The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.

Sclerotinia stem rot (SSR) caused by the phytopathogenic fungus Sclerotinia sclerotiorum is a major disease of oilseed rape (Brassica napus). During infection, large, white/grey lesions form on the stems of the host plant, perturbing seed development and decreasing yield. Due to its ability to produce long‐term storage structures called sclerotia, S. sclerotiorum inoculum can persist for long periods in the soil. Current SSR control relies heavily on cultural practices and fungicide treatments. Cultural control practices aim to reduce the number of sclerotia in the soil or create conditions that are unfavourable for disease development. These methods of control are under increased pressure in some regions, as rotations tighten and inoculum levels increase. Despite their ability to efficiently kill S. sclerotiorum, preventative fungicides remain an expensive gamble for SSR control, as their effectiveness is highly dependent on the ability to predict the establishment of microscopic infections in the crop. Failure to correctly time fungicide applications can result in a substantial cost to the grower. This review describes the scientific literature pertaining to current SSR control practices. Furthermore, it details recent advances in alternative SSR control methods including the generation of resistant varieties through genetic modification and traditional breeding, and biocontrol. The review concludes with a future directive for SSR control on oilseed rape.

BackgroundHemibiotrophic fungal pathogen Zymoseptoria tritici causes severe foliar disease in wheat. However, current knowledge of molecular mechanisms involved in plant resistance to Z. tritici and Z. tritici virulence factors is far from being complete. The present work investigated the proteome of leaf apoplastic fluid with emphasis on both host wheat and Z. tritici during the compatible and incompatible interactions.ResultsThe proteomics analysis revealed rapid host responses to the biotrophic growth, including enhanced carbohydrate metabolism, apoplastic defenses and stress, and cell wall reinforcement, might contribute to resistance. Compatibility between the host and the pathogen was associated with inactivated plant apoplastic responses as well as fungal defenses to oxidative stress and perturbation of plant cell wall during the initial biotrophic stage, followed by the strong induction of plant defenses during the necrotrophic stage. To study the role of anti-oxidative stress in Z. tritici pathogenicity in depth, a YAP1 transcription factor regulating antioxidant expression was deleted and showed the contribution to anti-oxidative stress in Z. tritici, but was not required for pathogenicity. This result suggests the functional redundancy of antioxidants in the fungus.ConclusionsThe data demonstrate that incompatibility is probably resulted from the proteome-level activation of host apoplastic defenses as well as fungal incapability to adapt to stress and interfere with host cell at the biotrophic stage of the interaction.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1549-6) contains supplementary material, which is available to authorized users.

The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.DOI: http://dx.doi.org/10.7554/eLife.22472.001

Summary Fungal plant pathogens secrete effector proteins and metabolites to cause disease. Additionally, some species transfer small RNAs (sRNAs) into plant cells to silence host mRNAs through complementary base pairing and suppress plant immunity. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about the molecular processes that govern interactions with its many hosts. In particular, evidence for the production of sRNAs by S. sclerotiorum during infection is lacking. We sequenced sRNAs produced by S. sclerotiorum in vitro and during infection of two host species, Arabidopsis thaliana and Phaseolus vulgaris . We found that S. sclerotiorum produces at least 374 distinct highly abundant sRNAs during infection, mostly originating from repeat‐rich plastic genomic regions. We predicted the targets of these sRNAs in A. thaliana and found that these genes were significantly more down‐regulated during infection than the rest of the genome. Predicted targets of S. sclerotiorum sRNAs in A. thaliana were enriched for functional domains associated with plant immunity and were more strongly associated with quantitative disease resistance in a genome‐wide association study (GWAS) than the rest of the genome. Mutants in A. thaliana predicted sRNA target genes SERK2 and SNAK2 were more susceptible to S. sclerotiorum than wild‐type, suggesting that S. sclerotiorum sRNAs may contribute to the silencing of immune components in plants. The prediction of fungal sRNA targets in plant genomes can be combined with other global approaches, such as GWAS, to assist in the identification of plant genes involved in quantitative disease resistance.

