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Frankfurt am Main, Germany

Thines M.,Integrative Fungal Research IPF | Thines M.,Biodiversity and Climate Research Center | Thines M.,Goethe University Frankfurt | Telle S.,Integrative Fungal Research IPF | And 5 more authors.
IMA Fungus

So far 19 genera of downy mildews have been described, of which seven are parasitic to grasses. Here, we introduce a new genus, Baobabopsis, to accommodate two distinctive downy mildews, B. donbarrettii sp. nov., collected on Perotis rara in northern Australia, and B. enneapogonis sp. nov., collected on Enneapogon spp. in western and central Australia. Baobabopsis donbarrettii produced both oospores and sporangiospores that are morphologically distinct from other downy mildews on grasses. Molecular phylogenetic analyses showed that the two species of Baobabopsis occupied an isolated position among the known genera of graminicolous downy mildews. The importance of the Poaceae for the evolution of downy mildews is highlighted by the observation that more than a third of the known genera of downy mildews occur on grasses, while more than 90 % of the known species of downy mildews infect eudicots. © 2015 International Mycological Association. Source

Sharma R.,Biodiversity and Climate Research Center | Sharma R.,Goethe University Frankfurt | Sharma R.,Center for Integrative Fungal Research | Xia X.,Biodiversity and Climate Research Center | And 25 more authors.
BMC Genomics

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. © 2015 Sharma et al. Source

Mishra B.,Biodiversity and Climate Research Center | Mishra B.,Goethe University Frankfurt | Solovyeva I.,Biodiversity and Climate Research Center | Schmuker A.,University of Hohenheim | And 3 more authors.
Mycological Progress

The basal immune system of plants fights pathogens by recognising conserved pathogen-associated molecular patterns. To bypass this, pathogens secrete effectors into the host plant, of which some are sensed by resistance genes, triggering host defence reactions. Plant pathogens diversify by host jumping and co-speciation. Little is known about the functional adaptations of effectors to new targets after host jumping, and how R-protein and target-mediated adaptations might differ. In this study, 40 coding sequences of the ATR1 effector from 3 different oomycete species, Hyaloperonospora thlaspeos-perfoliati, H. crispula and H. arabidopsidis have been analysed. Forty-six positively selected sites were identified, when sequences from all the organisms were analysed together. In H. arabidopsidis, more sites are under positive selection in comparison to the other species, owing to an evolutionary arms race of ATR1 with RPP1 resistance proteins from Arabidopsis thaliana. The availability of crystal structure of ATR1 of H. arabidopsidis facilitated homology modelling of the ATR1 of H. thlaspeos-perfoliati and H. crispula. It was found that in all species, more than 90 % of the positively selected residues are on the protein surface. Interestingly, variability of ATR1 was low in H. thlaspeos-perfoliati and H. crispula paralogs, suggesting the absence of a corresponding R-protein in their hosts. The distribution pattern of selected and altered residues differed for the changes incited by the evolutionary arms race and those changes that occurred after adaptation to a new target following a host jump. While in the first case, they were evenly distributed, they were more concentrated around specific domains in the latter case, highlighting that different forces have been shaping ATR1 evolution during arms races and after host jumps. © 2015, German Mycological Society and Springer-Verlag Berlin Heidelberg. Source

Sharma R.,Biodiversity and Climate Research Center | Sharma R.,Goethe University Frankfurt | Sharma R.,Integrative Fungal Research IPF | Thines M.,Biodiversity and Climate Research Center | And 2 more authors.
Mycological Progress

Next generation sequencing (NGS) technologies generate huge amounts of sequencing data. Several microbial genome projects, in particular for fungal whole genome sequencing, have used NGS techniques because of their cost efficiency. However, NGS techniques also require computational tools able to process and analyze huge datasets. Data processing steps, including quality and length filters, often lead to a remarkable improvement in the accuracy and quality of data analyses. Choosing appropriate parameters for this purpose is not always straightforward, as these will vary with the dataset. In this study we present the FastQFS (Fastq Quality Filtering and Statistics) tool, which can be used for both an assessment of filtering parameters and read filtering. There are several tools available, but an important asset of FastQFS is that it provides the information of filtering parameters that fit best to the raw dataset, prior to computationally expensive filtering. It generates statistics of reads meeting different quality and length thresholds, and also the expected coverage depth of the genome which would be achieved after applying different filtering parameters. Thus, the FastQFS tool will help researchers to make informed decisions on an NGS read filtering parameters, and avoiding time-consuming optimization of filtering criteria after initial analyses. The source code of the tool and related files are available from 10.12761/SGN.2015.4. © 2015, German Mycological Society and Springer-Verlag Berlin Heidelberg. Source

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