Chromosome-scale assembly and annotation of Phytophthora capsici isolate BYA5

Phytophthora capsici is a globally widespread oomycete pathogen that causes severe damage to diverse host plants, posing major agricultural challenges. Here, we present a high-quality, chromosome-level genome assembly of P. capsici isolate BYA5 using PacBio HiFi, ultralong Oxford Nanopore, and Hi-C sequencing data. The assembled genome spans 83.96 Mb and comprises 18 chromosomes, capturing all centromeres and most telomeres (32/36). The assembled genome exhibits a contiguous N50 of 3.84 Mb, representing the first chromosome-level genome sequence of a pathogenic P. capsici. A total of 15,688 protein-coding genes were annotated, including 337 RxLRs and 115 Crinkler (CRN) effectors. This high-quality reference genome provides a valuable resource for advancing our understanding of oomycete pathobiology and evolution, facilitating further research on virulence mechanisms and host-pathogen interactions.