Applied and Environmental Microbiology doi:10.1128/AEM.02221-16. Supplemental data: http://dx.doi.org/10.1128/AEM.02221-16 Received29 July 2016 Accepted22 September 2016 Genetic diversity and origins of the homoploid type hybrid Phytophthora ×alni Jaime Aguayo1*, Fabien Halkett2, Claude Husson2, Zoltán Á. Nagy3, András Szigethy3, József Bakonyi3, Pascal Frey2 and Benoit Marçais2 1 ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, Malzéville, France. 2 UMR IAM, INRA, Université de Lorraine, Nancy, France. 3 Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences. Budapest, Hungary. Running Head: Genetic structure of an homoploid pathogen *Address correspondence to Benoit Marçais,
[email protected] P.F. and B.M. co-directed this work Summary Assessing the process that gives rise to hybrid pathogens is central to understand the evolution of emerging plant diseases. Phytophthora ×alni, a pathogen of alder, results from the homoploid hybridization of two related species, Phytophthora uniformis and Phytophthora ×multiformis. Describing genetic characteristics of P. ×alni should help understanding how reproductive mechanisms and historical processes shaped the population structure of this emerging hybrid pathogen. The population genetic structure of P. ×alni and the relationship with its parental species was investigated using twelve microsatellites and one mitochondrial DNA (mtDNA) marker on a European collection of 379 isolates. Populations of P. ×alni were dominated by one multilocus genotype (MLG). The frequency of this dominant MLG increased after the disease emergence together with a decline in diversity, suggesting that it was favoured by a genetic mechanism such as drift or selection. Combined microsatellite and mtDNA results confirmed that P.