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Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.

Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, Klein J, Meijer HJ, Spring O, Win J, Zipper R, Bode HB, Govers F, Kamoun S, Schornack S, Studholme DJ, Van den Ackerveken G, Thines M - BMC Genomics (2015)

Bottom Line: Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species.This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic.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.

View Article: PubMed Central - PubMed

Affiliation: Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. rahul.sharma@senckenberg.de.

ABSTRACT

Background: Downy mildews are the most speciose 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 conservation of the dEER-motif. 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 evolution 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.

No MeSH data available.


Features of RxLR-dEER-like effectors and frequency of the RxLR and RxLR-dEER-like proteins in the genome of Pl. halstedii: a Sequence features of the RxLR-dEER-like proteins were calculated from predicted putative RxLR-like proteins. Numbers in brackets represent the minimum and maximum values of distances and number in italics represents the corresponding mean value. Multiple sequence alignments were performed by using Mafft and sequence logos were generated using jalview. b Bar plot representing the number of RxLR-like and RxLR-dEER-like proteins in the predicted secretome of Pl. halstedii
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Fig7: Features of RxLR-dEER-like effectors and frequency of the RxLR and RxLR-dEER-like proteins in the genome of Pl. halstedii: a Sequence features of the RxLR-dEER-like proteins were calculated from predicted putative RxLR-like proteins. Numbers in brackets represent the minimum and maximum values of distances and number in italics represents the corresponding mean value. Multiple sequence alignments were performed by using Mafft and sequence logos were generated using jalview. b Bar plot representing the number of RxLR-like and RxLR-dEER-like proteins in the predicted secretome of Pl. halstedii

Mentions: Candidate secreted proteins with RxLR-dEER-like domains were predicted using both regular expression and HMM-based methods (Additional file 2: Figure S21, S22A-B). A total of 260 candidate RxLR-like proteins were predicted from PSEP-en coding genes (Additional file 20). Out of these 260 RxLR-like proteins, 21 sequences had the exact RxLR-dEER motif. Features and occurrences of the RxLR-dEER like proteins were further analysed (Fig. 7a) and revealed an overrepresentation of some RxLR-dEER variants, e.g. KxLR-dEER and RxLK-dEER (Fig. 7b).Fig. 7


Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.

Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, Klein J, Meijer HJ, Spring O, Win J, Zipper R, Bode HB, Govers F, Kamoun S, Schornack S, Studholme DJ, Van den Ackerveken G, Thines M - BMC Genomics (2015)

Features of RxLR-dEER-like effectors and frequency of the RxLR and RxLR-dEER-like proteins in the genome of Pl. halstedii: a Sequence features of the RxLR-dEER-like proteins were calculated from predicted putative RxLR-like proteins. Numbers in brackets represent the minimum and maximum values of distances and number in italics represents the corresponding mean value. Multiple sequence alignments were performed by using Mafft and sequence logos were generated using jalview. b Bar plot representing the number of RxLR-like and RxLR-dEER-like proteins in the predicted secretome of Pl. halstedii
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4594904&req=5

Fig7: Features of RxLR-dEER-like effectors and frequency of the RxLR and RxLR-dEER-like proteins in the genome of Pl. halstedii: a Sequence features of the RxLR-dEER-like proteins were calculated from predicted putative RxLR-like proteins. Numbers in brackets represent the minimum and maximum values of distances and number in italics represents the corresponding mean value. Multiple sequence alignments were performed by using Mafft and sequence logos were generated using jalview. b Bar plot representing the number of RxLR-like and RxLR-dEER-like proteins in the predicted secretome of Pl. halstedii
Mentions: Candidate secreted proteins with RxLR-dEER-like domains were predicted using both regular expression and HMM-based methods (Additional file 2: Figure S21, S22A-B). A total of 260 candidate RxLR-like proteins were predicted from PSEP-en coding genes (Additional file 20). Out of these 260 RxLR-like proteins, 21 sequences had the exact RxLR-dEER motif. Features and occurrences of the RxLR-dEER like proteins were further analysed (Fig. 7a) and revealed an overrepresentation of some RxLR-dEER variants, e.g. KxLR-dEER and RxLK-dEER (Fig. 7b).Fig. 7

Bottom Line: Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species.This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic.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.

View Article: PubMed Central - PubMed

Affiliation: Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. rahul.sharma@senckenberg.de.

ABSTRACT

Background: Downy mildews are the most speciose 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 conservation of the dEER-motif. 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 evolution 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.

No MeSH data available.