduction and respond to selective pressure. Continued investigation of the sexual nature of microbial pathogens should facilitate both laboratory investigation and an understanding of the complex interplay between pathogens, hosts, vectors, and their environments.
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Affiliation(s)
- Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Moralejo E, Muñoz JAG, Descals E. Insights into Phytophthora ramorum sporulation: epidemiological and evolutionary implications. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1365-2338.2006.01016.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Becktell MC, Smart CD, Haney CH, Fry WE. Host-Pathogen Interactions Between Phytophthora infestans and the Solanaceous Hosts Calibrachoa × hybridus, Petunia × hybrida, and Nicotiana benthamiana. PLANT DISEASE 2006; 90:24-32. [PMID: 30786470 DOI: 10.1094/pd-90-0024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Late blight, caused by the pathogen Phytophthora infestans, is a devastating disease of potato and tomato, but can also damage other solanaceous hosts. To gain a better understanding of the interaction between P. infestans and these other hosts, the susceptibility of species in three solanaceous genera was investigated. Of the 10 Calibrachoa × hybridus cultivars tested, four were susceptible and six were resistant to the pathogen; susceptible cultivars supported only very limited growth of P. infestans. The majority of the Petunia × hybrida (petunia) cultivars were susceptible, although less so than susceptible potatoes or tomatoes. Two petunia cultivars displayed differential resistance, suggesting the presence of R genes against P. infestans. The hypersensitive response was present in susceptible, partially resistant, and resistant petunia-P. infestans interactions, but was predominant in the resistant interaction. Young petunias (3 weeks) were more susceptible than older petunias (7 weeks). Nicotiana benthamiana was susceptible to all four P. infestans isolates tested in the lab and became infected during a field epidemic. Several of these isolates were tested for the presence of the inf1 gene, and were found to have and express the gene in vitro. In addition, culture filtrate from these isolates contained 10-kDa proteins and also elicited the hypersensitive response in Nicotiana tabacum and N. benthamiana.
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Affiliation(s)
- M C Becktell
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853
| | - C D Smart
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853
| | - C H Haney
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853
| | - W E Fry
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853
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Avila-Adame C, Gómez-Alpizar L, Zismann V, Jones KM, Buell CR, Ristaino JB. Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Curr Genet 2005; 49:39-46. [PMID: 16328503 DOI: 10.1007/s00294-005-0016-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 07/22/2005] [Accepted: 07/28/2005] [Indexed: 11/24/2022]
Abstract
The mitochondrial genomes of haplotypes of the Irish potato famine pathogen, Phytophthora infestans, were sequenced. The genome sizes were 37,922, 39,870 and 39,840 bp for the type Ia, IIa and IIb mitochondrial DNA (mtDNA) haplotypes, respectively. The mitochondrial genome size for the type Ib haplotype, previously sequenced by others, was 37,957 bp. More than 90% of the genome contained coding regions. The GC content was 22.3%. A total of 18 genes involved in electron transport, 2 RNA-encoding genes, 16 ribosomal protein genes and 25 transfer RNA genes were coded on both strands with a conserved arrangement among the haplotypes. The type I haplotypes contained six unique open reading frames (ORFs) of unknown function while the type II haplotypes contained 13 ORFs of unknown function. Polymorphisms were observed in both coding and non-coding regions although the highest variation was in non-coding regions. The type I haplotypes (Ia and Ib) differed by only 14 polymorphic sites, whereas the type II haplotypes (IIa and IIb) differed by 50 polymorphic sites. The largest number (152) of polymorphic sites was found between the type IIb and Ia haplotypes. A large spacer flanked by the genes coding for tRNA-Tyr (trnY) and the small subunit RNA (rns) contained the largest number of polymorphic sites and corresponds to the region where a large indel that differentiates type II from type I haplotypes is located. The size of this region was 785, 2,666 and 2,670 bp in type Ia, IIa and IIb haplotypes, respectively. Among the four haplotypes, 81 mutations were identified. Phylogenetic and coalescent analysis revealed that although the type I and II haplotypes shared a common ancestor, they clearly formed two independent lineages that evolved independently. The type II haplotypes diverged earlier than the type I haplotypes. Thus our data do not support the previous hypothesis that the type II lineages evolved from the type I lineages. The type I haplotypes diverged more recently and the mutations associated with the evolution of the Ia and Ib types were identified.
