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

Citation

van de Vossenberg, B.T.L.H., Warris, S., Nguyen, H.D.T., van Gent-Pelzer, M.P.E., Joly, D.L., van de Geest, H.C., Bonants, P.J.M., Smith, D.S., Lévesque, C.A., van der Lee, T.A.J. (2019). Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. Scientific Reports, [online] 9(1), http://dx.doi.org/10.1038/s41598-019-45128-9

Plain language summary

The genome of the potato wart fungus was sequenced and compared with related fungi. One isolate from Prince Edward Island and another isolate, of a different race, from the Netherlands were sequenced and characterized in depth. Repeats and genes related to how the organism causes infection were determined by computer analyses. This study provides information essential for future research on the biology, genomics or detection of potato wart.

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.

Publication date

2019-12-01

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