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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #363776

Research Project: Management of Pathogens for Strawberry and Vegetable Production Systems

Location: Crop Improvement and Protection Research

Title: Comparative genomics of downy mildews

item FLETCHER, KYLE - University Of California
item Martin, Frank
item RIVERA, YAZMIN - Animal And Plant Health Inspection Service (APHIS)
item GIL, JULIANA - University Of California
item WOOD, KELSEY - University Of California
item DELA CUEVA, FE - University Of The Philippines
item Kandel, Shyam
item Luster, Douglas - Doug
item MAGILL, CLINT - Texas A&M University
item SHARMA, RAJAN - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Klosterman, Steven
item ABAD, GLORIA - Animal And Plant Health Inspection Service (APHIS)
item MICHELMORE, RICHARD - University Of California

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/6/2019
Publication Date: 7/10/2019
Citation: Fletcher, K., Martin, F.N., Rivera, Y., Gil, J., Wood, K., Dela Cueva, F., Kandel, S.L., Luster, D.G., Magill, C., Sharma, R., Klosterman, S.J., Abad, G., Michelmore, R. 2019. Comparative genomics of downy mildews. Oomycete Molecular Genetics Network Conference, July 10-12, 2019, Oban, Scotland.

Interpretive Summary:

Technical Abstract: We have sequenced the genomes of tropical and temperate downy mildew pathogens including at least one representative from Bremia, Peronospora, Sclerospora, Peronosclerospora and Perofascia. For some genera, it was possible to sequence multiple historical and contemporary isolates. A wide range of genome sizes coupled with recent expansions of repeats, the presence of more than two haplotypes, and varying levels of heterozygosity meant that some genomes were more difficult to assemble than others. When Hi-C data was used, assemblies approached chromosome scale contiguity. Data analyses revealed extensive synteny between downy mildews and Phytophthora spp. Maximum likelihood and multispecies coalescence trees support downy mildews as being polyphyletic. Orthology analysis revealed that major adaptations to biotrophy involve the loss of genes associated with transport, carbohydrate binding, and pathogenicity. However, sequences from the downy mildew pathogens have a reduced putative effector repertoire compared to Phytophthora spp.