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Affiliation(s)
- Cruz Avila-Adame
- Department of Plant Pathology, North Carolina State University, Box 7616, Raleigh, 27695, USA
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Kamoun S, Smart CD. Late Blight of Potato and Tomato in the Genomics Era. PLANT DISEASE 2005; 89:692-699. [PMID: 30791237 DOI: 10.1094/pd-89-0692] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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Adler NE, Erselius LJ, Chacón MG, Flier WG, Ordoñez ME, Kroon LPNM, Forbes GA. Genetic Diversity of Phytophthora infestans sensu lato in Ecuador Provides New Insight Into the Origin of This Important Plant Pathogen. PHYTOPATHOLOGY 2004; 94:154-162. [PMID: 18943538 DOI: 10.1094/phyto.2004.94.2.154] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT The metapopulation structure of Phytophthora infestans sensu lato is genetically diverse in the highlands of Ecuador. Previous reports documented the diversity associated with four putative clonal lineages of the pathogen collected from various hosts in the genus Solanum. This paper simultaneously analyzes diversity of the complete collection of isolates, including a large number that had not yet been reported. This analysis confirmed the existence of three pathogen populations, which all appear to be clonal lineages, and that correspond to those previously reported as US-1, EC-1, and EC-3. No evidence was found from the analyses of recently collected isolates that would contradict earlier reports about these three lineages. In contrast, new data from a group of isolates from several similar hosts caused us to modify the previous description of clonal lineage EC-2 and its previously proposed hosts, S. brevifolium and S. tetrapetalum. Given the uncertainty associated with the identification of these hosts, which all belong to the section Anarrhichomenum, we refer to them as the Anarrhichomenum complex, pending further taxonomic clarification. New pathogen genotypes associated with the Anarrhichomenum complex were isolated recently that are A1 mating type and Ia mitochondrial DNA (mtDNA) haplotype, and therefore differ from the previously described EC-2 lineage, which is A2 and Ic, respectively. Because of uncertainty on host identification, we do not know if the new genotypes are limited to one host species and therefore represent yet another host-adapted clonal lineage. For now, we refer to the new genotypes and previously described EC-2 genotypes, together, as the pathogen group attacking the Anarrhichomenum complex. Two A2 isolates identical to the previously described EC-2 archetype were collected from severely infected plants of pear melon (S. muricatum). Pear melon is generally attacked by US-1, and this is the first clear case we have documented in which two distinct pathogen genotypes have caused severe epidemics on the same host. Based on presence of unique marker alleles (restriction fragment length polymorphism [RFLP] and mtDNA) and genetic similarity analysis using RFLP and amplified fragment length polymorphism data, EC-3 and isolates from the Anarrhichomenum complex are genetically distinct from all genotypes of P. infestans that have been reported previously. No current theory of historical migrations for this pathogen can adequately support a Mexican origin for EC-3 and genotypes of the Anarrhichomenum complex and they may, therefore, be palaeoendemic to the Andean highlands. To date, we have identified 15 hosts in the genus Solanum, in addition to the Anarrhichomenum complex, and some unidentified species of P. infestans sensu lato in Ecuador. Five of the Solanum hosts are cultivated. One isolate was collected from Brugmansia sanguinea, which represents the first report from Ecuador of a host of this pathogen that is not in the genus Solanum. However, P. infestans sensu lato was only found on flower petals of B. sanguinea. This study provides new insights into the population structure of highly specialized genotypes of P. infestans sensu lato in the Andean highlands. The results are discussed in light of previous hypotheses regarding the geographic origin of the pathogen.
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Flier WG, Grünwald NJ, Kroon LPNM, Sturbaum AK, van den Bosch TBM, Garay-Serrano E, Lozoya-Saldaña H, Fry WE, Turkensteen LJ. The Population Structure of Phytophthora infestans from the Toluca Valley of Central Mexico Suggests Genetic Differentiation Between Populations from Cultivated Potato and Wild Solanum spp. PHYTOPATHOLOGY 2003; 93:382-90. [PMID: 18944351 DOI: 10.1094/phyto.2003.93.4.382] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
ABSTRACT The population structure of Phytophthora infestans in the Toluca Valley of central Mexico was assessed using 170 isolates collected from cultivated potatoes and the native wild Solanum spp., S. demissum and S. xendinense. All isolates were analyzed for mitochondrial DNA (mtDNA) haplotype and amplified fragment length polymorphism (AFLP) multi-locus fingerprint genotype. Isolate samples were monomorphic for mtDNA haplotype because all isolates tested were of the Ia haplotype. A total of 158 multilocus AFLP genotypes were identified among the 170 P. infestans isolates included in this study. P. infestans populations sampled in the Toluca Valley in 1997 were highly variable and almost every single isolate represented a unique genotype based on the analysis of 165 AFLP marker loci. Populations of P. infestans collected from the commercial potato-growing region in the valley, the subsistence potato production area along the slopes of the Nevado de Toluca, and the native Solanum spp. on the forested slopes of the volcano showed a high degree of genetic diversity. The number of polymorphic loci varied from 20.0 to 62.4% for isolates collected from the field station and wild Solanum spp. On average, 81.8% (135) of the AFLP loci were polymorphic. Hetero-zygosity varied between 7.7 and 19.4%. Significant differentiation was found at the population level between strains originating from cultivated potatoes and wild Solanum spp. (P = 0.001 to 0.022). Private alleles were observed in individual isolates collected from all three populations, with numbers of unique dominant alleles varying from 9 to 16 for isolates collected from commercial potato crops and native Solanum spp., respectively. Four AFLP markers were exclusively found present in isolates collected from S. demissum. Indirect estimation of gene flow between populations indicated restricted gene flow between both P. infestans populations from cultivated potatoes and wild Solanum hosts. There was no evidence found for the presence of substructuring at the subpopulation (field) level. We hypothesize that population differentiation and genetic isolation of P. infestans in the Toluca Valley is driven by host-specific factors (i.e., R-genes) widely distributed in wild Solanum spp. and random genetic drift.
