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 current reference 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, robust genome assemblies 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, DU054 and WA94.26. Independent genome assembly produced final genome sequences 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 94.4% and 91.5% of the stramenopile 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 analyses 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
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]. Sample collection and sequencing Two isolates of P. cinnamomi were selected from areas of infection on either side of the Australian continent: one from the Brisbane Ranges in southeastern Australia (DU054, A2 mating type)[5] and the other from southwestern Western Australia (WA94.26, A2 mating type), both Deakin University culture collection These isolates were selected to represent possible genetic diversity of P. cinnamomi in Australia arising from geographic isolation, and possible variation of selective pressures due to different host species. Genome assembly Raw sequencing data for each isolate was first pre-processed using Trimmomatic v0.336 with the following parameters: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:4 AVGQUAL:[30] MINLEN:[36], to remove Illumina adapters and filter reads based on quality scores (Phred score). We used the BUSCO (benchmarking universal single-copy orthologs) pipeline v1.2210 with the default e-value cutoff of 0.01, to assess the completeness of the assembled genomes and compared the results to the previously available Rans isolate. Preliminary genome annotation In the absence of any available high quality ESTs (expressed sequence tags) or transcriptome (gene expression) data for
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