Phytophthora cinnamomi is an extremely destructive phytopathogen that is the causative agent of dieback and root rot diseases in thousands of plant species worldwide. This fungi-like oomycete is a highly invasive endophyte, whose infections poses a serious threat to native biodiversity, forestry and agriculture. Exacerbation of its virulence and transmission is expected in a warming climate, increasing the need for the development of countermeasures against it, as current ones are largely ineffective. P. cinnamomi’s pathogenicity is dependent on its effector proteins that are secreted into the host’s tissues and allow for the establishment of a niche. The effectome is the collection of all effector proteins present in a genome, and they are under constant selective pressure, as the host species are in a race to develop resistance and co-evolve defences against the parasite. Therefore, understanding P. cinnamomi’s mechanisms of pathogenicity requires the identification of its rapidly evolving effectome.

To investigate the results of constant co-evolution in such an effective plant pathogen, genome assembly and annotation were used for effectome identification. By understanding the basis of P. cinnamomi’s pathogenicity, we hope to provide insights into the evolution of susceptibility and resistance in hosts which will contribute to the development of treatments. Specifically, this will be done by analysing the variation between effectomes of P. cinnamomi that have been isolated from different host species. Here the genomes of 10 isolates of P. cinnamomi that were obtained from various hosts in Aotearoa were assembled using long-read sequencing. The annotation of genomic information obtained through reference guided assembly of long sequence reads allows for the identification of effectomes present in these genomes. By comparing the 10 genomes and their annotated effectomes a deeper understanding into the co-evolution of P. cinnamomi and it hosts, as well as its mechanisms of pathogenicity.