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

Readers are alerted that there is currently a discussion regarding the use of some of the unpublished genomic data presented in this manuscript. Appropriate editorial action will be taken once this matter is resolved.
 Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.

/pdf/comparative-analysis-of-fungal-genomes-reveals-different-4a4yowqn3e.pdf

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi.

Any microorganism that attempts to colonize a plant must contend with the cell wall. One of the most conspicuous effects of microorganisms on plant cell walls is enzymic degradation. Our interpretation of the significance of this depends on our concept of the plant cell wall, which, however, is paradoxical. On the one hand, the wall is an inert mechanical support and barrier; on the other hand, the wall is a dynamic, metabolically active organelle (Robinson, 1991, and refs. therein). The wall is a nutritional source for microorganisms and animals, yet it contains noxious peroxidases, phenolics, and activated oxygen (Cooper, 1984). The wall is mainly carbohydrate, yet its proteins are disproportionately studied (Showalter, 1993). Degradation poses another paradox. On the one hand, plant cell walls are the world's most abundant source of Glc and other sugars; on the other hand, parts of it are resistant to degradation. Since all the polymers of a plant cell wall are eventually degraded by microorganisms, for every type of chemical bond in the wall there must be an enzyme that can cleave it. Some polysaccharidases such as a-amylase are widespread in nature; others, such as ligninase, are very restricted in their distribution.

Deconstructing the Cell Wall.

Accurate identification of fungal phytopathogens is essential for virtually all aspects of plant pathology, from fundamental research on the biology of pathogens to the control of the diseases they cause. Although molecular methods, such as polymerase chain reaction (PCR), are routinely used in the diagnosis of human diseases, they are not yet widely used to detect and identify plant pathogens. Here we review some of the diagnostic tools currently used for fungal plant pathogens and describe some novel applications. Technological advances in PCR-based methods, such as real-time PCR, allow fast, accurate detection and quantification of plant pathogens and are now being applied to practical problems. Molecular methods have been used to detect several pathogens simultaneously in wheat, and to study the development of fungicide resistance in wheat pathogens. Information resulting from such work could be used to improve disease control by allowing more rational decisions to be made about the choice and use of fungicides and resistant cultivars. Molecular methods have also been applied to the study of variation in plant pathogen populations, for example detection of different mating types or virulence types. PCR-based methods can provide new tools to monitor the exposure of a crop to pathogen inoculum that are more reliable and faster than conventional methods. This information can be used to improve disease control decision making. The development and application of molecular diagnostic methods in the future is discussed and we expect that new developments will increase the adoption of these new technologies for the diagnosis and study of plant disease.

Molecular diagnostics for fungal plant pathogens

Cytokinins were discovered in the 1950s by their ability to promote cell division in cultured plant cells. Recently, there have been significant breakthroughs in our understanding of the biosynthesis, metabolism, perception and signal transduction of this phytohormone. These advances, coupled with physiological and other approaches, have enabled remarkable progress to be made in our understanding of the interactions between cytokinin function and environmental inputs. In this review, we first highlight the most recent advances in our understanding of cytokinin biosynthesis, metabolism and signalling. We then discuss how various environmental signals interact with these pathways to modulate plant growth, development and physiology.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2009.01940.x

Environmental perception avenues: the interaction of cytokinin and environmental response pathways.

Evidence for the requirement of extracellular protease in the pathogenic interaction of Pyrenopeziza brassicae with oilseed rape

The mating type loci were cloned from Pyrenopeziza brassicae by chromosome walking from a mating type-linked polymerase chain reaction (PCR) fragment and shown to be idiomorphic by sequence analysis. The MAT 1-1 locus is approximately 3.2 kb and contains a single gene encoding a putative high-mobility group (HMG) domain protein. The MAT 1-2 locus is approximately 3.9 kb with three open reading frames (ORFs) encoding a putative HMG domain, an alpha-1 domain and metallothionein-like proteins. The putative alpha-1 domain ORF on MAT 1-2 is transcribed in the opposite orientation to the other two transcripts and extends into non-idiomorphic sequence. This is the first report of sequence analysis of the mating type loci from a discomycete fungus, which has revealed an interesting mating type infrastructure within the MAT 1-2 locus. Although metallothionein-like proteins have been implicated in a number of processes in animals and plants, they have not to date been implicated in the mating process of filamentous fungi. Possible roles for metallothionein-like proteins in the mating process are discussed.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2958.1999.01115.x

Cloning of the mating type loci from Pyrenopeziza brassicae reveals the presence of a novel mating type gene within a discomycete MAT 1-2 locus encoding a putative metallothionein-like protein

