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Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

Longmuir, Amy L, Beech, Peter and Richardson, Mark 2017, Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi, F1000research, vol. 6, pp. 1-10, doi: 10.12688/f1000research.12867.1.

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Title Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi
Formatted title Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi
Author(s) Longmuir, Amy L
Beech, PeterORCID iD for Beech, Peter orcid.org/0000-0003-1669-6623
Richardson, MarkORCID iD for Richardson, Mark orcid.org/0000-0002-1650-0064
Journal name F1000research
Volume number 6
Article ID 1972
Start page 1
End page 10
Total pages 10
Publisher F1000Research Ltd
Place of publication London, Eng.
Publication date 2017-11-08
ISSN 2046-1402
Keyword(s) Phytophthora cinnamomi
Phytophthora genome
plant pathogen
Summary 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.
Language eng
DOI 10.12688/f1000research.12867.1
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Related work DU:30102751
Copyright notice ©2017, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30105562

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.