Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1

In-depth comparative transcriptome analysis of Purpureocillium sp. CB1 under cadmium stress

Fungal bioremediation is a very attractive tool to cope with environmental pollution. We aimed to decipher the cadmium (Cd) response of Purpureocillium sp. CB1, isolated from polluted soil, at transcriptome level by RNA-sequencing (RNA-seq). We used 500 and 2500 mg/L of Cd²⁺ concentrations at two time points (t_6;36). RNA-seq determined 620 genes that were co-expressed in all samples. The highest number of differentially expressed genes (DEGs) was obtained within the first six h of exposure to 2500 mg/L of Cd²⁺. Several genes encoding transcriptional regulators, transporters, heat shock proteins, and oxidative stress-related genes were differentially expressed under Cd²⁺ stress. Remarkably, the genes that encode salicylate hydroxylase, which is involved in naphthalene biodegradation pathway, were significantly overexpressed. Utilization of diesel as the sole carbon source by CB1 even in the presence of Cd²⁺ supported concomitant upregulation of hydrocarbon degradation pathway genes. Furthermore, leucinostatin-related gene expression levels increased under Cd²⁺ stress. In addition, leucinostatin extracts from Cd²⁺-treated CB1 cultures showed higher antifungal activity than the control. Notably, Cd²⁺ in CB1 was mainly found as bound to the cell wall, thus confirming its adsorption potential. Cd²⁺ stress slightly reduced growth and led to mycelial malformation due to Cd²⁺ adsorption, especially at a concentration of 2500 mg/L at t₃₆. A strong correlation was recorded between RNA-seq and reverse-transcriptase-quantitative polymerase chain reaction (RT-qPCR) data. In conclusion, the study represents the first transcriptome analysis of Purpureocillium sp. under Cd²⁺ stress, providing insights into the primary targets for rational engineering to construct strains with remarkable bioremediation potency. KEY POINTS: • Upregulation of genes encoding salicylate hydroxylases under Cd²⁺ stress • Maximum Cd²⁺ adsorption at 500 mg/L at t₃₆ as tightly bound to the cell wall • Concordant bioremediation potential of CB1 on Cd²⁺ and diesel.

Entomopathogenic Strains of the Fungus Purpureocillium lilacinum Damage the Fungus Cultivar of Pest Leaf-Cutter Ants

Purpureocillium lilacinum (Hypocreales: Ophiocordycipitaceae) is a cosmopolitan fungus not only pathogenic to insect and nematode hosts but also to other fungi. Although having one organism with multiple effects would be desirable in a biocontrol strategy, few studies have looked at the multiple roles one strain could play. This work shows how three strains of P. lilacinum, previously proven to be entomopathogenic to leaf-cutter ants (LCA), could degrade several strains of Leucoagaricus sp., the fungus cultivated by LCA as their food source. We isolated four strains of Leucoagaricus sp. from Acromyrmex and Atta LCA species, and we determined their species molecularly, as well as their clade identity (Leucoagaricus gongylophorus, clade-A). We observed the effects on growth rates on Petri dishes and the interaction of microscopic structures of both fungi on slides. All three P. lilacinum strains inhibited the growth of L. gongylophorus. They also degraded all L. gongylophorus isolated from the Acromyrmex species, causing hyphae expansion and degradation of the cell wall. However, only one of them succeeded in degrading the L. gongylophorus strain isolated from the Atta species. The results confirm the damage to the hyphae of ant cultivars and highlight the need for future studies that reveal whether such behavior is due to P. lilacinum's mycoparasitic behavior. Using a single P. lilacinum strain with a dual function that includes the degradation of the cultivar of LCA of both genera would be a very promising strategy for the biocontrol of one of the worst herbivore pests in the Neotropics.

