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Oral: Oomycete Biology


What is a clone? Rethinking the ancestry of US clonal lineages of Phytophthora infestans using whole genome sequences
B. KNAUS (1), J. Tabima (2), Z. Kamvar (2), C. Davis (3), H. Judelson (3), N. Gr├╝nwald (1) (1) USDA ARS, Horticultural Crops Research Laboratory, U.S.A.; (2) Oregon State University, Botany and Plant Pathology, U.S.A.; (3) Univ. California, Plant Patholog

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Identifying genetic boundaries of a clone or clonal lineage is not straightforward. Identical multilocus genotypes can arise independently from unrelated clones. Similarly, lineages derived from the same ancestral clone can accumulate variants that distinguish them. Populations of the potato and tomato late blight pathogen, Phytophthora infestans, are well known for emerging as novel clonal lineages. These successions of clones have historically been named within the United States as lineages US1-US24, in order of appearance. Hypothetically, these lineages can emerge through divergence from other US lineages, recombination among US lineages or as novel, independent lineages. We used 32 whole genome sequences including dominant US clonal lineages and available samples from global populations. Based on the core orthologous genes located on supercontigs 1.1 and 1.5 we observed substantial amounts of variation shared among strains within clonal lineages. We found no support for emergence of any of the US lineages from a common ancestor shared with any other US lineages. Each of the US clonal lineages fit a model where populations of new clonal lineages emerge via migration from a source population that is sexual in nature and potentially located in central Mexico or elsewhere. This work provides novel insights into patterns of emergence of clonal lineages in plant pathogen genomes and provides an evolutionary framework for definition of clones in P. infestans.