Link to home

Copy number variation appears increased in clonal lineages over sexual lineages of Phytophthora infestans

Brian Knaus: USDA-ARS, Horticultural Crops Research Unit

<div>The Irish Potato Famine pathogen, <em>Phytophthora infestans</em> (Mont.) de Bary, continues to emerge causing epidemics globally. However, mechanisms that produce clonal lineages that are highly virulent remain uncharacterized. We used high throughput sequencing, from previously published sources as well as our own sequencing, to infer copy number variation, based on 200 kbp sliding windows of heterozygous sites, for <em>P. infestans</em> genomes from a global sample of isolates. 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. Many of the clonal lineages that have led to epidemics exhibit copy number increases, including US-1, US-8, US-11, US-23, and US-24. However, the lineage that is thought to have caused the Great Famine appeared diploid. Isolates collected from Mexico, the center of genetic diversity for <em>P. infestans</em> and a region where it is characterized as exhibiting a sexual mode of reproduction, were also predominantly diploid. These results indicate that no simple assumption about the role of copy number variation in <em>P. infestans</em> biology can be made and highlights the importance of inference of copy number prior to genetic analysis. Our results present a new perspective of <em>P. infestans</em> epidemics as frequently being accompanied by changes in copy number that may contribute to the pathogenicity of the lineage.</div>