The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens

Effectors of Plant Necrotrophic Fungi

Plant diseases caused by necrotrophic fungal pathogens result in large economic losses in field crop production worldwide. Effectors are important players of plant-pathogen interaction and deployed by pathogens to facilitate plant colonization and nutrient acquisition. Compared to biotrophic and hemibiotrophic fungal pathogens, effector biology is poorly understood for necrotrophic fungal pathogens. Recent bioinformatics advances have accelerated the prediction and discovery of effectors from necrotrophic fungi, and their functional context is currently being clarified. In this review we examine effectors utilized by necrotrophic fungi and hemibiotrophic fungi in the latter stages of disease development, including plant cell death manipulation. We define "effectors" as secreted proteins and other molecules that affect plant physiology in ways that contribute to disease establishment and progression. Studying and understanding the mechanisms of necrotrophic effectors is critical for identifying avenues of genetic intervention that could lead to improved resistance to these pathogens in plants.

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

Background

The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised – ToxA, Tox1 and Tox3.

Results

A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions.

Conclusions

We present an updated series of genomic resources for P. nodorum Sn15 – an important reference isolate and model necrotroph – with a comprehensive survey of its predicted pathogenicity content.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07699-8.

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

BACKGROUND

Sclerotinia sclerotiorum, the cause of Sclerotinia stem rot (SSR), is a host generalist necrotrophic fungus that can cause major yield losses in chickpea (Cicer arietinum) production. This study used RNA sequencing to conduct a time course transcriptional analysis of S. sclerotiorum gene expression during chickpea infection. It explores pathogenicity and developmental factors employed by S. sclerotiorum during interaction with chickpea.

RESULTS

During infection of moderately resistant (PBA HatTrick) and highly susceptible chickpea (Kyabra) lines, 9491 and 10,487 S. sclerotiorum genes, respectively, were significantly differentially expressed relative to in vitro. Analysis of the upregulated genes revealed enrichment of Gene Ontology biological processes, such as oxidation-reduction process, metabolic process, carbohydrate metabolic process, response to stimulus, and signal transduction. Several gene functional categories were upregulated in planta, including carbohydrate-active enzymes, secondary metabolite biosynthesis clusters, transcription factors and candidate secreted effectors. Differences in expression of four S. sclerotiorum genes on varieties with different levels of susceptibility were also observed.

CONCLUSION

These findings provide a framework for a better understanding of S. sclerotiorum interactions with hosts of varying susceptibility levels. Here, we report for the first time on the S. sclerotiorum transcriptome during chickpea infection, which could be important for further studies on this pathogen's molecular biology.

Genome sequencing and comparative genomic analysis of highly and weakly aggressive strains of Sclerotium rolfsii, the causal agent of peanut stem rot

BACKGROUND

Stem rot caused by Sclerotium rolfsii is a very important soil-borne disease of peanut. S. rolfsii is a necrotrophic plant pathogenic fungus with an extensive host range and worldwide distribution. It can infect peanut stems, roots, pegs and pods, leading to varied yield losses. S. rolfsii strains GP3 and ZY collected from peanut in different provinces of China exhibited a significant difference in aggressiveness on peanut plants by artificial inoculation test. In this study, de-novo genome sequencing of these two distinct strains was performed aiming to reveal the genomic basis of difference in aggressiveness.

RESULTS

Scleotium rolfsii strains GP3 and ZY, with weak and high aggressiveness on peanut plants, exhibited similar growth rate and oxalic acid production in laboratory. The genomes of S. rolfsii strains GP3 and ZY were sequenced by Pacbio long read technology and exhibited 70.51 Mb and 70.61 Mb, with contigs of 27 and 23, and encoded 17,097 and 16,743 gene models, respectively. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires, which might be associated with aggressiveness, differed between GP3 and ZY. There were 58 and 45 unique pathogen-host interaction (PHI) genes in GP3 and ZY, respectively. The ZY strain had more carbohydrate-active enzymes (CAZymes) in its secretome than GP3, especially in the glycoside hydrolase family (GH), the carbohydrate esterase family (CBM), and the polysaccharide lyase family (PL). GP3 and ZY also had different effector candidates and putative secondary metabolite synthetic gene clusters. These results indicated that differences in PHI, secreted CAZymes, effectors and secondary metabolites may play important roles in aggressive difference between these two strains.

CONCLUSIONS

The data provided a further understanding of the S. rolfsii genome. Genomic comparison provided clues to the difference in aggressiveness of S. rolfsii strains.

Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence

Brown rot is the most economically important fungal disease of stone fruits and is primarily caused by Monilinia laxa and Monlinia fructicola. Both species co-occur in European orchards although M. fructicola is considered to cause the most severe yield losses in stone fruit. This study aimed to generate a high-quality genome of M. fructicola and to exploit it to identify genes that may contribute to pathogen virulence. PacBio sequencing technology was used to assemble the genome of M. fructicola. Manual structural curation of gene models, supported by RNA-Seq, and functional annotation of the proteome yielded 10,086 trustworthy gene models. The genome was examined for the presence of genes that encode secreted proteins and more specifically effector proteins. A set of 134 putative effectors was defined. Several effector genes were cloned into Agrobacterium tumefaciens for transient expression in Nicotiana benthamiana plants, and some of them triggered necrotic lesions. Studying effectors and their biological properties will help to better understand the interaction between M. fructicola and its stone fruit host plants.

Sclerotinia Stem Rot Resistance in Rapeseed: Recent Progress and Future Prospects

Sclerotinia stem rot (SSR) of rapeseed (Brassica napus), caused by the soil-borne fungus Sclerotinia sclerotiorum, is one of the main diseases seriously affecting the yield and oil quality of infected rapeseed crops. The complexity of the inheritance of resistance and of the interaction mechanisms between rapeseed and S. sclerotiorum limits resistance gene identification and molecular breeding. In this review, the latest progress of research into resistance to SSR in B. napus is summarized from the following three directions: the pathogenesis mechanisms of S. sclerotiorum, the resistance mechanisms of B. napus toward S. sclerotiorum, and rapeseed breeding for resistance to SSR. This review aims to provide a theoretical basis and useful reference for analyzing the mechanism of the interaction between B. napus and S. sclerotiorum, searching for gene loci associated with the resistance response, and for achieving disease-resistance genetic manipulation and molecular design breeding in rapeseed.

Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi

The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.

Proteomic Analysis Reveals the Importance of Exudates on Sclerotial Development in Sclerotinia sclerotiorum

Sclerotinia sclerotiorum is a ubiquitous necrotrophic pathogenic fungus causing significant losses in a broad range of plant species. Sclerotia formed by S. sclerotiorum play important roles in both the fungal life cycle and the disease development cycle. Sclerotial exudation during sclerotial development is a characteristic feature of this fungus. In this study, a proteome-level investigation of proteins present in sclerotial exudates was conducted by high-throughput LC-MS/MS analysis. A total of 258 proteins were identified, in which 193 were annotated by GO annotation and 54 were classified by KEGG analysis. Four proteins related to plant cell wall degradation were further validated by measuring the corresponding enzymatic activity of the sclerotial exudates and/or by assessing the gene expression during sclerotial development. Results indicated that the proteins identified in sclerotial exudates help in the development of sclerotia and contribute to host cell necrosis caused by S. sclerotiorum. Furthermore, we proposed that sclerotial exudates can degrade plant cell walls to release carbohydrates that provide nutrition for fungal growth and possibly facilitate fungal cell wall assembly in developing sclerotia. This study also provides new insights on the morphogenesis and pathogenicity of other sclerotia-forming fungi.

Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum

Background

The fungicide fludioxonil over-stimulates the fungal response to osmotic stress, leading to over-accumulation of glycerol and hyphal swelling and bursting. Fludioxonil-resistant fungal strains that are null-mutants for osmotic stress response genes are easily generated through continual sub-culturing on sub-lethal fungicide doses. Using this approach combined with RNA sequencing, we aimed to characterise the effects of mutations in osmotic stress response genes on the transcriptional profile of the important agricultural pathogen Sclerotinia sclerotiorum under standard laboratory conditions. Our objective was to understand the impact of disruption of the osmotic stress response on the global transcriptional regulatory network in an important agricultural pathogen.

Results

We generated two fludioxonil-resistant S. sclerotiorum strains, which exhibited growth defects and hypersensitivity to osmotic stressors. Both had missense mutations in the homologue of the Neurospora crassa osmosensing two component histidine kinase gene OS1, and one had a disruptive in-frame deletion in a non-associated gene. RNA sequencing showed that both strains together differentially expressed 269 genes relative to the parent during growth in liquid broth. Of these, 185 (69%) were differentially expressed in both strains in the same direction, indicating similar effects of the different point mutations in OS1 on the transcriptome. Among these genes were numerous transmembrane transporters and secondary metabolite biosynthetic genes.

Conclusions

Our study is an initial investigation into the kinds of processes regulated through the osmotic stress pathway in S. sclerotiorum. It highlights a possible link between secondary metabolism and osmotic stress signalling, which could be followed up in future studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07402-x.

Genome Sequencing Analysis of Scleromitrula shiraiana, a Causal Agent of Mulberry Sclerotial Disease With Narrow Host Range

Scleromitrula shiraiana is a necrotrophic fungus with a narrow host range, and is one of the main causal pathogens of mulberry sclerotial disease. However, its molecular mechanisms and pathogenesis are unclear. Here, we report a 39.0 Mb high-quality genome sequence for S. shiraiana strain SX-001. The S. shiraiana genome contains 11,327 protein-coding genes. The number of genes and genome size of S. shiraiana are similar to most other Ascomycetes. The cross-similarities and differences of S. shiraiana with the closely related Sclerotinia sclerotiorum and Botrytis cinerea indicated that S. shiraiana differentiated earlier from their common ancestor. A comparative genomic analysis showed that S. shiraiana has fewer genes encoding cell wall-degrading enzymes (CWDEs) and effector proteins than that of S. sclerotiorum and B. cinerea, as well as many other Ascomycetes. This is probably a key factor in the weaker aggressiveness of S. shiraiana to other plants. S. shiraiana has many species-specific genes encoding secondary metabolism core enzymes. The diversity of secondary metabolites may be related to the adaptation of these pathogens to specific ecological niches. However, melanin and oxalic acid are conserved metabolites among many Sclerotiniaceae fungi, and may be essential for survival and infection. Our results provide insights into the narrow host range of S. shiraiana and its adaptation to mulberries.

Validation of an in vitro system to trigger changes in the gene expression of effectors of Sclerotinia sclerotiorum

AIMS

Sclerotinia sclerotiorum, the causal agent of white mold, can infect several host species, including economically important crops. In this study, we propose and validate a new in vitro system able to mimic the conditions of interaction with the host and promote the induction of S. sclerotiorum effectors.

METHODS AND RESULTS

For culture media production, we selected three plant species, common bean (Phaseolus vulgaris L, cv. Requinte.), maize (Zea mays, cv. BRS1030) and beggarticks (Bidens pilosa). To validate this system as an in vitro inducer of effectors, the qRT-PCR technique was used to investigate the expression profile of some S. sclerotiorum effector genes in each growth medium at different times after inoculation.

CONCLUSION

The results obtained in this study provide a validation of a new method to study S. sclerotiorum during mimetic interaction with different hosts. Although leaf extract does not fully represent the plant environment, the presence of plant components in the culture medium seems to induce effector genes, mimicking in planta conditions. The use of MEVM is simpler than in planta growth, bypasses problems such as the amount of mycelium produced, as well as contamination of host cells during transcriptomic and proteomic analyses.

SIGNIFICANCE AND IMPACT OF THE STUDY

We have devised MEVM media as a model mimicking the interaction of S. sclerotiorum and its hosts and used it to evaluate in vitro expression of effectors normally expressed only in planta.