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Wattier RAM, Gathercole LL, Assinder SJ, Gliddon CJ, Deahl KL, Shaw DS, Mills DI. Sequence variation of intergenic mitochondrial DNA spacers (mtDNA-IGS) of Phytophthora infestans (Oomycetes) and related species. ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1471-8286.2003.00378.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Shattock RC. Phytophthora infestans: populations, pathogenicity and phenylamides. PEST MANAGEMENT SCIENCE 2002; 58:944-950. [PMID: 12233186 DOI: 10.1002/ps.527] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Isolates of Phytophthora infestans (Mont) de Bary (the potato and tomato late blight pathogen) resistant to phenylamides appeared in Europe and North America in the late 1970s and early 1990s respectively. Concurrent, but coincidentally, with both these events there were radical structural shifts in the pathogen populations as immigrant genotypes from Mexico displaced the indigenous populations. Both A1 and A2 mating type isolates are now present in blighted crops, permitting alternative inoculum via germinating sexually produced oospores to influence dynamics of late blight populations. Studies of inheritance of ploidy, host-specific pathogenicity, mating type and resistance to antibiotics and phenylamide fungicides have provided insight into mechanisms of variation in this potent pathogen.
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Affiliation(s)
- Richard C Shattock
- School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, UK.
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Phytophthora ipomoeae sp. nov., a new homothallic species causing leaf blight on Ipomoea longipedunculata in the Toluca Valley of central Mexico. ACTA ACUST UNITED AC 2002. [DOI: 10.1017/s0953756202006123] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Sung JM, Choi YS, Shrestha B, Park YJ. Investigation on Artificial Fruiting of Cordyceps militaris. 한국균학회지 2002. [DOI: 10.4489/kjm.2002.30.1.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Perez WG, Gamboa JS, Falcon YV, Coca M, Raymundo RM, Nelson RJ. Genetic Structure of Peruvian Populations of Phytophthora infestans. PHYTOPATHOLOGY 2001; 91:956-965. [PMID: 18944122 DOI: 10.1094/phyto.2001.91.10.956] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Isolates of the late blight pathogen Phytophthora infestans (n = 327) from the central to southern Peruvian Andes were systematically collected in 1997 to 1999 and analyzed to determine the pathogen's population structure at its host's center of diversity. No isolates of the A2 mating type were detected. Cluster analysis of DNA fingerprinting data indicated that the collection consisted of five major groups that were interpreted to be clonal lineages. Two of the lineages (US-1 and EC-1) have been previously described, and three (PE-3, 5, and 6) are described here for the first time. Collections from three areas in the central Peruvian Andes, including two key sites used in an international potato breeding program, consisted of isolates of the EC-1 lineage, which has been reported to dominate the pathogen population in Andean countries to the north of Peru. The collections from Cusco and Puno were more diverse. More than one lineage was detected in 10 of the 20 fields sampled in Cusco. Data on virulence, metalaxyl sensitivity, and band data for allozymes, mitochondrial DNA, and ipiB1 suggested that PE-3 may have been produced through recombination events between US-1 and EC-1. Restriction fragment length polymorphism and amplified fragment length polymorphism marker data were not consistent with this hypothesis.
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Flier WG, Grünwald NJ, Fry WE, Turkensteen LJ. Formation, production and viability of oospores of Phytophthora infestans from potato and Solanum demissum in the Toluca Valley, central Mexico. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0953-7562(08)61958-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kamoun S. Nonhost resistance to Phytophthora: novel prospects for a classical problem. CURRENT OPINION IN PLANT BIOLOGY 2001; 4:295-300. [PMID: 11418338 DOI: 10.1016/s1369-5266(00)00176-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Members of the oomycete genus Phytophthora are the most devastating pathogens of dicot plants. Recent developments in the study of these organisms have led to improved understanding of their phylogenetic relationships and trends in their evolution. Molecular analyses of nonhost (species-level) resistance offer exciting prospects for disease management. A model that evokes a complex interplay of several layers of specific resistance, mediated by a set of ancient broad-spectrum R-gene loci, is sufficient to explain existing cellular and molecular data on nonhost resistance to Phytophthora.
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Affiliation(s)
- S Kamoun
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA.
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