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

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.

Metagenomics survey unravels diversities of biogas’ microbiomes with potential to enhance its’ productivity in Kenya

“…All these indicated Basidiomycota's species played wide metabolic roles in the AD systems. Interestingly, we also identified Chytridiomycota affiliates in reactor 9 and 10 and the members were capable of catabolizing pollen, chitin, keratin, and cellulose [185,186], which indicated the two treatments harbored the substrates. The detected Spizellomycetales, Cladochytriales and Rhizophydiales species in the two treatments, further revealed the presence of high decayed plant tissue concentration with high cellulose content.…”

“…Generally, Chytridiomycota species were basically carbohydrate metabolizers as previously revealed by the presence of glucose transporters and invertase activity in their systems [185,186]. The species used electron bifurcation mechanisms to conserve their energy and the mechanisms occured in the hydrogenosome [188].…”

TheSynchytrium endobioticumAvrSen1 triggers a Hypersensitive Response in Sen1 potatoes while natural variants evade detection

“…SeLEV6574_g04683. Both genomes were independently sequenced, assembled and annotated (31), and the gene prediction in the LEV6574 genome reflects the truncated AvrSen1 variant 2 that was identified from the AvrSen1 prediction pipeline. This indicates that not only the particular SNP is present in the Canadian genome, but also that the truncated gene model is expressed (Fig.…”

“…S1). Sequence reads were mapped (length fraction: 0.8, similarity fraction: 0.9) to the S. endobioticum pathotype 1(D1) isolate MB42 reference genome (31) in CLC genomics workbench v11.0.1 (Qiagen, the Netherlands), and mappings were improved with the local realignment tool (default settings) to better resolve the mapping in areas around insertions and deletions.…”

“…The recently annotated genomes of the pathotype 1(D1) isolate MB42 (QEAN00000000 v.1) and pathotype 6(O1) isolate LEV6574 (QEAM00000000 v.1) (31) open up the possibility to identify Avr gene candidates using a comparative genomic approach. Availability of S. endobioticum Avr genes will greatly advance our understanding and management of this challenging obligate biotrophic soilborne pathogenic fungus.…”