Characterisation of the genome and secretome of Phytophthora cryptogea and P. erythroseptica

<i>Phytophthoracryptogea</i> Pethybr. & Laff. and <i>P.erythroseptica</i> Pethybr. are oomycetes that cause root rot diseases of multiple plant species, including serious diseases of potato. These two species of <i>Phytophthora</i> were originally reported in Ireland more than 100 years ago and are closely related phylogenetically and morphologically similar. Both species have wide host ranges and can hybridise with each other. In this study, we sequenced whole genomes of the ex-type strain of <i>P.cryptogea</i> (CBS 113.19) and the authentic strain of <i>P.erythroseptica</i> (P6180). The genomes of the two isolates were assembled into 52.5 Mb and 74.7 Mb, respectively. A total of 11,654 protein-encoding genes were predicted for <i>P.cryptogea</i> and 15,970 for <i>P.erythroseptica</i>. Phylogenomic analyses of 2012 single-copy orthologous genes and 99 BUSCO genes from the stramenopiles dataset confirmed that they are sister species and show that they belong to <i>Phytophthora</i> clade 8. The secretome analysis of <i>P.erythroseptica</i> P6180, <i>P.cryptogea</i> CBS 418.71 and <i>P.cryptogea</i> CBS 113.19 may provide information for future research on resistance-breeding targets and strategies for pathogen control. This genomic characterisation of the two <i>Phytophthora</i> species provides additional reference data that might be useful for future studies on <i>Phytophthora</i> genetic variation, pathogenicity and biological traits.