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

LITERATURE CITED

• Abad ZG, Abad JA. 1997. Another look at the origin of late blight of potatoes, tomatoes, and pear melon in the Andes of South America. Plant Dis 81:682–688.
   Google Scholar
• Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Frederic S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup Ø, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Speigel FW, Taylor MFJR. 2005. The new higher-level classification of Eukarytotes with emphasis on the taxonomy of protists. J Eukary Microbiol 52:399–451.
   Google Scholar
• Adler NE, Erselius LJ, Chacon MG, Flier WG, Ordoñez ME, Kroon LPNM, Forbes GA. 2004. Genetic diversity of Phytophthora infestans sensu lato in Ecuador provides new insight into the origin of this important plant pathogen. Phytopathology 94:154–162.
   Google Scholar
• ———, Chacón G, Flier WG, Forbes GA. 2002. The Andean fruit crop, pear melon (Solanum muricatum), is a common host for A1 and A2 strains of Phytophthora infestans in Ecuador. Plant Pathol 51:802.
   Google Scholar
• Benson DM. 1991. Detection of Phytophthora cinnamomi in azalea with commercial serological assay kits. Plant Dis 75:478–482.
   Google Scholar
• Berkeley MJ. 1846. Observations, botanical and physiological on the potato murain. J Hort Soc London 1:9–34.
   Google Scholar
• Brasier CM, Hansen EM. 1992. Evolutionary biology of Phytophthora II: Phylogeny, speciation and population structure. Ann Rev Phytopathol 30:173–200.
   Google Scholar
• ———, Cooke DEL, Duncan JM. 1999. Origin of a new Phytophthora pathogen through interspecific hybridization. Proc Nat Acad Sci USA 96:5878–5883.
   Google Scholar
• ———, ———, ———, Hansen EM. 2003. Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides-P. megasperma ITS Clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile. Mycol Res 107:277–290.
   Google Scholar
• Cavalier-Smith TA. 1986. The kingdom Chromista: origin and systematics. In: Round FE, Chapman DJ, eds. Progress Phycological Research. Bristol, UK: Biopress Ltd. p 309–347.
   Google Scholar
• Chacón MG, Adler NE, Jarrin F, Flier WG, Gessler C, Forbes GA. 2006. Genetic structure of the population of Phytophthora infestans attacking Solanum ochranthum in the highlands of Ecuador. Eur J Plant Pathol 115: 235–245.
   Google Scholar
• Chen Y, Roxby R. 1996. Characterization of a Phytophthora infestans gene involved in vesicle transport. Gene 181: 89–94.
   Google Scholar
• Cooke DEL, Jung T, Williams NA, Schubert R, Bahnweg G, Oswald WF, Duncan JM. 1999. Molecular evidence supports Phytophthora quercina as a distinct species. Mycol Res 103:799–804.
   Google Scholar
• ———, Drenth A, Duncan JM, Wagels G, Brasier CM. 2000. A molecular phylogeny of Phytophthora and related oomycetes. Fungal Gen Biol 30:17–32.
   Google Scholar
• Correll DS. 1960. The potato and its wild relatives. Section Tuberarium of the genus Solanum, Botanical studies, Texas Research Foundation, Renner, Texas.
   Google Scholar
• Ersek T, Shoeltz JE, English JT. 1994. PCR amplification of species-specific DNA sequences can distinguish among Phytophthora species. Appl Envir Microbiol 60:2616–2621.
   Google Scholar
• Erwin DC, Ribeiro OK. 1996. Phytophthora diseases worldwide. St Paul, Minnesota: American Phytopathological Society Press. 562 p.
   Google Scholar
• Felsenstein J. 1985. Confidence limits on phylogenies: an approach using bootstrap. Evolution 39:783–791.
   Google Scholar
• Flier WG, Grnwald NK, Kroon LPNM, Sturbaum AK, van den Bosch TBM, Garay-Serrano E, Lozoya-Saldana H, Bonants PJM, Turkensteen LJ. 2002. Phytophthora ipomoeae sp. nov., a new homothallic species causing leaf blight on Ipomoea longipedunculata in the Toluca Valley of central Mexico. Mycol Res 106:848–856.
   Google Scholar
• ———, ———, ———, ———, ———, ———, ———, Fry WE, Turkensteen LJ. 2003. 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 93:382–390.
