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Genic copy number variation reveals an unexpected mosaic of varying ratios of diploidy and triploidy among isolates of Phytophthora infestans
Brian Knaus: USDA ARS; Javier Tabima: Oregon State University; Shankar Shakya: OREGON STATE UNIVERSITY; Howard Judelson: University of California; Nik Grunwald: USDA-ARS, Horticultural Crops Research Unit
<div>For almost as long as the potato has been cultivated, it has also been repeatedly subject to severe epidemics caused by the Irish Potato Famine pathogen, <i>Phytophthora infestans</i> (Mont.) de Bary. Fundamental to understanding the genetic architecture of traits such as fungicide resistance and mating type determination is knowledge of how many copies of each gene are expected (i.e., is a gene diploid, triploid, tetraploid or higher ploid). We used high throughput sequencing, from previously published sources as well as our own sequencing, to infer gene copy number for each of the annotated <i>P. infestans </i>genes. Instead of observing individuals that were predominantly diploid or triploid we observed individuals that represented a full spectrum of intermediate states from diploid to triploid. Comparison of gene copy number among samples did not result in large regions of conserved copy number but instead presented a surprisingly plastic genome. Previous perspectives that individuals are diploid at the species’ center of diversity and higher ploid in clonal epidemics are shown to be more ambiguous than previously thought. These results indicate that no simple assumption about gene copy number can be made within <i>P. infestans</i> and highlights the importance of inference of copy number prior to genetic analysis. Our findings present new perspectives on <i>P. infestans</i> as an organism with great variability in how many copies each gene it may contain.</div>

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