Biochemical and biophysical properties of a recombinant serine peptidase from Purpureocillium lilacinum

The industrial uses of peptidases have already been consolidated; however, their range of applications is increasing. Thus, the biochemical characterization of new peptidases could increase the range of their biotechnological applications. In silico analysis identified a gene encoding a putative serine peptidase from Purpureocillium lilacinum (Pl_SerPep), annotated as a cuticle-degrading enzyme. The Pl_SerPep gene product was expressed as a recombinant in a Komagataella phaffii (previously Pichia pastoris) expression system. The enzyme (rPl_SerPep) showed optimal pH and temperature of 8.0 and 60 °C, respectively. Moreover, rPl_SerPep has a higher thermal stability than the cuticle-degrading enzymes described elsewhere. The structural analysis indicated a conformational change in the rPl_SerPep secondary structure, which would allow an increase in catalytic activity at 60 °C. Komagataella phaffii secretes rPl_SerPep with the pro peptide in its inactive form. Low-resolution small-angle X-ray scattering (SAXS) analysis showed little mobility of the pro peptide portion, which indicates the apparent stability of the inactive form of the enzyme. The presence of 20 mM guanidine in the reaction resulted in the maintenance of activity, which was apparently a consequence of pro peptide structure flexibilization.

Virulence of the Bio-Control Fungus Purpureocillium lilacinum Against Myzus persicae (Hemiptera: Aphididae) and Spodoptera frugiperda (Lepidoptera: Noctuidae)

Eco-friendly entomopathogenic fungi are widely used to control agricultural insect pests. Purpureocillium lilacinum (Thom.) Luangsa-ard et al. (Hypocreales: Ophiocordycipitaceae) is a nematophagous fungus used for the bio-control of destructive root-knot nematodes. However, its insecticidal activities against agricultural insect pests haven't been widely studied. In this study, P. lilacinum PL-1 was isolated from soil (Hefei, China) and identified by molecular and morphological analyses. The growth rate, spore production, proteinase, and chitinase activities of the isolate were analyzed. Virulence tests against green peach aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae) and fall armyworm (FAW), Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae) were performed. The median lethal concentration (LC50) and median lethal time (LT50) against aphids (via immersion) and LT50 against FAW (via injection) were determined. FAW eggs immersed in aqueous conidia suspension were infected after 60 h. Differentially expressed genes (DEGs) in the infection of FAW larvae by P. lilacinum were analyzed by quantitative reverse transcription PCR. The significantly upregulated DEGs include FAW immune genes (antimicrobial peptides, C-type lectins, lysozymes, prophenoloxidase, and peptidoglycan recognition proteins) and fungal pathogenic genes (ligase, chitinase, and hydrophobin). Our data demonstrate that P. lilacinum can be used as an entomopathogenic fungus against agricultural insect pests.

Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu

Daqu and wheat Qu are saccharification and fermenting agents in Chinese huangjiu and baijiu production. This study aimed to investigate the difference between Daqu and wheat Qu in physicochemical indices, microbial communities, functional genes, and the metabolic network of key microbes responsible for flavor synthesis by whole-metagenome sequencing and metabolite analysis. Herein, physicochemical indices indicated that compared with wheat Qu, Daqu exhibited higher protease and cellulase activity and acidity, and lower glucoamylase and amylase enzyme activity. Metagenomic sequencing reveals that although Daqu and wheat Qu community composition have significant differences at species level, they have similar functional genes. Daqu were enriched in Pediococcus pentosaceus, Weissella paramesenteroides, Rasamsonia emersonii and Byssochlamys spectabilis (22.48% of the total abundance), while wheat Qu harbored greater abundances of Saccharopolyspora (54.78%, Saccharopolyspora rectivirgula, Saccharopolyspora shandongensis, Saccharopolyspora hirsuta, Saccharopolyspora spinose, and Saccharopolyspora erythraea). From a functional perspective, the important functions of Daqu and wheat Qu are both amino acid metabolism and carbohydrate metabolism. Meanwhile, a combined analysis among microbiota, functional genes, and dominant flavors indicated S. shandongensis, S. rectivirgula, and S. spinose might be the main contributor to the synthesis of flavor compounds in wheat Qu, while R. emersonii, W. paramesenteroides, Leuconostoc citreum, Leuconostoc mesenteroides, Weissella cibaria and P. pentosaceus may make the greatest contribution to flavor compounds synthesis in Daqu. This study reveals the microbial and functional dissimilarities of Daqu and wheat Qu, and helps elucidating different metabolic roles of microbes during flavor formation.