Spontaneous and Fungicide-Induced Genomic Variation in Sclerotinia sclerotiorum

Stress from exposure to sublethal fungicide doses may cause genomic instability in fungal plant pathogens, which may accelerate the emergence of fungicide resistance or other adaptive traits. In a previous study, five strains of Sclerotinia sclerotiorum were exposed to sublethal doses of four fungicides with different modes of action, and genotyping showed that such exposure induced mutations. The goal of the present study was to characterize genome-wide mutations in response to sublethal fungicide stress in S. sclerotiorum and study the effect of genomic background on the mutational repertoire. The objectives were to determine the effect of sublethal dose exposure and genomic background on mutation frequency/type, distribution of mutations, and fitness costs. Fifty-five S. sclerotiorum genomes were sequenced and aligned to the reference genome. Variants were called and quality filtered to obtain high confidence calls for single nucleotide polymorphisms (SNPs), insertions/deletions (INDELs), copy number variants, and transposable element (TE) insertions. Results suggest that sublethal fungicide exposure significantly increased the frequency of INDELs in two strains from one genomic background (P value ≤ 0.05), while TE insertions were generally repressed for all genomic backgrounds and under all fungicide exposures. The frequency and/or distribution of SNPs, INDELs, and TE insertions varied with genomic background. A propensity for large duplications on chromosome 7 and aneuploidy of this chromosome were observed in the S. sclerotiorum genome. Mutation accumulation did not significantly affect the overall in planta strain aggressiveness (P value > 0.05). Understanding factors that affect pathogen mutation rates can inform disease management strategies that delay resistance evolution.

Genome-wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families

Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant-pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3' receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high-confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection.

Tackling Control of a Cosmopolitan Phytopathogen: Sclerotinia

Phytopathogenic members of the Sclerotinia genus cause widespread disease across a broad range of economically important crops. In particular, Sclerotinia sclerotiorum is considered one of the most destructive and cosmopolitan of plant pathogens. Here, were review the epidemiology of the pathogen, its economic impact on agricultural production, and measures employed toward control of disease. We review the broad approaches required to tackle Sclerotinia diseases and include cultural practices, crop genetic resistance, chemical fungicides, and biological controls. We highlight the benefits and drawbacks of each approach along with recent advances within these controls and future strategies.

Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis

Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8-39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.

Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era

Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.

Activity of the Succinate Dehydrogenase Inhibitor Fungicide Penthiopyrad Against Sclerotinia sclerotiorum

In present study, the morphological and physiological characteristics of Sclerotinia sclerotiorum (Lib.) de Bary to a novel succinate dehydrogenase inhibitor (SDHI) fungicide penthiopyrad has been reported. The baseline sensitivity of S. sclerotiorum to penthiopyrad was determined using 119 strains by inhibition of mycelial growth. The median effective concentration (EC₅₀) values for penthiopyrad ranged from 0.0096 to 0.2606 μg/ml, and the mean value was 0.0578 (±0.0626) μg/ml. After 1 μg/ml penthiopyrad treatment, mycelia of S. sclerotiorum strains showed increased apical branching and were denser compared with control, and cell membrane permeability significantly increased. In addition, glycerol content, oxalic acid (OA), and exopolysaccharide (EPS) content decreased markedly and mycelial respiration was distinctly inhibited. The number and dry weight of sclerotia significantly decreased after being treated with 2 μg/ml penthiopyrad. Penthiopyrad exhibited both protective and curative activity on the detached rapeseed leaves. Importantly, the above results will provide us more information on penthiopyrad for management of diseases caused by S. sclerotiorum and increase our understanding of action of penthiopyrad against S. sclerotiorum.

Sclerotinia sclerotiorum utilizes host-derived copper for ROS detoxification and infection

Necrotrophic plant pathogen induces host reactive oxygen species (ROS) production, which leads to necrosis in the host, allowing the pathogen to absorb nutrients from the dead tissues. Sclerotinia sclerotiorum is a typical necrotrophic pathogen that causes Sclerotinia stem rot in more than 400 species, resulting in serious economic losses. Here, we found that three S. sclerotiorum genes involved in copper ion import/transport, SsCTR1, SsCCS and SsATX1, were significantly up-regulated during infection of Brassica oleracea. Function analysis revealed that these genes involved in fungal ROS detoxification and virulence. On the host side, four genes putatively involved in copper ion homeostasis, BolCCS, BolCCH, BolMT2A and BolDRT112, were significantly down-regulated in susceptible B. oleracea, but stably expressed in resistant B. oleracea during infection. Their homologs were found to promote resistance to S. sclerotiorum and increase antioxidant activity in Arabidopsis thaliana. Furthermore, copper concentration analysis indicated that copper flow from healthy area into the necrotic area during infection. A model was proposed that S. sclerotiorum utilizes host copper to detoxify ROS in its cells, whereas the resistant hosts may restrict the supply of essential copper nutrients to S. sclerotiorum by maintaining copper ion homeostasis during infection.

Comparative transcriptome analysis of Sclerotinia sclerotiorum revealed its response mechanisms to the biological control agent, Bacillus amyloliquefaciens

Biological control mechanisms of plant diseases have been intensively studied. However, how plant pathogens respond to and resist or alleviate biocontrol agents remains largely unknown. In this study, a comparative transcriptome analysis was performed to elucidate how the pathogen of sclerotinia stem rot, Sclerotinia sclerotiorum, responds and resists to the biocontrol agent, Bacillus amyloliquefaciens. Results revealed that a total of 2,373 genes were differentially expressed in S. sclerotiorum samples treated with B. amyloliquefaciens fermentation broth (TS) when compared to control samples (CS). Among these genes, 2,017 were upregulated and 356 were downregulated. Further analyses indicated that various genes related to fungal cell wall and cell membrane synthesis, antioxidants, and the autophagy pathway were significantly upregulated, including glucan synthesis, ergosterol biosynthesis pathway, fatty acid synthase, heme-binding peroxidase related to oxidative stress, glutathione S-transferase, ABC transporter, and autophagy-related genes. These results suggest that S. sclerotiorum recruits numerous genes to respond to or resist the biocontrol of B. amyloliquefaciens. Thus, this study serves as a valuable resource regarding the mechanisms of fungal pathogen resistance to biocontrol agents.

Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14

Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.

Rapid identification of an Arabidopsis NLR gene as a candidate conferring susceptibility to Sclerotinia sclerotiorum using time-resolved automated phenotyping

The broad host range necrotrophic fungus Sclerotinia sclerotiorum is a devastating pathogen of many oil and vegetable crops. Plant genes conferring complete resistance against S. sclerotiorum have not been reported. Instead, plant populations challenged by S. sclerotiorum exhibit a continuum of partial resistance designated as quantitative disease resistance (QDR). Because of their complex interplay and their small phenotypic effect, the functional characterization of QDR genes remains limited. How broad host range necrotrophic fungi manipulate plant programmed cell death is for instance largely unknown. Here, we designed a time-resolved automated disease phenotyping pipeline enabling high-throughput disease lesion measurement with high resolution, low footprint at low cost. We could accurately recover contrasted disease responses in several pathosystems using this system. We used our phenotyping pipeline to assess the kinetics of disease symptoms caused by seven S. sclerotiorum isolates on six A. thaliana natural accessions with unprecedented resolution. Large effect polymorphisms common to the most resistant A. thaliana accessions identified highly divergent alleles of the nucleotide-binding site leucine-rich repeat gene LAZ5 in the resistant accessions Rubezhnoe and Lip-0. We show that impaired LAZ5 expression in laz5.1 mutant lines and in A. thaliana Rub natural accession correlate with enhanced QDR to S. sclerotiorum. These findings illustrate the value of time-resolved image-based phenotyping for unravelling the genetic bases of complex traits such as QDR. Our results suggest that S. sclerotiorum manipulates plant sphingolipid pathways guarded by LAZ5 to trigger programmed cell death and cause disease.

A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N₅₀ of 2,649.7 kbp and N₉₀ of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

Phylotranscriptomics of the Pentapetalae Reveals Frequent Regulatory Variation in Plant Local Responses to the Fungal Pathogen Sclerotinia sclerotiorum

Quantitative disease resistance (QDR) is a conserved form of plant immunity that limits infections caused by a broad range of pathogens. QDR has a complex genetic determinism. The extent to which molecular components of the QDR response vary across plant species remains elusive. The fungal pathogen Sclerotinia sclerotiorum, causal agent of white mold diseases on hundreds of plant species, triggers QDR in host populations. To document the diversity of local responses to S. sclerotiorum at the molecular level, we analyzed the complete transcriptomes of six species spanning the Pentapetalae (Phaseolus vulgaris, Ricinus communis, Arabidopsis [Arabidopsis thaliana], Helianthus annuus, Solanum lycopersicum, and Beta vulgaris) inoculated with the same strain of S. sclerotiorum About one-third of plant transcriptomes responded locally to S. sclerotiorum, including a high proportion of broadly conserved genes showing frequent regulatory divergence at the interspecific level. Evolutionary inferences suggested a trend toward the acquisition of gene induction relatively recently in several lineages. Focusing on a group of ABCG transporters, we propose that exaptation by regulatory divergence contributed to the evolution of QDR. This evolutionary scenario has implications for understanding the QDR spectrum and durability. Our work provides resources for functional studies of gene regulation and QDR molecular mechanisms across the Pentapetalae.

An effector of a necrotrophic fungal pathogen targets the calcium-sensing receptor in chloroplasts to inhibit host resistance

SsITL, a secretory protein of the necrotrophic phytopathogen Sclerotinia sclerotiorum, was previously reported to suppress host immunity at the early stages of infection. However, the molecular mechanism that SsITL uses to inhibit plant defence against S. sclerotiorum has not yet been elucidated. Here, we report that SsITL interacted with a chloroplast-localized calcium-sensing receptor, CAS, in chloroplasts. We found that CAS is a positive regulator of the salicylic acid signalling pathway in plant immunity to S. sclerotiorum and CAS-mediated resistance against S. sclerotiorum depends on Ca²⁺ signalling. Furthermore, we showed that SsITL could interfere with the plant salicylic acid (SA) signalling pathway and SsITL-expressing transgenic plants were more susceptible to S. sclerotiorum. However, truncated SsITLs (SsITL-NT1 or SsITL-CT1) that lost the ability to interact with CAS do not affect plant resistance to S. sclerotiorum. Taken together, our findings reveal that SsITL inhibits SA accumulation during the early stage of infection by interacting with CAS and then facilitating the infection by S. sclerotiorum.

ORF Ι of Mycovirus SsNSRV-1 is Associated with Debilitating Symptoms of Sclerotinia sclerotiorum

We previously identified Sclerotinia sclerotiorum negative-stranded virus 1 (SsNSRV-1), the first (-) ssRNA mycovirus, associated with hypovirulence of its fungal host Sclerotinia sclerotiorum. In this study, functional analysis of Open Reading Frame Ι (ORF Ι) of SsNSRV-1 was performed. The integration and expression of ORF Ι led to defects in hyphal tips, vegetative growth, and virulence of the mutant strains of S. sclerotiorum. Further, differentially expressed genes (DEGs) responding to the expression of ORF Ι were identified by transcriptome analysis. In all, 686 DEGs consisted of 267 up-regulated genes and 419 down-regulated genes. DEGs reprogramed by ORF Ι were relevant to secretory proteins, pathogenicity, transcription, transmembrane transport, protein biosynthesis, modification, and metabolism. Alternative splicing was also detected in all mutant strains, but not in hypovirulent strain AH98, which was co-infected by SsNSRV-1 and Sclerotinia sclerotiorum hypovirus 1 (SsHV-1). Thus, the integrity of SsNSRV-1 genome may be necessary to protect viral mRNA from splicing and inactivation by the host. Taken together, the results suggested that protein ORF Ι could regulate the transcription, translation, and modification of host genes in order to facilitate viral proliferation and reduce the virulence of the host. Therefore, ORF Ι may be a potential gene used for the prevention of S. sclerotiorum.

Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae

Fungal effector proteins facilitate host-plant colonization and have generally been characterized as small secreted proteins (SSPs). We classified and functionally tested SSPs from the secretomes of three closely related necrotrophic phytopathogens: Ciborinia camelliae, Botrytis cinerea, and Sclerotinia sclerotiorum. Alignment of predicted SSPs identified a large protein family that share greater than 41% amino acid identity and that have key characteristics of previously described microbe-associated molecular patterns (MAMPs). Strikingly, 73 of the 75 SSP family members were predicted within the secretome of the host-specialist C. camelliae with single-copy homologs identified in the secretomes of the host generalists S. sclerotiorum and B. cinerea. To explore the potential function of this family of SSPs, 10 of the 73 C. camelliae proteins, together with the single-copy homologs from S. sclerotiorum (SsSSP3) and B. cinerea (BcSSP2), were cloned and expressed as recombinant proteins. Infiltration of SsSSP3 and BcSSP2 into host tissue induced rapid necrosis. In contrast, only one of the 10 tested C. camelliae SSPs was able to induce a limited amount of necrosis. Analysis of chimeric proteins consisting of domains from both a necrosis-inducing and a non-necrosis-inducing SSP demonstrated that the C-terminus of the S. sclerotiorum SSP is essential for necrosis-inducing function. Deletion of the BcSSP2 homolog from B. cinerea did not affect growth or pathogenesis. Thus, this research uncovered a family of highly conserved SSPs present in diverse ascomycetes that exhibit contrasting necrosis-inducing functions.

Transcriptome analysis of the plant pathogen Sclerotinia sclerotiorum interaction with resistant and susceptible canola (Brassica napus) lines

Sclerotinia stem rot is an economically important disease of canola (Brassica napus) and is caused by the fungal pathogen Sclerotinia sclerotiorum. This study evaluated the differential gene expression patterns of S. sclerotiorum during disease development on two canola lines differing in susceptibility to this pathogen. Sequencing of the mRNA libraries derived from inoculated petioles and mycelium grown on liquid medium generated approximately 164 million Illumina reads, including 95 million 75-bp-single reads, and 69 million 50-bp-paired end reads. Overall, 36% of the quality filter-passed reads were mapped to the S. sclerotiorum reference genome. On the susceptible line, 1301 and 1214 S. sclerotiorum genes were differentially expressed at early (8-16 hours post inoculation (hpi)) and late (24-48 hpi) infection stages, respectively, while on the resistant line, 1311 and 1335 genes were differentially expressed at these stages, respectively. Gene ontology (GO) categories associated with cell wall degradation, detoxification of host metabolites, peroxisome related activities like fatty acid ß-oxidation, glyoxylate cycle, oxidoreductase activity were significantly enriched in the up-regulated gene sets on both susceptible and resistant lines. Quantitative RT-PCR of six selected DEGs further validated the RNA-seq differential gene expression analysis. The regulation of effector genes involved in host defense suppression or evasion during the early infection stage, and the expression of effectors involved in host cell death in the late stage of infection provide supporting evidence for a two-phase infection model involving a brief biotrophic phase during early stages of infection. The findings from this study emphasize the role of peroxisome related pathways along with cell wall degradation and detoxification of host metabolites as the key mechanisms underlying pathogenesis of S. sclerotiorum on B. napus.

Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean (Vicia faba L.)

Chocolate spot is a major fungal disease of faba bean caused by the ascomycete fungus, Botrytis fabae. B. fabae is also implicated in botrytis gray mold disease in lentils, along with B. cinerea. Here we have isolated and characterized two B. fabae isolates from chocolate spot lesions on faba bean leaves. In plant disease assays on faba bean and lentil, B. fabae was more aggressive than B. cinerea and we observed variation in susceptibility among a small set of cultivars for both plant hosts. Using light microscopy, we observed a spreading, generalized necrosis response in faba bean toward B. fabae. In contrast, the plant response to B. cinerea was localized to epidermal cells underlying germinated spores and appressoria. In addition to the species characterization of B. fabae, we produced genome assemblies for both B. fabae isolates using Illumina sequencing. Genome sequencing coverage and assembly size for B. fabae isolates, were 27x and 45x, and 43.2 and 44.5 Mb, respectively. Following genome assembly and annotation, carbohydrate-active enzyme (CAZymes) and effector genes were predicted. There were no major differences in the numbers of each of the major classes of CAZymes. We predicted 29 effector genes for B. fabae, and using the same selection criteria for B. cinerea, we predicted 34 putative effector genes. For five of the predicted effector genes, the pairwise dN/dS ratio between orthologs from B. fabae and B. cinerea was greater than 1.0, suggesting positive selection and the potential evolution of molecular mechanisms for host specificity in B. fabae. Furthermore, a homology search of secondary metabolite clusters revealed the absence of the B. cinerea phytotoxin botrydial and several other uncharacterized secondary metabolite biosynthesis genes from B. fabae. Although there were no obvious differences in the number or proportional representation of different transposable element classes, the overall proportion of AT-rich DNA sequence in B. fabae was double that of B. cinerea.

Host Transcriptional Response of Sclerotinia sclerotiorum Induced by the Mycoparasite Coniothyrium minitans

Mycoparasite Coniothyrium minitans parasitizes specifically the mycelia or sclerotia of Sclerotinia sclerotiorum, a worldwidely spread plant fungal pathogen causing serious diseases on crops. The interaction of C. minitans with S. sclerotiorum remains reciprocal and complex and little is known, especially on the side of the host (S. sclerotiorum). In this study, the early transcriptional response of S. sclerotiorum to the mycoparasitism by C. minitans was explored and the differentially expressed genes (DEGs) were analyzed. Based on GO ontology, KEGG pathway and fungal categories database, 887 up-regulated DEGs were enriched in the growth related function (i.e., rRNA processing, ribosome biogenesis, binding and transport), while the 546 down-regulated DEGs were enriched in the stress-related functions (i.e., oxidoreductase, response to stress and heat and the chorismate biosynthetic process). The expression of shikimate pathway and the biosynthesis of phenylalanine involving genes was significantly suppressed. Furthermore, 581 unenriched DEGs were explored in the parasitizing process and were mapped on the Pfam domains of redox enzymes, Alpha/Beta hydrolase, haloacid dehalogenase, and other universal conserved domain containing proteins. Thirty-two DEGs encoding candidate effectors, with 16 up-regulated and 16 down-regulated, were observed with diverse function. SS1G_11912 (encoding SsNEP2) was significantly up-regulated and may function in the parasitism. The involving of the shikimate pathway of phenylalanine biosynthesis and effector candidates were discussed. The results provide a basal understand on the interaction of S. sclerotiorum and C. minitans.

