Dataset Identification

Citation
Sharma R Thines M Xia X
Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora
Document ID: rsharma.26.4
Document URL: http://dataportal-senckenberg.de/database/metacat/rsharma.26.4/bikf


General Information

Abstract:
Background Downy mildews are the most specious group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. Results Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the dEER-motif in effector translocation. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolutionary trajectories of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. Conclusions The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
Keywords:
  • Comparative genomics, core effectors, downy mildew, evolution, microsatellites, obligate biotroph, oomycetes, phytohormones, plant pathogen, promotor, RxLR effectors
Data Table and Publications
Other Data:P.halstedii_protein_sequences ( View Metadata | Download File )
Other Data:P.halstedii_CDS ( View Metadata | Download File )
Other Data:P.halstedii_EMBL_file ( View Metadata | Download File )
Other Data:Tree file ( View Metadata | Download File )
Other Data:Phals repeatmasked genome ( View Metadata | Download File )
Other Data:Phals unmasked genome ( View Metadata | Download File )
Other Data:Phals Secretome ( View Metadata | Download File )
Other Data:Phals.gff ( View Metadata | Download File )

Involved Parties

Data Set Owners
Individual:Mr Rahul Sharma
Organization:IPF, Bik-F, Senckenberg
Position:Phd student
Individual:Prof. Dr. Marco Thines
Address:
Georg-Voigt-Strasse 14-16,
Frankfurt am main, 60325
Individual: Xiaojuan Xia
Organization:Bik-F, Senckenberg
Position:Phd student
Data Set Contacts
Individual:Prof. Dr. Marco Thines
Address:
Georg-Voigt-Strasse 14-16,
Frankfurt am main, 60325 Germany

Distribution Information

Authentification
Auth System:knb
Order:allowFirst
Allow: [read] public
Download Metadata: Ecological Metadata Language (EML) File