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Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi
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posted on 2017-11-08, 00:00 authored by Amy Longmuir, Peter BeechPeter Beech, Mark RichardsonMark RichardsonBackground: 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.
History
Journal
F1000researchVolume
6Article number
1972Pagination
1 - 10Publisher
F1000Research LtdLocation
London, Eng.Publisher DOI
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ISSN
2046-1402Language
engPublication classification
C1 Refereed article in a scholarly journal; C Journal articleCopyright notice
2017, Longmuir AL et al.Usage metrics
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