A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres

Ellwood, Simon R.; Liu, Zhaohui; Syme, Robert A.; Lai, Zhibing; Hane, James K.; Keiper, Felicity; Moffat, Caroline S.; Oliver, Richard P.; Friesen, Timothy L.

doi:10.1186/gb-2010-11-11-r109

Cited by 93 publications

(73 citation statements)

References 76 publications

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“…The 14 new Dothideomycete genomes discussed here are also deposited to DDBJ/EMBL/GenBank under the following accessions numbers Alternaria brassicicola ATCC 96836: ACIW00000000, Baudoinia compniacensis UAMH 10762: AEIF00000000, Cladosporium fulvum CBS131901 (race 0WU): AMRR00000000, Cochliobolus heterostrophus ATCC 48331 (race T, strain C4): AIHU00000000, Cochliobolus heterostrophus ATCC 48331 (race O, strain C5): AIDY00000000, Cochliobolus sativus ND90Pr: AEIN00000000, Dothistroma septosporum CBS128990 (NZE10): AIEN00000000, Hysterium pulicare CBS 123377: PRJNA81797, Mycosphaerella fijiensis CIRAD86: AIHZ00000000, Mycosphaerella populicola P02.02b: AIDU00000000, Mycosphaerella populorum SO2202: AEFD00000000, Pyrenophora tritici-repentis Pt-1C-BFP: AAXI00000000, Rhytidhysteron rufulum CBS 306.38: PRJNA81799, Setosphaeria turcica Et28A: AIHT00000000. The four additional genomes of Leptosphaeria maculans JN3 [23], Mycosphaerella graminicola IPO323 [24], Pyrenophora teres f. teres 0–1 [22], and Stagonospora nodorum SN15 [21] used in the comparative analyses were published earlier.…”

Section: Methodsmentioning

confidence: 99%

“…Here we report new genome sequences of 14 dothideomycete genomes and use them in comparative analyses with those of four Dothideomycetes published previously [21], [22], [23], [24], plus representative outgroups from the Ascomycota and Basidiomycota (Table 1), a total of 39 genomes. Among the 18 sequenced dothideomycete genomes, nine are from species of the order Pleosporales , seven from the order Capnodiales and two from the order Hysteriales .…”

Section: Introductionmentioning

confidence: 99%

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Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

et al. 2012

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The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

et al. 2012

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“…Data from this study and from [10]–[12], [157], [158].1PKS: PolyKetide Synthase.2NRPS: Non-Ribosomal Peptide Synthetase.3PKS-NRPS: PolyKetide Synthase - Non-Ribosomal Peptide Synthase hybrid.4CHS: CHalcone Synthase.5DMATS: DiMethyl Allyl Tryptophan Synthase.6STC: SesquiTerpene Cyclase.7DTC: DiTerpene Cyclase.…”

Section: Resultsmentioning

confidence: 99%

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

et al. 2011

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Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea–specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.

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“…Protein FASTA files were downloaded from the genome sequences of: Pyrenophora teres - NCBI (Ellwood et al 2010); Stagonospora nodorum - Broad Institute [Annotation Update 2011-05-06 (Hane et al 2007)]; Mycosphaerella graminicola - Joint Genome Institute (Goodwin et al 2011); Colletotrichum (Glomerella) graminicola - Broad Institute; Fusarium graminearum - Broad Institute (Cuomo et al 2007); and Puccinia graminis - Broad Institute (Duplessis et al 2011). A stringent Pfam domain prediction (E < 1e-20) was performed for each organism with HMMER3 (Finn et al 2011).…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of a Plant-Pathogenic Fungus,Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Manning

Pandelova

Dhillon

et al. 2013

G3 Genes|Genomes|Genetics

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146

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Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.

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A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres

Cited by 93 publications

References 76 publications

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Comparative Genomics of a Plant-Pathogenic Fungus,Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

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