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Whole Genome Sequencing for Development of PCR specific detection of Monilinia species for Quarantine applications.

Subodh Srivastava: USDA-APHIS-PPQ-S&T-CPHST

<div><em>Monilinia</em> species cause important and economically devastating brown fruit rot diseases of pome and stone fruits and blossom blights. Two <em>Monilinia</em> species, <em>M. fructigena </em>and <em>M. polystroma,</em> are of regulatory concern to US Agriculture, but cannot be easily distinguished from native species. To help us improve diagnostics methods, we sequenced the genome of <em>Monilinia fructigena</em> with both Illumina Mi-Seq and PacBio platforms to compare quality and enhance marker discovery. We generated 20 million and 1.08 million reads to assemble into 1,635 and 1,324 contigs with over 150X and 50X coverage for the Illumina and PacBio platforms, respectively. We used CLC and Canu assemblers to assemble these Illumina and PacBio reads, respectively, and PacBio reads were further polished to improve the quality of bases with Illumina using PILON (hybrid correction/polisher). The Illumina assembly covers 93.67% of PacBio assembly, meaning we added 7% more genome using PacBio assembled contigs. We observed 41.2% in Accessory Genetic Material (AGM), or unique sequences, and 58.8% Core Genetic Material (CGM) when this assembly is compared to <em>M. fructicola</em>. We also observed 23.8 % unique (CGM 76.2%) when compared with <em>M. laxa</em>, and 11.2% unique (CGM 88.8%) when compared with <em>M. polystroma</em>. We plan to annotate these genomes (AGM as well as CGM) and analyze for identification of uniqueness between these closely related species to develop DNA based markers for quarantine applications.</div>