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

Rahul Sharma,Xiaojuan Xia,Miloslav Kitner,Otmar Spring,Stan Oome,Guido Van Den Ackerveken,Joe Win,Sophien Kamoun,Marco Thines,Helge B Bode,David J Studholme,Eric Kemen,Reinhard Zipper,Christine Sambles,Liliana Cano ,D.j Van Den Hoogen ,F Govers ,Howard S Judelson ,Joel D Klein ,H.j.g Meijer ,Sebastián Schornack ,Édouard Evangelisti

doi:10.1186/s12864-015-1904-7

Abstract

BackgroundDowny 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.ResultsHere 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1904-7) contains supplementary material, which is available to authorized users.

Highlights

Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance
Illumina standard adapter and primer sequences were removed from these reads and further quality control (QC) trimming was performed using an average phred quality score cut-off of 20 and a minimum length threshold of 72 bp
All reads were assembled using the Velvet [41] genome assembler v1.2.09 and the resulting scaffolds were compared to the National center for biotechnology information (NCBI) nt database using Blast to check for bacterial and host plant contamination (Additional file 1)

Summary

Introduction

Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. Oomycetes include devastating pathogens of plants and animals that can be found in almost all ecosystems and show a variety of different lifestyles [1,2,3]. They often cause serious infections on their hosts and are responsible for huge economic losses [4]. Considering the devastating effects on the sunflower crop, it is crucial to develop genomic resources for Pl. halstedii to achieve a better understanding of its infection biology and reveal new strategies for avoiding the loss of sunflower crop to this pathogen

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Conclusion