Evidence for a role of cutinase in pathogenicity of Pyrenopeziza brassicae on brassicas

Recent evidence has suggested that cutinase is required for cuticular penetration and, therefore, is essential for pathogenicity of Pyrenopeziza brassicae, the causal organism of light leaf spot disease of oilseed rape and other brassicas. In order to acquire molecular evidence for the role of cutinase in pathogenesis, the single-copy P. brassicae cutinase gene Pbc1 was disrupted by a transformation-mediated approach. Southern hybridization analysis revealed that in one mutant, NH10-1224, the disruption was due to a tandem insertion of two copies of the disruption vector into the 5' coding region of Pbc1. In contrast to the wild type, no expression of Pbc1 was detected during in planta growth or in cutin-induced mycelium of NH10-1224 and no cutinase activity was detected in culture supernatants from NH10-1224 using p-nitrophenyl butyrate as substrate. Scanning electron microscopy of Brassica napus cotyledons infected with wild-type P. brassicae confirmed that entry into the host is by direct penetration of the cuticle. In contrast, the cutinase-deficient mutant NH10-1224 failed to penetrate the cuticular layer and was unable to develop disease symptoms. This evidence is consistent with the hypothesis that Pbc1 is required for P. brassicae to penetrate the plant cuticle. Demonstration that complementation of NH10-1224 with the Pbc1 wild-type gene restores both cutinase activity and pathogenicity will be required to definitively establish that cutinase is required for successful pathogenesis of brassicas by P. brassicae.

https://apsjournals.apsnet.org/doi/pdfplus/10.1094/MPMI.2003.16.6.545

Molecular evidence that the extracellular cutinase Pbc1 is required for pathogenicity of Pyrenopeziza brassicae on oilseed rape.

In previous work, four genes involved in mating-type determination were cloned from reference strains of Pyrenopeziza brassicae; three genes, PAD1, PMT1, and PHB1 (re-named henceforth as MAT-1-1, MAT-1-4, and MAT1-3, respectively), are encoded by the MAT-1 idiomorph, and one gene, PHB2 (re-named MAT-2), by the corresponding MAT-2 idiomorph. To assess MAT gene organisation within field-populations of P. brassicae, 30 field-isolates of both mating-types from different geographical locations were analysed by PCR using primers designed for the MAT genes of P. brassicae. The results indicate that mating-type gene structure and organisation within these isolates is conserved and is consistent with the mating-type designations established by crossing experiments. The four P. brassicae MAT genes were then used as probes against gel blots of the genomic DNA of a discomycete Tapesia yallundae from the same family (Dermateaceae, order Helotiales) and one, Ascobolus stercorarius, from a distantly related family (Ascobolaceae, order Pezizales), in order to determine whether P. brassicae MAT-gene homologs were present. MAT-specific hybridisation signals were obtained with T. yallundae using all four probes. In particular, MAT-1 DNA of T. yallundae gave a strongly hybridising signal with MAT-1-4 (PMT1), a putative metallothionein gene found in the P. brassicae MAT-1 idiomorph but not in any other MAT idiomorph examined to-date. No MAT-specific hybridisation was obtained with A. stercorarius. A fragment of the MAT-2 gene of T. yallundae was obtained by PCR using degenerate primers designed to amplify the high-mobility group (HMG) domain present in other ascomycete MAT genes. Sequencing of this PCR product revealed similarities to MAT HMG domains from other ascomycetes with the greatest degree of similarity exhibited with P. brassicae. The T. yallundae HMG-DNA sequence was shown to co-segregate with mating type (MAT-2) in progeny from a sexual cross.

Intra-specific and inter-specific conservation of mating-type genes from the discomycete plant-pathogenic fungi Pyrenopeziza brassicae and Tapesia yallundae.

A.M. Ashby

Papers

Evidence for the requirement of extracellular protease in the pathogenic interaction of Pyrenopeziza brassicae with oilseed rape

Cloning of the mating type loci from Pyrenopeziza brassicae reveals the presence of a novel mating type gene within a discomycete MAT 1-2 locus encoding a putative metallothionein-like protein

Evidence for a role of cutinase in pathogenicity of Pyrenopeziza brassicae on brassicas

Molecular evidence that the extracellular cutinase Pbc1 is required for pathogenicity of Pyrenopeziza brassicae on oilseed rape.

Intra-specific and inter-specific conservation of mating-type genes from the discomycete plant-pathogenic fungi Pyrenopeziza brassicae and Tapesia yallundae.