Increased Pathogenicity of the Nematophagous Fungus Drechmeria coniospora Following Long-Term Laboratory Culture

Domestication provides a window into adaptive change. Over the course of 2 decades of laboratory culture, a strain of the nematode-specific fungus Drechmeria coniospora became more virulent during its infection of Caenorhabditis elegans. Through a close comparative examination of the genome sequences of the original strain and its more pathogenic derivative, we identified a small number of non-synonymous mutations in protein-coding genes. In one case, the mutation was predicted to affect a gene involved in hypoxia resistance and we provide direct corroborative evidence for such an effect. The mutated genes with functional annotation were all predicted to impact the general physiology of the fungus and this was reflected in an increased in vitro growth, even in the absence of C. elegans. While most cases involved single nucleotide substitutions predicted to lead to a loss of function, we also observed a predicted restoration of gene function through deletion of an extraneous tandem repeat. This latter change affected the regulatory subunit of a cAMP-dependent protein kinase. Remarkably, we also found a mutation in a gene for a second protein of the same, protein kinase A, pathway. Together, we predict that they result in a stronger repression of the pathway for given levels of ATP and adenylate cyclase activity. Finally, we also identified mutations in a few lineage-specific genes of unknown function that are candidates for factors that influence virulence in a more direct manner.

Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein (PlRPS15) in filamentous fungi

The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into pre-ribosomal particles are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, whose expression is up-regulated during abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 co-translationally interacted with the unassembled small ribosomal subunit protein, PlRPS15 (uS19). PlRPS15 contained an eukaryote-specific N-terminal extension that mediated the interaction with PlCYP5. PlCYP5 increased the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. Consistently, the phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g. growth and ribosome biogenesis defects). PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botrytis cinerea and Metarhizium anisopliae were identified. Notably, PlCYP5-PlRPS15 homologs from three filamentous fungi interacted with each other but not those from other species. In summary, our data disclosed a unique dedicated chaperone system for RPs by cyclophilin in filamentous fungi.

Isolation and Characterization of the Polyhexamethylene Biguanide Hydrochloride-Resistant Fungus, Purpureocillium lilacinum

We isolated a fungus from a 20% (= 200,000 µg/mL) aqueous solution of polyhexamethylene biguanide hydrochloride (PHMB), a widely used antimicrobial and examined its morphology and drug resistance profile. Based on the sequence of the internal transcribed spacer region of ribosomal DNA, the fungus was identified as Purpureocillium lilacinum. Although the P. lilacinum type and resistant strains showed similar morphology, the latter had extremely low PHMB susceptibility and was able to grow in 20% aqueous solution of PHMB, which eliminated the type strain. The minimum inhibitory concentration (MIC) of PHMB for the resistant strain was significantly higher than that of the type strain and other pathogenic filamentous fungi and yeasts. The susceptibility to antimicrobial agents and antifungal agents other than PHMB was similar to that of the type strain, therefore the drug resistance of the isolate was specific to PHMB. Furthermore, we sequenced the genome of the isolate to predict PHMB resistance-related genes. Despite its high resistance to PHMB, no well-known genes homologous to fungal PHMB-resistant genes were detected in the genome of the resistant strain. In summary, P. lilacinum was found to be significantly more resistant to PHMB than previously reported, via an unidentified mechanism of drug resistance.