Target the core: durable plant resistance against filamentous plant pathogens through effector recognition

Plant pathogens colonize their host through the secretion of effector proteins that modulate plant metabolism and immune responses to their benefit. Plants evolve towards effector recognition, leading to host immunity. Typically, pathogen effectors are targets for recognition through plant receptors that are encoded by resistance genes. Resistance gene mediated crop immunity puts a tremendous pressure on pathogens to adapt and alter their effector repertoire to overcome recognition. We argue that the type of effector that is recognized by the host may have considerable implications on the durability of resistance against filamentous plant pathogens. Effector genes that are conserved among pathogens and reside in core genome regions are most likely to hold indispensable virulence functions. Consequently, the cost for the pathogen to overcome recognition by the host is higher than for diversified, host-specific effectors with a quantitative impact on virulence. Consequently, resistance genes that directly target conserved effector proteins without the interception of other effector proteins are potentially excellent resistance resources. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Fusarium virguliform e Transcriptional Plasticity Is Revealed by Host Colonization of Maize versus Soybean

We exploited the broad host range of Fusarium virguliforme to identify differential fungal responses leading to either an endophytic or a pathogenic lifestyle during colonization of maize (Zea mays) and soybean (Glycine max), respectively. To provide a foundation to survey the transcriptomic landscape, we produced an improved de novo genome assembly and annotation of F. virguliforme using PacBio sequencing. Next, we conducted a high-resolution time course of F. virguliforme colonization and infection of both soybean, a symptomatic host, and maize, an asymptomatic host. Comparative transcriptomic analyses uncovered a nearly complete network rewiring, with less than 8% average gene coexpression module overlap upon colonizing the different plant hosts. Divergence of transcriptomes originating from host specific temporal induction genes is central to infection and colonization, including carbohydrate-active enzymes (CAZymes) and necrosis inducing effectors. Upregulation of Zn(II)-Cys6 transcription factors were uniquely induced in soybean at 2 d postinoculation, suggestive of enhanced pathogen virulence on soybean. In total, the data described herein suggest that F. virguliforme modulates divergent infection profiles through transcriptional plasticity.

A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence

Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high-quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison, resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes, examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions, consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in subtelomeric regions of chromosomes, with 10 of the 14 accessory region QTL localizing to subtelomeric regions. Comparative analysis of the subtelomeric regions of P. teres f. teres chromosomes revealed translocation events in which homology was detected between nonhomologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the subtelomeric accessory genomic compartments not only harbor most of the known virulence loci but, also, that these regions have the capacity to rapidly evolve.

A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

BACKGROUND

The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.

RESULTS

We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.

CONCLUSIONS

These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

Receptor-Like Kinases BAK1 and SOBIR1 Are Required for Necrotizing Activity of a Novel Group of Sclerotinia sclerotiorum Necrosis-Inducing Effectors

Sclerotinia sclerotiorum is a characteristic necrotrophic plant pathogen and is dependent on the induction of host cell death for nutrient acquisition. To identify necrosis-inducing effectors, the genome of S. sclerotiorum was scanned for genes encoding small, secreted, cysteine-rich proteins. These potential effectors were tested for their ability to induce necrosis in Nicotiana benthamiana via Agrobacterium-mediated expression and for cellular localization in host cells. Six novel proteins were discovered, of which all but one required a signal peptide for export to the apoplast for necrotizing activity. Virus-induced gene silencing revealed that the five necrosis-inducing effectors with a requirement for secretion also required the plant co-receptor-like kinases Brassinosteroid Insensitive 1-Associated Receptor Kinase 1 (BAK1) and Suppressor of BAK1-Interacting Receptor-like Kinase 1 (SOBIR1) for the induction of necrosis. S. sclerotiorum necrosis-inducing effector 2 (SsNE2) represented a new class of necrosis-inducing proteins as orthologs were identified in several other phytopathogenic fungi that were also capable of inducing necrosis. Substitution of conserved cysteine residues with alanine reduced, but did not abolish, the necrotizing activity of SsNE2 and full-length protein was required for function as peptides spanning the entire protein were unable to induce necrosis. These results illustrate the importance of necrosis-inducing effectors for S. sclerotiorum virulence and the role of host extracellular receptor(s) in effector-triggered susceptibility to this pathogen.

The host generalist phytopathogenic fungus Sclerotinia sclerotiorum differentially expresses multiple metabolic enzymes on two different plant hosts

Sclerotinia sclerotiorum is a necrotrophic fungal pathogen that infects upwards of 400 plant species, including several economically important crops. The molecular processes that underpin broad host range necrotrophy are not fully understood. This study used RNA sequencing to assess whether S. sclerotiorum genes are differentially expressed in response to infection of the two different host crops canola (Brassica napus) and lupin (Lupinus angustifolius). A total of 10,864 of the 11,130 genes in the S. sclerotiorum genome were expressed. Of these, 628 were upregulated in planta relative to in vitro on at least one host, suggesting involvement in the broader infection process. Among these genes were predicted carbohydrate-active enzymes (CAZYmes) and secondary metabolites. A considerably smaller group of 53 genes were differentially expressed between the two plant hosts. Of these host-specific genes, only six were either CAZymes, secondary metabolites or putative effectors. The remaining genes represented a diverse range of functional categories, including several associated with the metabolism and efflux of xenobiotic compounds, such as cytochrome P450s, metal-beta-lactamases, tannases and major facilitator superfamily transporters. These results suggest that S. sclerotiorum may regulate the expression of detoxification-related genes in response to phytotoxins produced by the different host species. To date, this is the first comparative whole transcriptome analysis of S. sclerotiorum during infection of different hosts.