   Google Scholar
• Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordoñez ME, Fry BA, Doucett K, Fry WE. 1997. Population genetic structure of Phytophthora infestans in Ecuador. Phytopathology 87:375–380.
   Google Scholar
• Forster H, Oudemans P, Coffey MD. 1990. Mitochondrial and nuclear DNA diversity within six species of Phytophthora. Exp Mycol 12:18–31.
   Google Scholar
• Galindo J, Hohl RH. 1985. Phytophthora mirabilis, a new species of Phytophthora. Sydowia 38:87–96.
   Google Scholar
• Garry G, Forbes GA, Salas A, Santa Cruz M, Perez WG, Nelson RJ. 2005. Genetic diversity and host differentiation among isolates of Phytophthora infestans from cultivated potato and wild solanaceous hosts in Peru. Plant Pathol 54:740–748.
   Google Scholar
• Gepts P. 1998. Origin and evolution of common bean: past events and recent trends. Hort Sci 33:1124–1130.
   Google Scholar
• Gómez-Alpizar L, Carbone I, Ristaino JB. 2007. An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies. Proc Nat Acad Sci USA 104:3306–3311.
   Google Scholar
• Goodwin SB, Fry W. 1994. Genetic analysis of interspecific hybrids between Phytophthora infestans and Phytophthora mirabilis. Exp Mycol 18:20–32.
   Google Scholar
• ———, Spielman LJ, Matuszak JM, Bergeron SN, Fry WE. 1992. Clonal diversity and genetic differentiation of Phytophthora infestans populations in northern and central Mexico. Phytopathology 82:955–961.
   Google Scholar
• ———, Legard DE, Smart CD, Levy M, Fry WE. 1999. Gene flow analysis of molecular markers confirms that Phytophthora mirabilis and Phytophthora infestans are separate species. Mycologia 91:796–810.
   Google Scholar
• Griffith GW, Shaw DS. 1998. Polymorphisms in Phytophthora infestans: four mitochondrial haplotypes are detected after PCR amplification of DNA from pure cultures or from host lesions. Appl Envir Micro 64:4007–4014.
   Google Scholar
• Grünwald NJ, Flier WG. 2005. The biology of Phytophthora infestans at its center of origin. Annu Rev Phytopathol 43:171–190.
   Google Scholar
• ———, ———, Sturbaum AK, Garay-Serrano E, van den Bosch TBM, Smart CD, Matuzak JM, Lozoya-Saldana H, Turkensteen LJ, Fry WE. 2001. Population structure of Phytophthora infestans within the Tolluca Valley region of central Mexico. Phytopathology 91:882–890.
   Google Scholar
• Gunderson JH, Elwood H, Ingold A, Kindle K, Sogin ML. 1987. Phylogenetic relationships between chlorophytes, chrysophytes and oomycetes. Proc Nat Acad Sci USA 84:5823–5827.
   Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nuc Acids Symp 41:95–98.
   Google Scholar
• Huelsenbeck JP, Ronquist F. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–4.
   Google Scholar
• Jung T, Nechwatal J, Cooke DEL, Hartmann G, Blaschke M, Oswald WF, Duncan JM, Delatour C. 2003. Phytophthora pseudosyringae sp. nov., a new species causing root and collar rot of deciduous tree species in Europe. Mycol Res 107:772–789.
   Google Scholar
• Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120.
   Google Scholar
• Kong P, Hong C, Richardson PA, Gallegly ME. 2003. Single-strand-conformation polymorphism of the ribosomal DNA for rapid species differentiation in the genus Phytophthora. Fungal Gen Biol 39:238–249.
   Google Scholar
• Kroon LPNM, Bakker FT, van den Bosch GBM, Bonants PJM, Flier WG. 2004. Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Gen Biol 41:766–782.
   Google Scholar
• Kumar S, Tamura K, Jakobsen IB, Nei M. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245.
   Google Scholar
• Lang BF, Forget L. 1993. The mitochondrial genome of Phytophthora infestans. In: O’Brien SJ, ed. Genetic maps: locus maps of complex genomes. New York: Cold Spring Harbor Laboratory Press. p 3.133–3.135.
   Google Scholar
• Martin FN, Tooley PW. 2003. Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes. Mycologia 95:269–284.
   Google Scholar
• ———, ———. 2004. Identification of Phytophthora isolates to species level using restriction fragment length polymorphism analysis of polymerase chain reaction-amplified region of mitochondrial DNA. Phytopathology 94:983–991.