Transcriptomic studies on Purpureocillium lilacinum reveal molecular mechanisms of response to fluconazole and itraconazole

Filamentous fungus Purpureocillium lilacinum is an emerging pathogen that infects immunocompromised and immunocompetent individuals and is resistant to several azole molecules. Although azole resistance mechanisms are well studied in Aspergillus sp. and Candida sp., there are no studies to date reporting P. lilacinum molecular response to these molecules. The aim of this study was to describe P. lilacinum molecular mechanisms involved in antifungal response against fluconazole and itraconazole. Transcriptomic analyses showed that gene expression modulation takes place when P. lilacinum is challenged for 12 h with fluconazole (64 μg/mL) or itraconazole (16 μg/mL). The antifungals acted on the ergosterol biosynthesis pathway, and two homologous genes coding for cytochrome P450 51 enzymes were upregulated. Genes coding for efflux pumps, such as the major facilitator superfamily transporter, also displayed increased expression in the treated samples. We propose that P. lilacinum develops antifungal responses by raising the expression levels of cytochrome P450 enzymes and efflux pumps. Such modulation could confer P. lilacinum high levels of target enzymes and could lead to the constant withdrawal of antifungals, which would force an increase in the administration of antifungal medications to achieve fungal morbidity or mortality. The findings in this work could aid in the decision-making for treatment strategies in cases of P. lilacinum infection.

Understanding the Transcriptional Changes During Infection of Meloidogyne incognita Eggs by the Egg-Parasitic Fungus Purpureocillium lilacinum

The egg-pathogenic fungus Purpureocillium lilacinum parasitizes on nematode eggs, and thus, it is used as a good biocontrol agent against plant root-knot nematodes. However, little is known about the transcriptional response of P. lilacinum while infecting nematode eggs. This study presents the whole transcriptome sequencing of P. lilacinum and transcriptome-wide gene expression analysis of P. lilacinum upon infecting the eggs of Meloidogyne incognita compared to non-infecting controls. A transcriptomic library of P. lilacinum was used as reference gene set and six transcriptomic libraries of the non-infecting control and P. lilacinum infecting M. incognita eggs were constructed, respectively, comprising three biological replicates of each. A total of 1,011 differently expressed genes (DEGs) were identified in the infecting samples, including 553 up-regulated and 458 down-regulated genes compared to the non-infecting control samples. Furthermore, functional enrichment analysis exhibited that these DEGs were primarily involved in oxidative phosphorylation, oxidoreductase activity, and metabolic processes. Fifteen DEGs were randomly selected to verify the RNA sequencing results through quantitative real-time polymerase chain reaction (qPCR). The study focused on P. lilacinum genes that were strongly expressed upon infecting M. incognita eggs. These DEGs were primarily involved in detoxification, parasitic behavior, and nutritional utilization. This study contributes significantly to the understanding of the molecular mechanisms underlying the parasitic action of P. lilacinum on nematode eggs and provides a valuable genetic resource for further research on parasitic behavior of P. lilacinum. Notably, this study examined the transcriptomics of P. lilacinum infecting M. incognita eggs at only one time point. Since there were fungi at different stages of the infection process at that time point, the transcriptional profiles are not precisely examining one specific stage in this process.

Haplotype Diversity of NADPH-Cytochrome P450 Reductase Gene of Ophiocordyceps sinensis and the Effect on Fungal Infection in Host Insects

Ophiocordyceps sinensis Berk. is a fungal parasite that parasitizes the larvae of Hepialidae and is used as a traditional Chinese medicine. However, it is not clear how O. sinensis infects its host. The encoding gene haplotype diversity and predicted function of the nicotinamide adenine dinucleotide phosphate (NADPH)-cytochrome P450 reductase (CPR) related to the fungal pathogenicity was analyzed for 219 individuals from 47 O. sinensis populations. Two NADPH CPR genes of O. sinensis were detected and their dominant haplotypes were widely distributed throughout the entire distribution range in Western China. Only 5.43% of all O. sinensis individuals possessed the specific private haplotypes of NADPH CPR-1 and CPR-2 genes. Bioinformatic analyses predicted that the phosphorylation sites, motifs, and domains of NADPH CPR of O. sinensis were different between those encoding by the dominant and private gene haplotypes. The one-to-one match fungus–host correspondence of the same individual suggested that the widely distributed O. sinensis with the dominant NADPH CPR gene haplotypes may strongly infect almost all host insects through a random infection by oral or respiratory pores. Conversely, O. sinensis with the specific private NADPH CPR gene haplotypes is likely to infect only a few corresponding host insects by breaching the cuticle, due to the changed NADPH CPR structure and function.

