Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans

Makkonen, Jenny; Vesterbacka, Arto; Martin, Frank N.; Jussila, Japo; Diéguez-Uribeondo, Javier; Kortet, Raine; Kokko, Hanna

doi:10.1038/srep36089

Cited by 20 publications

(25 citation statements)

References 58 publications

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“…The locations of the four species-specific putative ORFs between rns and cox2 were the same as in P. tabacina and P. cubensis . Inverted repeats (IRs) have been observed in the mitochondrial genomes of the Peronosporomycete Pythium and Saprolegniomycetes Saprolegnia, Achyla, Thraustotheca and Aphanomyces, but these typically represent between 34 to 73% of the genome and encode the large and small ribosomal RNAs [ 37 – 39 , 41 , 59 , 60 ]. While an IR is present in P. effusa, it is atypical for an oomycete because it is less than 900 bp and does not encode rRNA.…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of downy mildews reveals potential adaptations to biotrophy

et al. 2018

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BackgroundSpinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years.ResultsWe virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp.ConclusionsWe present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5214-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Comparative genomics of downy mildews reveals potential adaptations to biotrophy

et al. 2018

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“…As a positive control, DNA extracted from a pure culture of the A . astaci strain AP03 [ 42 ], was used; distilled Milli-Q water was used as a negative control. Amplified products were analyzed by electrophoresis in 1% agarose TAE gels stained with SBYR ® Safe (Thermo Fisher Scientific, Waltham, MA, USA).…”

Section: Methodsmentioning

confidence: 99%

Crayfish plague in Japan: A real threat to the endemic Cambaroides japonicus

Martín-Torrijos

Kawai²,

Makkonen

et al. 2018

PLoS ONE

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Global introductions of aquatic species and their associated pathogens are threatening worldwide biodiversity. The introduction of two North American crayfish species, Procambarus clarkii and Pacifastacus leniusculus, into Japan in 1927 seems to have negatively affected native Japanese crayfish populations of Cambaroides japonicus. Several studies have shown the decline of these native populations due to competition, predation and habitat colonization by the two invasive North American crayfish species. Here, we identify an additional factor contributing to this decline. We report the first crayfish plague outbreaks in C. japonicus populations in Japan, which were diagnosed using both histological and molecular approaches (analyses of the internal transcribed spacer region). Subsequent analyses of the mitochondrial ribosomal rnnS and rnnL regions of diseased specimens indicate that these outbreaks originated from a P. clarkii population and identify a novel haplotype of Aphanomyces astaci, d3-haplotype, hosted by P. clarkii. Overall, our findings demonstrate the first two cases of crayfish plague in Japan, and the first case in a non-European native crayfish species, which originated from the red swamp crayfish P. clarkii. This finding is a matter of concern for the conservation of the native freshwater species of Japan and also highlights the risk of introducing crayfish carrier species into biogeographic regions harboring species susceptible to the crayfish plague.

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“…For the challenge experiments, the AP03 strain of A . astaci , recently genome sequenced (GenBank accession number KX405004), was used [ 27 ]. This strain was isolated from specimens of a population of P .…”

Section: Methodsmentioning

confidence: 99%

“…This strain was isolated from specimens of a population of P . clarkii located in the surroundings of the Garrotxa Natural Park [ 27 ]. This strain belongs to the Pc genotype and is deposited at the RJB-CSIC culture collection.…”

Section: Methodsmentioning

confidence: 99%

Resistance to the crayfish plague, Aphanomyces astaci (Oomycota) in the endangered freshwater crayfish species, Austropotamobius pallipes

Martín-Torrijos

Llach²,

Pou‐Rovira³

et al. 2017

PLoS ONE

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The pathogen Aphanomyces astaci Schikora 1906 is responsible for the decline of the native crayfish species of Europe, and their current endangered status. This pathogenic species is native to North America and only colonizes aquatic decapods. The North American crayfish species have a high resistance to this pathogen, while species from other regions are highly susceptible. However, recent field and laboratory observations indicate that there might exist some populations with resistance against this disease. The objective of this study was to test the susceptibility of 8 selected native European crayfish populations of Austropotamobius pallipes Lereboullet 1858 from the Pyrenees. We challenged them against the genome sequenced strain AP03 of A. astaci isolated from a North American red swamp crayfish, Procambarus clarkii Girard 1852, in the Garrotxa Natural Park, Girona. The results showed that there are significant differences (P<0,001) among populations, although most of them show high mortality rates after the zoospore challenge with A. astaci. However, one population from Girona exhibited a 100% survival during a four-month monitoring period under the experimental conditions tested. Histological analyses revealed a high immune reaction in tissues examined, i.e., encapsulation and melanization of hyphae, similar to that found in North American resistant crayfish species. These results represent the first observation of a native European crayfish population showing high resistance towards the most virulent genotype of this pathogen, i.e., genotype Pc. The identification of this population is of key importance for the management of these endangered species, and represents a crucial step forward towards the elucidation of the factors involved in the immune reaction against this devastating pathogen.

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Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans

Cited by 20 publications

References 58 publications

Comparative genomics of downy mildews reveals potential adaptations to biotrophy

Comparative genomics of downy mildews reveals potential adaptations to biotrophy

Crayfish plague in Japan: A real threat to the endemic Cambaroides japonicus

Resistance to the crayfish plague, Aphanomyces astaci (Oomycota) in the endangered freshwater crayfish species, Austropotamobius pallipes

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