Draft assembly of Phytopthora capsici from long-read sequencing uncovers complexity

Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as host and fungicide, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits wide-spread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here we leverage Oxford Nanopore Technology (ONT) and existing short read resources, to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in > 1.25 million reads with an N50 of 13 kb. The resulting assembly is 124 Mbp in 906 scaffolds with an N50 length of 232 kb. This assembly is 92% bigger than the current draft genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 96.5% complete orthologs (39.7% duplicated). Evolutionary analysis supports a recent whole genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.