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The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.

Schwelm A, Fogelqvist J, Knaust A, Jülke S, Lilja T, Bonilla-Rosso G, Karlsson M, Shevchenko A, Dhandapani V, Choi SR, Kim HG, Park JY, Lim YP, Ludwig-Müller J, Dixelius C - Sci Rep (2015)

Bottom Line: Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways.Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes.This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden.

ABSTRACT
Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.

No MeSH data available.


Related in: MedlinePlus

Protein families in Rhizaria and P. brassicae.(a) Venn diagramm of OrthoMCL protein families predicted for P. brassicae, S. subterranea and the the non-pathogenic Rhizarian B. natans and R. filosa. A Rhizarian core set was defined by common familes of B. natans, R. filosa and P. brassicae (groups E + F). Groups A-D build P. brassicae specific proteins. The S. subterranea predicted models were not regarded for the definition of the core set and P. brassicae specific set as no complete genome information is available. Numbers in the table show the number of OrthoMCL families and in brackets the number of P. brassicae proteins in each family. (b) Functional annotation of the P. brassicae proteins according to KOG functional categories. Rhizaria core set and P. brassicae-specific genes are defined as in (a).
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f2: Protein families in Rhizaria and P. brassicae.(a) Venn diagramm of OrthoMCL protein families predicted for P. brassicae, S. subterranea and the the non-pathogenic Rhizarian B. natans and R. filosa. A Rhizarian core set was defined by common familes of B. natans, R. filosa and P. brassicae (groups E + F). Groups A-D build P. brassicae specific proteins. The S. subterranea predicted models were not regarded for the definition of the core set and P. brassicae specific set as no complete genome information is available. Numbers in the table show the number of OrthoMCL families and in brackets the number of P. brassicae proteins in each family. (b) Functional annotation of the P. brassicae proteins according to KOG functional categories. Rhizaria core set and P. brassicae-specific genes are defined as in (a).

Mentions: OrthoMCL17 analysis defined a Rhizaria core set of 1,863 protein families common to P. brassicae, R. filosa and B. natans of which 1,338 families were shared with S. subterranea (Fig. 2). The specific set of P. brassicae contained 2,161 protein families out of 5,605 proteins with no orthologues in R. filosa and B. natans. KOG-term analysis showed that high proportions of the proteins in the Plasmodiophorids are poorly characterized and the majority of the P. brassicae specific genes have no assigned function (Fig. 2; Supplementary Fig. S5). The P. brassicae-specific genes were diversely expressed in the different developmental stages, whereas the Rhizarian core genes were most active in the plasmodial stage, when P. brassicae was already established inside the plant root (Supplementary Fig. S6).


The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.

Schwelm A, Fogelqvist J, Knaust A, Jülke S, Lilja T, Bonilla-Rosso G, Karlsson M, Shevchenko A, Dhandapani V, Choi SR, Kim HG, Park JY, Lim YP, Ludwig-Müller J, Dixelius C - Sci Rep (2015)

Protein families in Rhizaria and P. brassicae.(a) Venn diagramm of OrthoMCL protein families predicted for P. brassicae, S. subterranea and the the non-pathogenic Rhizarian B. natans and R. filosa. A Rhizarian core set was defined by common familes of B. natans, R. filosa and P. brassicae (groups E + F). Groups A-D build P. brassicae specific proteins. The S. subterranea predicted models were not regarded for the definition of the core set and P. brassicae specific set as no complete genome information is available. Numbers in the table show the number of OrthoMCL families and in brackets the number of P. brassicae proteins in each family. (b) Functional annotation of the P. brassicae proteins according to KOG functional categories. Rhizaria core set and P. brassicae-specific genes are defined as in (a).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4471660&req=5

f2: Protein families in Rhizaria and P. brassicae.(a) Venn diagramm of OrthoMCL protein families predicted for P. brassicae, S. subterranea and the the non-pathogenic Rhizarian B. natans and R. filosa. A Rhizarian core set was defined by common familes of B. natans, R. filosa and P. brassicae (groups E + F). Groups A-D build P. brassicae specific proteins. The S. subterranea predicted models were not regarded for the definition of the core set and P. brassicae specific set as no complete genome information is available. Numbers in the table show the number of OrthoMCL families and in brackets the number of P. brassicae proteins in each family. (b) Functional annotation of the P. brassicae proteins according to KOG functional categories. Rhizaria core set and P. brassicae-specific genes are defined as in (a).
Mentions: OrthoMCL17 analysis defined a Rhizaria core set of 1,863 protein families common to P. brassicae, R. filosa and B. natans of which 1,338 families were shared with S. subterranea (Fig. 2). The specific set of P. brassicae contained 2,161 protein families out of 5,605 proteins with no orthologues in R. filosa and B. natans. KOG-term analysis showed that high proportions of the proteins in the Plasmodiophorids are poorly characterized and the majority of the P. brassicae specific genes have no assigned function (Fig. 2; Supplementary Fig. S5). The P. brassicae-specific genes were diversely expressed in the different developmental stages, whereas the Rhizarian core genes were most active in the plasmodial stage, when P. brassicae was already established inside the plant root (Supplementary Fig. S6).

Bottom Line: Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways.Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes.This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden.

ABSTRACT
Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.

No MeSH data available.


Related in: MedlinePlus