The Notorious Soilborne Pathogenic Fungus Sclerotinia sclerotiorum: An Update on Genes Studied with Mutant Analysis

Ascomycete Sclerotinia sclerotiorum (Lib.) de Bary is one of the most damaging soilborne fungal pathogens affecting hundreds of plant hosts, including many economically important crops. Its genomic sequence has been available for less than a decade, and it was recently updated with higher completion and better gene annotation. Here, we review key molecular findings on the unique biology and pathogenesis process of S. sclerotiorum, focusing on genes that have been studied in depth using mutant analysis. Analyses of these genes have revealed critical players in the basic biological processes of this unique pathogen, including mycelial growth, appressorium establishment, sclerotial formation, apothecial and ascospore development, and virulence. Additionally, the synthesis has uncovered gaps in the current knowledge regarding this fungus. We hope that this review will serve to build a better current understanding of the biology of this under-studied notorious soilborne pathogenic fungus.

Repeat-Induced Point Mutations Drive Divergence between Fusarium circinatum and Its Close Relatives

The Repeat-Induced Point (RIP) mutation pathway is a fungal-specific genome defense mechanism that counteracts the deleterious effects of transposable elements. This pathway permanently mutates its target sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence of RIP in the pitch canker pathogen, Fusarium circinatum, and its close relatives in the Fusarium fujikuroi species complex (FFSC). Our results showed that the examined fungi all exhibited hallmarks of RIP, but that they differed in terms of the extent to which their genomes were affected by this pathway. RIP mutations constituted a large proportion of all the FFSC genomes, including both core and dispensable chromosomes, although the latter were generally more extensively affected by RIP. Large RIP-affected genomic regions were also much more gene sparse than the rest of the genome. Our data further showed that RIP-directed sequence diversification increased the variability between homologous regions of related species, and that RIP-affected regions can interfere with homologous recombination during meiosis, thereby contributing to post-mating segregation distortion. Taken together, these findings suggest that RIP can drive the independent divergence of chromosomes, alter chromosome architecture, and contribute to the divergence among F. circinatum and other members of this economically important group of fungi.

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Background

Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts.

Results

We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half including telomeres. Both genomes were annotated with MAKER using transcript evidence generated in this study with over 13,000 protein-coding genes predicted. Unique groups of genes for each isolate were identified when compared to closely related fungal species. Structural comparisons between the isolates reveal large-scale rearrangements including chromosomal inversions and translocations. To include isolates representing a range of pathogen genotypes, an additional 30 isolates were sequenced with Illumina, assembled, and compared to the strawberry genotype assembly. Within the limits of comparing Illumina and PacBio assemblies, no conserved structural rearrangements were identified among the isolates from the strawberry genotype compared to those from other hosts, but some candidate genes were identified that were largely present in isolates of the strawberry genotype and absent in other genotypes.

Conclusions

High-quality reference genomes of M. phaseolina have allowed for the identification of structural changes associated with a genotype that has a host preference toward strawberry and will enable future comparative genomics studies. Having more complete assemblies allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes. Work with Illumina data from additional isolates suggests that some genes are predominately present in isolates of the strawberry genotype, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs identified in the strawberry genotype assembly and to determine if unique genes in the strawberry genotype play a role in pathogenicity.

New High-Quality Draft Genome of the Brown Rot Fungal Pathogen Monilinia fructicola

Brown rot is a worldwide fungal disease of stone and pome fruit that is caused by several Monilinia species. Among these, Monilinia fructicola can cause severe preharvest and postharvest losses, especially for stone fruit. Here, we present a high-quality draft genome assembly of M. fructicola Mfrc123 strain obtained using both Illumina and PacBio sequencing technologies. The genome assembly comprised 20 scaffolds, including 29 telomere sequences at both ends of 10 scaffolds, and at a single end of 9 scaffolds. The total length was 44.05 Mb, with a scaffold N50 of 2,592 kb. Annotation of the M. fructicola assembly identified a total of 12,118 genes and 13,749 proteins that were functionally annotated. This newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within Monilinia species.

The Formaldehyde Dehydrogenase SsFdh1 Is Regulated by and Functionally Cooperates with the GATA Transcription Factor SsNsd1 in Sclerotinia sclerotiorum

S. sclerotiorum is a pathogenic fungus with sclerotium and infection cushion development, making S. sclerotiorum one of the most challenging agricultural pathogens with no effective control method. We identified important sclerotium and compound appressorium formation determinants, SsNsd1 and SsFdh1, and investigated their regulatory mechanism at the molecular level. SsNsd1 and SsFdh1 are zinc finger motif-containing proteins and associate with each other in the nucleus. On other hand, SsNsd1, as a GATA transcription factor, directly binds to GATA-box DNA in the promoter region of Ssfdh1. The SsNsd1-SsFdh1 interaction and nuclear translocation were found to prevent efficient binding of SsNsd1 to GATA-box DNA. Our results provide insights into the role of the GATA transcription factor and its regulation of formaldehyde dehydrogenase in stress resistance, fungal sclerotium and compound appressorium development, and pathogenicity.

GATA transcription factors (TFs) are common eukaryotic regulators, and glutathione-dependent formaldehyde dehydrogenases (GD-FDH) are ubiquitous enzymes with formaldehyde detoxification activity. In this study, the formaldehyde dehydrogenase Sclerotinia sclerotiorum Fdh1 (SsFdh1) was first characterized as an interacting partner of a GATA TF, SsNsd1, in S. sclerotiorum. Genetic analysis reveals that SsFdh1 functions in formaldehyde detoxification, nitrogen metabolism, sclerotium development, and pathogenicity. Both SsNsd1 and SsFdh1 harbor typical zinc finger motifs with conserved cysteine residues. SsNsd1 regulates SsFdh1 in two distinct manners. SsNsd1 directly binds to GATA-box DNA in the promoter region of Ssfdh1; SsNsd1 associates with SsFdh1 through disulfide bonds formed by conserved Cys residues. The SsNsd1-SsFdh1 interaction and nuclear translocation were found to prevent efficient binding of SsNsd1 to GATA-box DNA. Site-directed point mutation of these Cys residues influences the SsNsd1-SsFdh1 interaction and SsNsd1 DNA binding capacity. SsFdh1 is regulated by and functions jointly with the SsNsd1 factor, providing new insights into the complex transcriptional regulatory mechanisms of GATA factors.

