Copy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3a

• Published in: PloS one 2009-04, Vol.4 (4), p.e5066-e5066
• Main Authors: Qutob, Dinah, Tedman-Jones, Jennifer, Dong, Suomeng, Kuflu, Kuflom, Pham, Hai, Wang, Yuanchao, Dou, Daolong, Kale, Shiv D, Arredondo, Felipe D, Tyler, Brett M, Gijzen, Mark
• Format: Article
• Language: English
• Subjects: Agriculture; Algal Proteins - chemistry; Algal Proteins - genetics; Amino Acid Sequence; avirulence genes; Avr1a gene; Avr3a gene; Bioinformatics; chromosome mapping; Cloning; Cloning, Molecular; Copy number; copy number variation; Deoxyribonucleic acid; Disease; DNA; effector genes; Effectors; Evolution; Fitness; Food; fungal diseases of plants; Gangrene; Gene amplification; gene deletion; gene duplication; Gene expression; gene expression regulation; Gene sequencing; Genes; Genes, Fungal; Genetic aspects; Genetic diversity; Genetic polymorphisms; Genomes; Genomics; Glycine max; Immune system; Laboratories; microbial genetics; Microbiology/Microbial Evolution and Genomics; Microbiology/Plant-Biotic Interactions; Molecular Sequence Data; Molecular weight; Oligonucleotide Array Sequence Analysis; Oomycetes; Pathogens; Phenotypic variations; physical chromosome mapping; Phytophthora; Phytophthora - genetics; Phytophthora - pathogenicity; Phytophthora sojae; Plant Biology/Agricultural Biotechnology; Plant Biology/Plant Genomes and Evolution; Plant Biology/Plant-Biotic Interactions; plant pathogenic fungi; Plant pathology; Polymorphism, Genetic; Proteins; Reproduction (copying); Reproductive fitness; RNA, Messenger - genetics; Sequence Homology, Amino Acid; Soybeans; Strains (organisms); Surveillance; Transcription; transcription (genetics); Transcription, Genetic; Virulence; Virulence (Microbiology)
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0005066

The importance of segmental duplications and copy number variants as a source of genetic and phenotypic variation is gaining greater appreciation, in a variety of organisms. Now, we have identified the Phytophthora sojae avirulence genes Avr1a and Avr3a and demonstrate how each of these Avr genes display copy number variation in different strains of P. sojae. The Avr1a locus is a tandem array of four near-identical copies of a 5.2 kb DNA segment. Two copies encoding Avr1a are deleted in some P. sojae strains, causing changes in virulence. In other P. sojae strains, differences in transcription of Avr1a result in gain of virulence. For Avr3a, there are four copies or one copy of this gene, depending on the P. sojae strain. In P. sojae strains with multiple copies of Avr3a, this gene occurs within a 10.8 kb segmental duplication that includes four other genes. Transcriptional differences of the Avr3a gene among P. sojae strains cause changes in virulence. To determine the extent of duplication within the superfamily of secreted proteins that includes Avr1a and Avr3a, predicted RXLR effector genes from the P. sojae and the P. ramorum genomes were compared by counting trace file matches from whole genome shotgun sequences. The results indicate that multiple, near-identical copies of RXLR effector genes are prevalent in oomycete genomes. We propose that multiple copies of particular RXLR effectors may contribute to pathogen fitness. However, recognition of these effectors by plant immune systems results in selection for pathogen strains with deleted or transcriptionally silenced gene copies.