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

dc.contributorVirginia Techen
dc.contributor.authorQutob, Dinahen
dc.contributor.authorTedman-Jones, Jenniferen
dc.contributor.authorDong, Suomengen
dc.contributor.authorKuflu, Kuflomen
dc.contributor.authorPham, Haien
dc.contributor.authorWang, Yuanchaoen
dc.contributor.authorDou, Daolongen
dc.contributor.authorKale, Shiv D.en
dc.contributor.authorArredondo, Felipe D.en
dc.contributor.authorTyler, Brett M.en
dc.contributor.authorGijzen, Marken
dc.description.abstractThe 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 enes 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.en
dc.description.sponsorshipThis research was supported by grants to MG from Agriculture and Agri-Food Canada, Canadian Crop Genomics Initiative, and to BMT from the National Research Initiative of the United States Department of Agriculture (2001-35319-14251, 2002-35600-12747, 2007-35319-18100 and 2007-35600-18530) and from the United States National Science Foundation (MCB-0242131 and MCB-0731969). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.identifier.citationQutob D, Tedman-Jones J, Dong S, Kuflu K, Wang Y, Dou D, Kale SD, Arredondo FD, Tyler BM, Gijzen M (2009) Copy number variation and transcriptional polymorphisms of Phytophthora sojae RXLR effector genes. PLoS ONE 4(4): e5066. doi: 10.1371/journal.pone.0005066.en
dc.publisherPublic Library of Scienceen
dc.rightsIn Copyrighten
dc.subjectDNA sequencesen
dc.subjectGene predictionen
dc.subjectGenetic locien
dc.subjectGenoome evolutionen
dc.subjectProbe hybridizationen
dc.subjectSequence assembly toolsen
dc.subjectSequence motif analysisen
dc.titleCopy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3aen
dc.title.serialPLoS ONEen
dc.typeArticle - Refereeden


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