IMPORTANCES. sclerotiorum is a pathogenic fungus with sclerotium and infection cushion development, making S. sclerotiorum one of the most challenging agricultural pathogens with no effective control method. We identified important sclerotium and compound appressorium formation determinants, SsNsd1 and SsFdh1, and investigated their regulatory mechanism at the molecular level. SsNsd1 and SsFdh1 are zinc finger motif-containing proteins and associate with each other in the nucleus. On other hand, SsNsd1, as a GATA transcription factor, directly binds to GATA-box DNA in the promoter region of Ssfdh1. The SsNsd1-SsFdh1 interaction and nuclear translocation were found to prevent efficient binding of SsNsd1 to GATA-box DNA. Our results provide insights into the role of the GATA transcription factor and its regulation of formaldehyde dehydrogenase in stress resistance, fungal sclerotium and compound appressorium development, and pathogenicity.

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

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.

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Background

Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea – both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts.

Results

Genomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents.

Conclusions

Detection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5774-2) contains supplementary material, which is available to authorized users.

A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.

Comparative genomics of plant pathogenic Botrytis species with distinct host specificity

BACKGROUND

Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae.

RESULTS

Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed.

CONCLUSIONS

Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.

Gene regulation of Sclerotinia sclerotiorum during infection of Glycine max: on the road to pathogenesis

BACKGROUND

Sclerotinia sclerotiorum is a broad-host range necrotrophic pathogen which is the causative agent of Sclerotinia stem rot (SSR), and a major disease of soybean (Glycine max). A time course transcriptomic analysis was performed in both compatible and incompatible soybean lines to identify pathogenicity and developmental factors utilized by S. sclerotiorum to achieve pathogenic success.

RESULTS

A comparison of genes expressed during early infection identified the potential importance of toxin efflux and nitrogen metabolism during the early stages of disease establishment. The later stages of infection were characterized by an apparent shift to survival structure formation. Analysis of genes highly upregulated in-planta revealed a temporal regulation of hydrolytic and detoxification enzymes, putative secreted effectors, and secondary metabolite synthesis genes. Redox regulation also appears to play a key role during the course of infection, as suggested by the high expression of genes involved in reactive oxygen species production and scavenging. Finally, distinct differences in early gene expression were noted based on the comparison of S. sclerotiorum infection of resistant and susceptible soybean lines.

CONCLUSIONS

Although many potential virulence factors have been noted in the S. sclerotiorum pathosystem, this study serves to highlight soybean specific processes most likely to be critical in successful infection. Functional studies of genes identified in this work are needed to confirm their importance to disease development, and may constitute valuable targets of RNAi approaches to improve resistance to SSR.

Intercellular cooperation in a fungal plant pathogen facilitates host colonization

Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.

A Sclerotinia sclerotiorum Transcription Factor Involved in Sclerotial Development and Virulence on Pea

Sclerotinia sclerotiorum is a plant-pathogenic ascomycete fungus and infects over 400 host plants, including pea (Pisum sativum L.). The fungus causes white mold on pea, and substantial yield loss is attributed to the disease. To improve white mold management, further understanding of S. sclerotiorum pathogenicity is crucial. In this study, 389 transcription factors (TFs) were mined from the complete genome sequence of S. sclerotiorum and their in planta expression patterns were determined in susceptible and partially resistant pea lines and compared to in vitro expression patterns on culture medium. One of the transcription factors was significantly induced in planta at 24 and 48 h postinfection compared to the expression in vitro This putative C6 transcription factor of S. sclerotiorum (SsC6TF1) was knocked down using a gene-silencing approach to investigate its functions in vegetative growth and sclerotial development as well as its virulence and pathogenicity in pea. While the SsC6TF1 knockdown mutants had hyphal growth rates identical to those of the wild-type strain and were capable of infection, the knockdown mutants produced no sclerotia or significantly fewer and smaller sclerotia on the culture medium and exhibited reduced virulence on both pea lines. This study profiled genome-wide expression for S. sclerotiorum transcription factors in planta and in vitro and functionally characterized a novel transcription factor, SsC6TF1, which positively regulates sclerotial development and virulence on pea. The finding provides molecular insights into S. sclerotiorum biology and interaction with pea and other economically important crops.IMPORTANCE White mold, caused by Sclerotinia sclerotiorum, is a destructive disease on important legume species such as soybean, dry bean, and pea. This study investigated expression levels of transcription factors in S. sclerotiorumin planta (pea lines) and in vitro (culture medium). One transcription factor displaying high expression in planta was found to be involved in sclerotial development and virulence on pea. This report provides a new understanding regarding transcription factors of S. sclerotiorum in development and virulence.

Manipulation of Phytohormone Pathways by Effectors of Filamentous Plant Pathogens

Phytohormones regulate a large variety of physiological processes in plants. In addition, salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are responsible for primary defense responses against abiotic and biotic stresses, while plant growth regulators, such as auxins, brassinosteroids (BRs), cytokinins (CKs), abscisic acid (ABA), and gibberellins (GAs), also contribute to plant immunity. To successfully colonize plants, filamentous pathogens like fungi and oomycetes have evolved diverse strategies to interfere with phytohormone pathways with the help of secreted effectors. These include proteins, toxins, polysaccharides as well as phytohormones or phytohormone mimics. Such pathogen effectors manipulate phytohormone pathways by directly altering hormone levels, by interfering with phytohormone biosynthesis, or by altering or blocking important components of phytohormone signaling pathways. In this review, we outline the various strategies used by filamentous phytopathogens to manipulate phytohormone pathways to cause disease.