Complete mitochondrial genome of the important bio-control fungus Purpureocillium lilacinum (Ophiocordycipitaceae, Hypocreales) and its phylogenetic analysis

Purpureocillium lilacinum is widely used as commercialized bio-control agents for controlling plant parasitic nematodes, as well as other insects and plant pathogens. In this study, the complete mitogenome of P. lilacinum was determined using the next-generation sequencing technology. The mitogenome is a circular molecule of 23,495 bp containing 15 protein-coding genes (PCGs), 2 rRNA (rnl and rns) genes and 22 tRNA genes. The overall base composition is 35.5% A, 36.0% T, 12.9% C and 15.6% G, with a CG content of 28.5%. Phylogenetic analysis inferred from 14 concatenated PCGs of 47 taxa shows that P. lilacinum is clustered with the genus Tolypocladium of Ophiocordycipitaceae and forms a separate clade with strong statistical support. This study contributes to our understanding about sytematics and evolutionary biology of cordycipitoid fungi.

Genome-Wide Identification and Characterization of the Cyclophilin Gene Family in the Nematophagous Fungus Purpureocillium lilacinum

Purpureocillium lilacinum has been widely used as a commercial biocontrol agent for the control of plant parasitic nematodes. Whole genome analysis promotes the identification of functional genes and the exploration of their molecular mechanisms. The Cyclophilin (CYP) gene family belongs to the immunophillin superfamily, and has a conserved cyclophilin-like domain (CLD). CYPs are widely identified in prokaryotes and eukaryotes, and can be divided into single- and multi-domain proteins. In the present study, 10 CYP genes possessing the CLD, named PlCYP1-P10, were identified from the genome of P. lilacinum strain 36-1. Those 10 PlCYPs were predicted to have different cellular localizations in P. lilacinum. Phylogenetic and gene structure analysis revealed the evolutionary differentiation of CYPs between Ascomycotina and Saccharomycotina fungi, but conservation within the Ascomycotina fungi. Motif and gene structure distributions further support the result of phylogenetic analysis. Each PlCYP gene had a specific expression pattern in different development stages of P. lilacinum and its parasitism stage on eggs of Meloidogyne incognita. In addition, the 10 PlCYP genes exhibited different expression abundances in response to abiotic stresses, among which PlCYP4 was highly expressed at a high temperature (35 °C), while PlCYP6 was up-regulated under 5 mM of H₂O₂ stress. Furthermore, the heterologous expression of PlCYP4 and PlCYP6 in Escherichia coli enhanced the cellular tolerance against a high temperature and H₂O₂. In summary, our study indicates the potential functions of PlCYPs in virulence and the stress response, and also provides a frame for further analysis of the CYP gene family in Ascomycotina fungi.

Micromycetes as colonizers of mineral building materials in historic monuments and museums

Complex of microfungi colonizing mineral building materials, i.e. limestone and plaster, in interiors of cultural heritage was characterized. Wide-scale investigation was carried out with fourteen objects studied. We have revealed a specific culturable community. We have analyzed role of obtained microfungi in biodeterioraton process on the basis of our tests (pH and water activity preferences, ability to solubilize CaCO₃) and literature data (substrate preferences and enzyme activities). The species most actively developing in mineral materials in indoor environments were Acremonium charticola, Acremonium furcatum, Lecanicillium sp., Parengyodontium album, Purpureocillium lilacinum and Sarocladium kiliense. Considering this fact and their ability to develop successfully at extremely wide range of pH values from slightly acidic to alkaline ones and their high enzymatic activities we conclude that the listed species are of high interest in seeking the cause of biodeterioration. These species can actively develop in materials penetrating for years deep into the substrates and causing their deterioration in conditions of considerably heightened moisture content. In this group, A. charticola and Lecanicillium sp. were able to solubilize CaCO₃.

