Abstract:
BACKGROUND: Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the
most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There is
currently a lack of a high-quality reference genome for this species despite several attempts that have been made
towards sequencing its genome. The lack of a good quality genome sequence has been a setback for various
genetic and genomic research to be done on this species. As a consequence, little is known regarding its genome
characteristics and how these contribute to its pathogenicity and invasiveness.
RESULTS: In this work we generated a high-quality genome sequence and annotation for P. cinnamomi using a
combination of Oxford Nanopore and Illumina sequencing technologies. The annotation was done using RNA-Seq
data as supporting gene evidence. The final assembly consisted of 133 scaffolds, with an estimated genome size of
109.7 Mb, N50 of 1.18 Mb, and BUSCO completeness score of 97.5%. Genome partitioning analysis revealed that P.
cinnamomi has a two-speed genome characteristic, similar to that of other oomycetes and fungal plant pathogens.
In planta gene expression analysis revealed up-regulation of pathogenicity-related genes, suggesting their
important roles during infection and host degradation.
CONCLUSION: This study has provided a high-quality reference genome and annotation for P. cinnamomi. This is
among the best assembled genomes for any Phytophthora species assembled to date and thus resulted in
improved identification and characterization of pathogenicity-related genes, some of which were undetected in
previous versions of genome assemblies. Phytophthora cinnamomi harbours a large number of effector genes which
are located in the gene-poor regions of the genome. This unique genomic partitioning provides P. cinnamomi with
a high level of adaptability and could contribute to its success as a highly invasive species. Finally, the genome
sequence, its annotation and the pathogenicity effectors identified in this study will serve as an important resource
that will enable future studies to better understand and mitigate the impact of this important pathogen.