In a collection of 735 Botrytis isolates sampled from Australian wine grape‐growing regions, a single isolate from clade I and group I (based on Bc‐hch RFLP analysis) was found. As many Botrytis species are known to live sympatrically, it was hypothesized that this isolate might be a new Botrytis species. After phenotypic and molecular assays supported this hypothesis, the species was designated B. medusae. Phylogenetic analyses using the nuclear genes G3PDH, HSP60, RPB2, NEP1 and NEP2 consistently placed B. medusae in an early‐diverging clade I Botrytis spp. lineage. Botrytis medusae produced white aerial mycelium, grew faster at 30 °C and produced long‐branched conidiophore extensions, compared with B. cinerea and B. pseudocinerea. Botrytis medusae was only able to infect wounded grape leaves and was significantly less virulent on wounded leaves and berries than B. cinerea. Botrytis medusae also lacked villiform appendages on the conidial surface and long conidiophores, which are defining features of B. sinoviticola and B. californica, respectively. Identification and characterization of new cryptic Botrytis species living in sympatry on grapevines could potentially provide information to assist disease management strategies for B. cinerea.

Sclerotinia sclerotiorum is a fungal pathogen that causes stem rot in oilseed rape (Brassica napus). Previously, B. napus accessions with partial stem resistance to a Canadian S. sclerotiorum isolate (#321) were identified using a stem test in which flowering plants were inoculated with mycelium plugs. The present study examined the partial stem resistance of four of these accessions, PAK54, PAK93, DC21 and K22, following inoculation with Australian isolates. Mycelial compatibility groups and intergenic spacer (IGS) region haplotypes were identified among 71 isolates from Australian oilseed rape and lupin fields. Eleven genetically diverse isolates showed differences in aggressiveness when inoculated onto nine oilseed rape varieties and one Chinese accession. Isolates CU8.24, CU10.17 and CU11.19 were selected based on genetic diversity, growth rate in vitro and high aggressiveness in the initial screen and subsequently inoculated onto the four B. napus accessions. These accessions developed significantly smaller lesions compared with the susceptible control varieties ('AV Garnet' and 'Westar'), with the average frequency of soft and collapsed lesions being less than 20% in PAK54, DC21 and K22, 29% in PAK93 and greater than 88% in the susceptible controls. Microscopic examination revealed that hyphae were typically confined to the stem cortex in the smallest lesions, but could be found in the stem pith in larger lesions. These results show that B. napus accessions PAK54, PAK93, DC21 and K22 can be used in Australia for development of varieties with partial stem resistance to S. sclerotiorum.Résumé: Sclerotinia sclerotiorum est un agent pathogène fongique qui cause la pourriture sclérotique chez le colza oléagineux (Brassica napus). Auparavant, les accessions de B. napus possédant une résistance partielle à la pourriture causée par l'isolat canadien de S. sclerotiorum (n°321) étaient identifiées à l'aide d'un test spécifique de la pourriture au cours duquel les plants en fleur étaient inoculés avec des chevilles de mycélium. Cette étude examine la résistance partielle à la pourriture des quatre accessions suivantes, PAK54, PAK93, DC21 et K22, après inoculation avec des isolats australiens. Les groupes de compatibilité mycélienne et les haplotypes des régions des espaceurs intergéniques ont été identifiés chez 71 isolats provenant de champs de colza oléagineux et de lupin australiens. Onze isolats génétiquement différents ont affiché des variations quant à leur agressivité lorsqu'ils ont été utilisés pour inoculer neuf variétés de colza oléagineux et une accession chinoise. Les isolats CU8.24, CU10.17 et CU11.19 ont été choisis en fonction de leur diversité génétique, de leur taux de croissance in vitro et de leur énorme agressivité lors du criblage initial, puis ont servi à inoculer les quatre accessions de B. napus. Ces accessions ont développé des lésions particulièrement petites comparativement aux variétés témoins réceptives ('AV Garnet' et 'Westar'), avec une fréquence moyenne de moins de 20% de lésions molles...