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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #364020
Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: Genome-wide increased copy number is associated with emergence of dominant clones of the Irish potato famine pathogen Phytophthora infestans

Author
item KNAUS, BRIAN - Oregon State University
item TABIMA, JAVIER - Oregon State University
item SHAKYA, SHANKAR - Oregon State University
item JUDELSON, HOWARD - University Of California, Davis
item Grunwald, Niklaus - Nik

Submitted to: mBio
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2020
Publication Date: 6/23/2020
Citation: Knaus, B.J., Tabima, J.F., Shakya, S.K., Judelson, H.S., Grunwald, N.J. 2020. Genome-wide increased copy number is associated with emergence of dominant clones of the Irish potato famine pathogen Phytophthora infestans. mBio. 11(3). https://doi.org/10.1128/mBio.00326-20.
DOI: https://doi.org/10.1128/mBio.00326-20

Interpretive Summary: The plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages (asexual reproduction). In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a comparative analysis of 47 samples of the pathogen based on sequencing all of the DNA in each sample. We included samples from sexual populations at the center of origin as well as several asexual populations collected from around the world. We conclude that sexual populations at the center of origin typically contain the expected two sets of genetic information, while modern clonal lineages unexpectedly have a third copy of genetic information. We also found variation in the number of copies of individual genes. This work provides evidence that plant pathogens can reemerge in agriculture by increasing DNA content.

Technical Abstract: The plant pathogen that caused the Irish potato famine, Phytophthora infestans, continues to reemerge globally. These modern epidemics are caused by clonally reproducing lineages. In contrast, a sexual mode of reproduction is observed at its center of origin in Mexico. We conducted a comparative genomic analysis of 47 high coverage genomes to infer changes in genic copy number. We included samples from sexual populations at the center of origin as well as several dominant clonal lineages sampled worldwide. We conclude that sexual populations at the center of origin are diploid as was the lineage that caused the famine, while modern clonal lineages showed increased copy number (3x). Copy number variation (CNV) was found genome-wide and did not to adhere to the two-speed genome hypothesis. Although previously reported, tetraploidy was not found in any of the genomes evaluated. We propose a model of superclone emergence supported by the epidemiological record (e.g., EU_13_A2, US-11, US-23) whereby higher copy number provides fitness leading to replacement of prior clonal lineages.