   Google Scholar
• May K, Ristaino JB. 2004. Identity of the mtDNA haplotype(s) of Phytophthora infestans in historical specimens from the Irish potato famine. Mycol Res 108:471–479.
   Google Scholar
• Mills SD, Forster H, Coffey MD. 1991. Taxonomic structure of Phytophthora cryptogea and P. dreschsleri based on isozyme and mitochondrial DNA analysis. Mycol Res 95: 31–48.
   Google Scholar
• Newhook FJ, Waterhouse GM, Stamps OJ. 1976. Tabular key to the species of Phytophthora. Mycotaxon 32:199–217.
   Google Scholar
• Niederhauser JS. 1991. Phytophthora infestans: the Mexican connection. In: Lucas JA, Shattock RC, Shaw DS, Cooke LR, eds. Phytophthora. Cambridge, UK: Cambridge University Press. p 25–45.
   Google Scholar
• Oliva RF, Erselius LJ, Adler NE, Forbes GA. 2002. Potential of sexual reproduction among host-adapted populations of Phytophthora infestans sensu lato in Ecuador. Plant Pathol 51:710–719.
   Google Scholar
• Ordoñez ME, Hohl HR, Velasco A, Ramon MP, Oyarzun PJ, Smart CD, Fry WE, Forbes GA, Erselius LJ. 2000. A novel population of Phytophthora, similar to P. infestans, attacks wild Solanum species in Ecuador. Phytopathology 90:197–202.
   Google Scholar
• Ospina-Giraldo MD, Jones RW. 2003. Characterization of the glucose-6-phosphate isomerase gene in Phytophthora infestans reveals the presence of multiple alleles. Fungal Gen Biol 40:197–206.
   Google Scholar
• Pieterse CM, van’t Klooster J, van den Berg-Velthuis GC, Govers F. 1995. NiaA, the structural nitrate reductase gene of Phytophthora infestans: isolation, characterization and expression analysis in Aspergillus nidulans. Curr Gen 27:359–366.
   Google Scholar
• Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818.
   Google Scholar
• Rajapakse S, Nilmalgoda SD, Molnar M, Ballard RE, Austin DF, Bohac JR. 2004. Phylogenetic relationships of the sweet potato in Ipomoea series Batatas (Convolvulaceae) based on nuclear b-amylase gene sequences. Mol Phylogenet Evol 30:623–632.
   Google Scholar
• Ristaino JB, Madritch M, Trout CL, Parra G. 1998. PCR amplification of ribosomal DNA species identification in the plant pathogen genus Phytophthora. Appl Envir Micro 64:948–954.
   Google Scholar
• ———, Groves CT, Parra GR. 2001. PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 411:695–697.
   Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690.
   Google Scholar
• Stamps DJ, Waterhouse GM, Newhook FJ, Hall GS. 1990. Revised tabular key to the species of Phytophthora. Commonwealth Agricultural Bureaux International Mycological Institute (UK). No. 162. 28 p.
   Google Scholar
• Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599.
   Google Scholar
• Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and species concepts in Fungi. Fungal Gen Biol 31:21–32.
   Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acid Res 24:4876–4882.
   Google Scholar
• Trout CL, Ristaino JB, Madritch M, Wangsomboondee T. 1997. Rapid detection of Phytophthora infestans in late blight-infected potato and tomato using PCR. Plant Dis 81:1042–1048.
   Google Scholar
• Waterhouse GM. 1963. Key to the species of Phytophthora de Bary. Mycol Paper 162:1–22.
   Google Scholar
• Wattier RAM, Gathercole LL, Assinder SJ, Gliddon CJ, Deahl KL, Shaw DS, Mills DI. 2003. Sequence variation of inter-genic mitochondrial DNA spacers (mtDNA-IGS) of Phytophthora infestans (Oomycetes) and related species. Mol Ecol Note 3:136–138.
   Google Scholar
• White TJ, Bruns T, Lee SB, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky J, White TJ, eds. PCR protocols: a guide to methods and applications. San Diego: Academic Press. p 315–322.
   Google Scholar
• Yoon HS, Hackett JD, Pinto G, Bhattacharya D. 2002. The single, ancient origin of chromist plastids. Proc Nat Acad Sci USA 99:15507–15512.
   Google Scholar