Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

• Published in: PeerJ (San Francisco, CA) Vol. 5; p. e3266
• Main Authors: Wallace, Emma C, Quesada-Ocampo, Lina M
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 02.05.2017; PeerJ, Inc; PeerJ Inc
• Subjects: Agricultural Science; Bioinformatics; Comparative genomics; Computational biology; Downy mildew; Epidemics; Epidemiology; Gene expression; Genes; Genetic resources; Genomes; Genomic analysis; Genomics; Hyaloperonospora arabidopsidis; Identification; Identification and classification; Laboratories; Methods; Microsatellites; Mildew; Molecular Biology; Pathogenic microorganisms; Pathogens; Pesticides; Phylogenetics; Plant diseases; Plant pathology; Plant Science; Population; Population genetics; Population structure; Pseudoperonospora cubensis; Pseudoperonospora humuli; Simple Sequence Repeats; Studies; United States > US; Comparative genomics; Microsatellites; Simple Sequence Repeats; Downy mildew; Pseudoperonospora cubensis; Population genetics
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.3266

Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete , causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, , since no draft genome is available for this species. We also compared the microsatellite repertoire of to that of the model organism , which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from transcripts differed significantly from . The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in isolates, and 83 microsatellites demonstrated transferability to . Eleven microsatellites were found to be polymorphic and consistently amplified in isolates. Analysis of isolates from diverse hosts and locations revealed higher diversity in compared to isolates. These microsatellites will be useful in efforts to better understand relationships within species and on a population level.