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 3Ј 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.

Comparative Genomics of a Plant-Pathogenic Fungus,Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

“…Recombination can lead to domain swapping between virulence proteins as has been shown in the oomycete Crinkler family of modular proteins, which exhibit domain swapping and chimera formation (Haas et al 2009), and in the NRPSs of Ptr . TE-mediated duplications can lead to copy number variation (CNV), which in Phytophthora sojae has been associated with silencing of effectors (Qutob et al 2009) and in P. infestans has been proposed to contribute to the assembly of novel genes (Jiang et al 2006). In Ptr , CNV of the HST gene, ToxB , correlates with isolate virulence.…”

Mechanisms and Evolution of Virulence in Oomycetes

“…These effector genes are frequently rearranged, duplicated, or expanded, www.annualreviews.org • Virulence in Oomycetes 309 and they are enriched in dynamic genomic regions (41)(42)(43)77). For example, most of the hundreds of RxLR effector genes are located in regions without conserved synteny (44).…”

Presence/absence, differential expression and sequence polymorphisms between PiAVR2 and PiAVR2‐like in Phytophthora infestans determine virulence on R2 plants

“…Copy number variation has been a feature of avirulence loci in P. infestans and P. sojae and has contributed to phenotypic variation (Jiang et al, 2006;Qutob et al, 2009;Dong et al, 2009). This is well documented particularly for PsAvr1a and PsAvr3a, with some avirulent P. sojae isolates containing multiple copies and some virulent isolates revealing complete deletion of recognized forms .…”