Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential

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.

Expression of several Phytophthora cinnamomi putative RxLRs provides evidence for virulence roles in avocado

“…Several genomes of Phytophthora species contain hundreds of candidate RxLR effectors [20][21][22]29], and many of these effectors have been demonstrated by functional studies to contribute to virulence during host infection. In P. cinnamomi, recent studies have identified candidate RxLRs in the pathogen's genome [1,[23][24][25] but it remains unclear whether these putative effector genes are expressed during plant infection to contribute to virulence, and functions have yet to be assigned to any P. cinnamomi effectors. To that end, this study identified 61 candidate P. cinnamomi RxLR effector genes which are specifically expressed during the initial infection of avocado.…”

“…In this study, a compilation of predicted candidate RxLRs in P. cinnamomi was created using data produced in previous studies [1,[23][24][25] as well as the set of 192 candidate RxLRs we identified in the P. cinnamomi genome using the pipeline developed by Win et al [22]. The final dataset consisted of 238 putative P. cinnamomi RxLRs with confirmed signal peptides.…”

“…A library of putative P. cinnamomi RxLR effector genes was constructed using available sequence lists of candidates predicted in recent literature [1,[23][24][25] as well as a set of 192 candidate RxLRs predicted in this study using a bioinformatics pipeline adapted from Win et al [22]. Gene names for the full list of candidates were determined using a BLAST search of the recently available P. cinnamomi genome [25], and redundant sequences were removed. The final compiled library contained 322 candidate RxLR sequences from the P. cinnamomi GKB4 genome.…”

“…Based on their expression profiles and initial phylogenetic analyses, 71 putative RxLRs were retained for further investigation and several of these genes had multiple hits to different contigs of the P. cinnamomi genome [25]. In most cases, the hits differed slightly in their overall similarity scores, leading to the hypothesis that the hits represented duplications of the candidate RxLRs, rather than errors in the genome assembly.…”

“…A study by Hardham & Blackman [1] predicted 171 candidate RxLRs in the P. cinnamomi genome, based on similarity to candidate RxLRs in Phytophthora infestans. Most recently, 181 putative RxLR genes have been predicted in a new genomic analysis of P. cinnamomi, and 41 of these had altered expression profiles 5 days after inoculation of avocado [25]. This is the only study conducted to date which highlights which predicted RxLRs may have virulence roles in avocado, though the use of a single late timepoint in that study means that many questions remain unanswered regarding which P. cinnamomi RxLR effectors may specifically contribute to virulence during the establishing of PRR in avocado.…”