Improving Genomic Resources for the Detection of Macrophomina phaseolina Infection of Strawberry

Macrophomina phaseolina is a haploid fungus that typically causes charcoal rot on a wide range of hosts, although a group of strawberry host-specific isolates has recently been identified. Isolates recovered from other hosts were not pathogenic on strawberry. Hundreds of M. phaseolina isolates were collected from strawberry and different hosts, and an SSR analysis revealed that, with few exceptions, the strawberry isolates were the same genotype. To understand this host specificity from a genomic level, we sequenced M. phaseolina isolates from strawberry and from alfalfa using PacBio data and Illumina paired end and mate pair data. The current genome assembly from the strawberry isolate using HGAP3 to assemble PacBio reads and PILON to error correct with the paired end and mate pair data has an N50 of 3.3 Mb with 143 contigs and ~150x genome coverage. Over 90% of the genome is represented on the 15 longest contigs. The assembly of the alfalfa isolate and genome annotation of both isolates is underway with the intention of using comparative genomics to identify genes that could be responsible for strawberry host specificity. Additional sequencing with Illumina and genome assembly with CLC Workbench was done on eleven isolates, and a unique locus within the M. phaseolina strawberry specific genotype was identified using comparative genomics. Specific primers were designed for this locus and are being used for a nested TaqMan qPCR assay to quantify M. phaseolina in the soil, and an isothermal recombinase polymerase amplification assay is being developed to detect infection in plants.