Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families.

species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is , the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, (New Zealand kauri). A deeper understanding of how pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of , the only other completely assembled genome sequence of an oomycete. All chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed . Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against and other species, ultimately helping decipher how pathogens have evolved to shape their effector repertoires and how they might adapt in the future.