title: Amplification generates modular diversity at an avirulence locus in the pathogen Phytophthora.
abstract: The destructive late blight pathogen Phytophthora infestans is notorious for its rapid adaptation to circumvent detection mediated by plant resistance (R) genes. We performed comparative genomic hybridization on microarrays (array-CGH) in a near genome-wide survey to identify genome rearrangements related to changes in virulence. Six loci with copy number variation were found, one of which involves an amplification colocalizing with a previously identified locus that confers avirulence in combination with either R gene R3b, R10, or R11. Besides array-CGH, we used three independent approaches to find candidate genes at the Avr3b-Avr10-Avr11 locus: positional cloning, cDNA-AFLP analysis, and Affymetrix array expression profiling. This resulted in one candidate, pi3.4, that encodes a protein of 1956 amino acids with regulatory domains characteristic for transcription factors. Amplification is restricted to the 3' end of the full-length gene but the amplified copies still contain the hallmarks of a regulatory protein. Sequence comparison showed that the amplification may generate modular diversity and assist in the assembly of novel full-length genes via unequal crossing-over. Analyses of P. infestans field isolates revealed that the pi3.4 amplification correlates with avirulence; isolates virulent on R3b, R10, and R11 plants lack the amplified gene cluster. The ancestral state of 3.4 in the Phytophthora lineage is a full-length, single-copy gene. In P. infestans, however, pi3.4 is a dynamic gene that is amplified and has moved to other locations. Modular diversity could be a novel mechanism for pathogens to quickly adapt to changes in the environment.
authors.affiliation: Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, NL-5-6709 PD Wageningen and Graduate School Experimental Plant Sciences, The Netherlands.
authors.forename: Rays H Y
authors.initials: RH
authors.lastname: Jiang
authors.forename: Rob
authors.initials: R
authors.lastname: Weide
authors.forename: Peter J I
authors.initials: PJ
authors.lastname: van de Vondervoort
authors.forename: Francine
authors.initials: F
authors.lastname: Govers
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D020451:Contig Mapping; D003433:Crosses, Genetic; D004271:DNA, Fungal / Q000235:genetics; D018628:Gene Dosage; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D005809:Genes, Regulator; D008040:Genetic Linkage; D005819:Genetic Markers; D014644:Genetic Variation; D006239:Haplotypes; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010838:Phytophthora / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism / Q000472:pathogenicity*; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA; D026801:Synteny; D014774:Virulence / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D005819:Genetic Markers