Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum

Bart T.L.H. van de Vossenberg, Sven Warris, Hai D.T. Nguyen, Marga P.E. van Gent-Pelzer, David L. Joly, Henri C. van de Geest, Peter J.M. Bonants, Donna S. Smith, André C. Lévesque, Theo A.J. van der Lee

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.

LanguageEnglish
Article number8672
JournalScientific Reports
Volume9
Issue number1
DOIs
Publication statusPublished - 17 Jun 2019

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Synchytrium endobioticum
Chytridiomycota
lifestyle
genomics
fungi
genome
warts
guanine
point mutation
purines
Basidiomycota
mutagenesis
Ascomycota
plant pathogens
introns
pathogenicity
genes
cell walls
potatoes
enzymes

Cite this

van de Vossenberg, Bart T.L.H. ; Warris, Sven ; Nguyen, Hai D.T. ; van Gent-Pelzer, Marga P.E. ; Joly, David L. ; van de Geest, Henri C. ; Bonants, Peter J.M. ; Smith, Donna S. ; Lévesque, André C. ; van der Lee, Theo A.J. / Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. In: Scientific Reports. 2019 ; Vol. 9, No. 1.
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abstract = "Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.",
author = "{van de Vossenberg}, {Bart T.L.H.} and Sven Warris and Nguyen, {Hai D.T.} and {van Gent-Pelzer}, {Marga P.E.} and Joly, {David L.} and {van de Geest}, {Henri C.} and Bonants, {Peter J.M.} and Smith, {Donna S.} and L{\'e}vesque, {Andr{\'e} C.} and {van der Lee}, {Theo A.J.}",
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Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. / van de Vossenberg, Bart T.L.H.; Warris, Sven; Nguyen, Hai D.T.; van Gent-Pelzer, Marga P.E.; Joly, David L.; van de Geest, Henri C.; Bonants, Peter J.M.; Smith, Donna S.; Lévesque, André C.; van der Lee, Theo A.J.

In: Scientific Reports, Vol. 9, No. 1, 8672, 17.06.2019.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - van de Vossenberg, Bart T.L.H.

AU - Warris, Sven

AU - Nguyen, Hai D.T.

AU - van Gent-Pelzer, Marga P.E.

AU - Joly, David L.

AU - van de Geest, Henri C.

AU - Bonants, Peter J.M.

AU - Smith, Donna S.

AU - Lévesque, André C.

AU - van der Lee, Theo A.J.

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AB - Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.

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