The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum

The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and "two-speed" genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.

Variability in Protein Expression in Marine-Derived Purpureocillium lilacinum Subjected to Salt and Chromium Stresses

Abiotic factors can cause substantial limitation of growth of microbes. A combination of salinity stress along with chromium (Cr+6), one of the carcinogen, can pose an immediate threat to any living system. To understand how salinity (0, 35 and 100 PSU) and Cr(VI) stress (0, 100 and 500 ppm), affects cells at the molecular level, the cellular response of Purpureocillium lilacinum to the individual as well the combination of both the stresses were studied by peptide mass fingerprinting technique. The study reports 1412 proteins, of which 105 proteins were found to be present across all conditions. The most prevalent functional class expressed was genetic information processing. Proteins involved in free radical scavenging were up-regulated in response to the oxidative stress generated due to both the applied stresses while expression of metal chelators, transporters systems, indicated towards multiple stress tolerance mechanisms to combat synergistic effects of salt and Cr stress.

Managing the plant microbiome for biocontrol fungi: examples from Hypocreales

Feeding an increasing global population requires continued improvements in agricultural efficiency and productivity. Meeting estimated future production levels requires the adoption of practices that increase output without environmental degradation associated with external inputs to supplement nutrition or control pests. Enriching the community of microbes associated with plants in agricultural systems for those providing ecosystem services such as pest control is one possible component towards achieving sustainable productivity increases. In this review we explore the current state of knowledge for Hypocreales fungi used in biological control. Advances in understanding the field ecology, diversity and genetic determinants of host range and virulence of hypocrealean fungi provide the means to improve their efficacy.

Comparative Transcriptomic Analysis of Virulence Factors in Leptosphaeria maculans during Compatible and Incompatible Interactions with Canola

Leptosphaeria maculans is a hemibiotrophic fungus that causes blackleg of canola (Brassica napus), one of the most devastating diseases of this crop. In the present study, transcriptome profiling of L. maculans was performed in an effort to understand and define the pathogenicity genes that govern both the biotrophic and the necrotrophic phase of the fungus, as well as those that separate a compatible from an incompatible interaction. For this purpose, comparative RNA-seq analyses were performed on L. maculans isolate D5 at four different time points following inoculation on susceptible cultivar Topas-DH16516 or resistant introgression line Topas-Rlm2. Analysis of 1.6 billion Illumina reads readily identified differentially expressed genes that were over represented by candidate secretory effector proteins, CAZymes, and other pathogenicity genes. Comparisons between the compatible and incompatible interactions led to the identification of 28 effector proteins whose chronology and level of expression suggested a role in the establishment and maintenance of biotrophy with the plant. These included all known Avr genes of isolate D5 along with eight newly characterized effectors. In addition, another 15 effector proteins were found to be exclusively expressed during the necrotrophic phase of the fungus, which supports the concept that L. maculans has a separate and distinct arsenal contributing to each phase. As for CAZymes, they were often highly expressed at 3 dpi but with no difference in expression between the compatible and incompatible interactions, indicating that other factors were necessary to determine the outcome of the interaction. However, their significantly higher expression at 11 dpi in the compatible interaction confirmed that they contributed to the necrotrophic phase of the fungus. A notable exception was LysM genes whose high expression was singularly observed on the susceptible host at 7 dpi. In the case of TFs, their higher expression at 7 and 11 dpi on susceptible Topas support an important role in regulating the genes involved in the different pathogenic phases of L. maculans. In conclusion, comparison of the transcriptome of L. maculans during compatible and incompatible interactions has led to the identification of key pathogenicity genes that regulate not only the fate of the interaction but also lifestyle transitions of the fungus.