Abstract
Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The currently available genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, more robust assemblies of the genomes of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings: Some 308 million raw reads were generated for the two strains. Independent genome assembly produced final genomes of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 82.5% and 81.8% of the eukaryote universal single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analysis and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.
Highlights
Phytophthora cinnamomi is a highly virulent plant pathogen that has a devastating impact of the Australian ecosystem, namely in the south-western areas of Western Australia and much of the south and east coasts of Victoria and New South Wales[1]
In the south west Botanical Province of Western Australia, alone, over 40% of the 5710 plant species present have been shown to be susceptible to P. cinnamomi[2]
Significant genetic and phenotypic variation can occur within a signal clonal linage of P. cinnamomi[3] and susceptibility of a given host plant species has been shown to vary from site to site[4]
Summary
1. Nicolás Daniel Ayub , National Scientific and Technical Research Council, Buenos Aires, Argentina. 2. Erik Andreasson, Swedish University of Agricultural Sciences, Alnarp, Sweden Laura Grenville Briggs, Swedish University of Agricultural Sciences, Alnarp, Sweden. University of Exeter, Any reports and responses or comments on the article can be found at the end of the article. This article is included in the Agriculture, Food and Nutrition gateway
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