Oral: Fungal Diseases
Improving genomic resources for the detection of Macrophomina phaseolina infection of strawberry
A. BURKHARDT (1), K. Childs (2), M. Ramon (1), F. Martin (1) (1) USDA, U.S.A.; (2) Michigan State University, U.S.A.
Macrophomina phaseolina is the causal agent of charcoal rot, which is characterized by wilting, stunting, and crown discoloration. It has had an increasingly devastating impact on strawberry production in California as treatment methods have shifted from broadcast pre-plant fumigation with methyl bromide+chloropicrin to individual bed treatment with alternative fumigants. Hundreds of M. phaseolina isolates were collected from infected hosts in multiple countries and states, including many from California. An SSR analysis revealed that, with few exceptions, the strawberry isolates were a single genotype (isolates from other hosts were not pathogenic on strawberry). To quickly identify the strawberry genotype, genotype-specific primers were developed with the end goal of implementing a diagnostic assay from soil prior to planting. These primers were designed by sequencing multiple isolates and using comparative genomics to identify genotype-specific loci. However, the complexity of the differences in the genomes of strawberry and non-strawberry isolates cannot be fully resolved with this approach. Therefore, PacBio sequencing was used to assemble a strawberry isolate reference genome. The draft assembly has an N50 of 3.3 Mb with 143 contigs and ~150x genome coverage. Ongoing work to improve and annotate this assembly is being done so that it can be used to identify additional strawberry-specific loci and to understand host specificity through comparative genomics.