Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

Spanu, Pietro D.; Abbott, James; Amselem, Joëlle; Burgis, Timothy A.; Soanes, Darren M.; Stüber, Kurt; Themaat, Emiel Ver Loren van; Brown, J. K. M.; Butcher, Sarah; Gurr, Sarah J.; Lebrun, Marc; Ridout, Christopher J.; Schulze‐Lefert, Paul; Talbot, Nicholas J.; Ahmadinejad, Nahal; Ametz, Christian; Barton, Geraint; Benjdia, Mariam; Bidzinski, Przemyslaw; Bindschedler, Laurence V.; Both, Maike; Brewer, Marin Talbot; Cadle‐Davidson, Lance; Cadle-Davidson, Molly; Collemare, Jérôme; Cramer, Rainer; Frenkel, Omer; Godfrey, Dale I.; Harriman, James; Hoede, Claire; King, Brian Christopher; Klages, Sven; Kleemann, Jochen; Knoll, Daniela; Koti, Prasanna S.; Kreplak, Jonathan; Lopez‐Ruiz, Francisco J.; Lu, Xunli; Maekawa, Takaki; Mahanil, Siraprapa; Micali, Cristina; Milgroom, Michael G.; Montana, Giovanni; Noir, Sandra; O’Connell, Richard J.; Oberhaensli, Simone; Parlange, Francis; Pedersen, Carsten; Quesneville, Hadi; Reinhardt, Richard; Rott, Matthias; Sacristán, Soledad; Schmidt, Sarah M.; Schön, Moritz; Skamnioti, Pari; Sommer, Hans; Stephens, Amber; Takahara, Hiroyuki; Thordal‐Christensen, Hans; Vigouroux, Marielle; Weßling, Ralf; Wicker, Thomas; Panstruga, Ralph

doi:10.1126/science.1194573

Cited by 715 publications

(827 citation statements)

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“…The present analyses suggest that microsporidian species may have been derived from an ancestor organism with high gene compaction and that due to the acquisition of DNA (that is, TEs), some have evolved towards larger genomes. Furthermore, such genome invasion by TEs has recently been described for Blumeria graminis, a filamentous plant pathogenic fungus 36 . In this species, the TEs were evenly distributed throughout the genome, and the protein-coding genes are, consequently, in small clusters, as in the A. algerae genome.…”

Section: Discussionmentioning

confidence: 98%

Annotation of microsporidian genomes using transcriptional signals

et al. 2012

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High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DnA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidianhost relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.

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Section: Discussionmentioning

confidence: 98%

Annotation of microsporidian genomes using transcriptional signals

et al. 2012

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“…npg l e t t e r s Both Colletotrichum species encode markedly more secondary metabolism enzymes (103 in C. higginsianum and 74 in C. graminicola) than other sequenced fungi (2-58 in ascomycetes 24,25 ) ( Supplementary Fig. 10a and Supplementary Table 8).…”

Section: E T T E R Smentioning

confidence: 99%

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

et al. 2012

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Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types

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“…In many cases, the three-dimensional structure of the protein, the disulfide bond pattern, and the cysteine spacing have been used to identify protease and/or protease inhibitors as putative effectors in obligate biotrophic soil-born plant pathogens [34,51,52]. These effectors target host proteins/proteases during infection, thereby manipulating the host response to infection.…”

Section: Where and How To Look For Effectors?mentioning

confidence: 99%

Identification of Plasmodiophora brassicae effectors — A challenging goal

et al. 2018

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Clubroot is an economically important disease affecting Brassica plants worldwide. Plasmodiophora brassicae is the protist pathogen associated with the disease, and its soil-borne obligate parasitic nature has impeded studies related to its biology and the mechanisms involved in its infection of the plant host. The identification of effector proteins is key to understanding how the pathogen manipulates the plant’s immune response and the genes involved in resistance. After more than 140 years studying clubroot and P. brassicae, very little is known about the effectors playing key roles in the infection process and subsequent disease progression. Here we analyze the information available for identified effectors and suggest several features of effector genes that can be used in the search for others. Based on the information presented in this review, we propose a comprehensive bioinformatics pipeline for effector identification and provide a list of the bioinformatics tools available for such.

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Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

Cited by 715 publications

References 13 publications

Annotation of microsporidian genomes using transcriptional signals

Annotation of microsporidian genomes using transcriptional signals

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

Identification of Plasmodiophora brassicae effectors — A challenging goal

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