Biology subjects

Seidl, M. F.

Publications and source records attributed to Seidl, M. F..

At least 19 recordsLinked to original sources

bioRxiv2026

Consolidating species boundaries in the Fusarium oxysporum species complex based on genomic evidence

The Fusarium oxysporum species complex (FOSC) comprises numerous plant pathogens infecting crops such as tomato, lettuce, melon, and banana. Despite its economic and ecological importance and decades of research, the species names linked to different phylogenetic lineages within this species complex remain largely controversial. Earlier taxonomic frameworks relied on a limited number of marker genes, variable taxon sampling and inconsistent species definitions, leading to a fragmented and unstable taxonomy. To address these challenges, we here analysed nearly 2,500 conserved marker genes from 660 genomes, including genome assemblies from 22 ex-type strains that were sequenced using long-read sequencing technology, representing nearly half of the 51 currently described species within FOSC. Maximum likelihood- and coalescence-based analyses of the full phylogenomic data matrix as well as subsets yielded a robust phylogeny of FOSC, which was furthermore corroborated by whole genome comparisons. Many previously described species are redundant, while two novel lineages remain undescribed. Direct comparisons to traditional marker gene-based approaches demonstrate their inadequacy for species delimitation in FOSC. We show that our phylogenomic framework can guide the detection of novel marker genes able to distinguish the major lineages within FOSC, which will be essential for taxon delineation and classification in future studies. Thus, our phylogenomic analyses provide a stable cornerstone for revising FOSC taxonomy and offers a critical resource for the broader research community.

evolutionary biology↗

bioRxiv2026

An expanded urine culturing workflow to cultivate and characterize diverse urobiome isolates

Despite increased recognition of the diverse resident microbiome of the urinary tract (i.e., the urobiome) in postmenopausal women, the roles and functions of these microbes remain largely unknown. Further empirical research is needed to understand the physiology, interactions, and antibiotic resistance evolution of urobiome members with pathogenic potential. However, experimental work relies on viable, culturable isolates. Standard urine culturing practices are designed for identifying a narrow set of known urinary microbes, and are thus poorly suited for cultivating taxa from the resident urobiome. Here we expand the urine culturing toolkit to reliably recover diverse urobiome taxa for downstream empirical research. Urine samples collected from postmenopausal women with recurrent urinary tract infections were shipped at ambient temperature to a central point for culturing. Microbial viability was maintained using boric acid preservative tubes during multi-day transport of sample aliquots. Selective media incubated under specialized conditions were used to promote recovery of diverse urobiome members, including fastidious taxa. Under 5% CO2 -enriched atmospheric conditions and with longer incubation times, we leveraged a chromogenic agar (UTIC) to further differentiate isolates based on colony color and morphology. We evaluated the workflow for its ability to isolate and characterize urobiome taxa, as determined by morphological differentiation and taxonomic identification. Across 108 urine samples, 6.3 {+/-} 3.2 distinct isolates were recovered, with no detectable relationship between sample shipment duration and isolate richness. On chromogenic agar, colony growth and color intensity was improved with CO2 -enriched atmospheric conditions and extended incubation times. We identified diverse taxa that are typically underrepresented in standard diagnostic culture and provide novel morphological characterizations for members of the genera Actinotignum, Aerococcus, Facklamia, Lactobacillus, Latilactobacillus, Limosilactobacillus, and Streptococcus species, which have not been previously described on UTIC chromogenic agar. Using this novel workflow, we recovered a diverse collection of urobiome isolates from urine samples shipped over multiple days. We also demonstrated the utility of a chromogenic agar for the visual differentiation of key urobiome taxa. While sequencing approaches have enhanced our understanding of urobiome composition, culturing is needed to investigate microbial interactions, virulence mechanisms, and antimicrobial susceptibility. This protocol adds to the growing toolkit for the cultivation of diverse urobiome isolates needed to support downstream empirical studies and advance urinary tract infection research.

microbiology↗

bioRxiv2026

Cross-study metagenomics analysis reveals distinct microbial signatures of urinary tract infections

BackgroundUrinary tract infections (UTIs) represent a major public health concern, increasingly complicated by rising antibiotic resistance, diminishing treatment efficacy, and increasing prevalence of recurrence. The urinary tract microbiome (urobiome) remains poorly characterized, despite its potential role in UTIs. ResultsTo provide a comprehensive overview of the urobiome, we here integrated seven publicly available shotgun metagenomics studies, linking microbial composition to clinical infection status or diagnostics. Community-level analyses revealed distinct urobiome clusters, defined by one predominant bacterial taxon. Genome-resolved metagenomics allowed recovery of high-quality metagenome-assembled genomes (MAGs), enabling phylogenetic reconstruction, prediction of pathogenic potential, and profiling of antimicrobial resistance genes across multiple taxa. We then analyzed the pangenome of the clinically significant Escherichia coli species and found that its genomic variation is driven more by phylotype than isolation source or UTI status, supporting a model of opportunistic infection. ConclusionsTaken together, our analyses represent a systematic, cross-study view of the urobiome that emphasizes the ecological complexity of the urobiome and the importance of integrating functional and phylogenetic information when studying UTIs.

microbiology↗

bioRxiv2026

A structurally unique effector shared between Verticillium dahliae and Fusarium oxysporum is involved in cotton defoliation and virulence on other hosts

Defoliating (D) strains of the vascular wilt fungus Verticillium dahliae cause severe yield losses in cotton and olive worldwide, yet the genetic basis underlying this pathotype has remained unknown. Here, we combined comparative genomics, functional genetics, structural analysis, and phylogenomics to uncover the molecular determinant of defoliation. We identified a small, D pathotype-specific genomic region encoding two duplicated secreted effector genes. Simultaneous deletion of both gene copies abolished pathogenicity and defoliation in cotton, olive, Nicotiana benthamiana, and Arabidopsis thaliana, whereas single deletions reduced virulence and genetic complementation restored disease symptoms. Conversely, expression of the D effector in non-defoliating strains was sufficient to induce defoliation. Moreover, or exogenous application of the purified protein, induced wilting and defoliation as well. Structural analyses revealed that D homologs share a conserved but previously uncharacterized protein fold and are distributed across Verticillium and Fusarium species, exhibiting functional diversification and host-specific activity. Phylogenomic and genomic context analyses indicate repeated horizontal transfer events mediated by giant transposable elements known as Starships. Together, our findings identify the D effector as a central pathogenicity factor that drives defoliation and virulence, and demonstrate how Starship-mediated horizontal gene transfer shapes the emergence and dissemination of an agriculturally devastating fungal trait.

plant biology↗

bioRxiv2025

Extensive horizontal transfer of transposable elements shape fungal mobilomes

Transposons impact eukaryotic genome size and evolution. Horizontal transfer of transposons (HTT) is important for their long-term persistence, but has only been systematically studied in animals, and thus the abundance, impact, and factors that shape HTTs in lineages outside animals is unknown. Fungi are at least as ancient and diverse as animals and are characterized by extensive genome size variation caused by transposons. Here, we screened 1,348 genomes across fungal biodiversity, genome sizes, and lifestyles to detect extensive HTTs, that generated on average 7% but up to 70% of the transposon content in some taxa. We in total identified at least 5,518 independent HTTs, mostly involving Tc1/Mariner DNA transposons. While the majority of HTTs occur between closely related taxa, irrespective of their lifestyles, HTTs were particularly common in Mucoromycotina, Sordariomycetes, Dothideomycetes, and Leotiomycetes. Importantly, species lacking fungal-specific defense mechanisms against transposons and those with gene-sparse and repeat-rich genomic compartments are involved in significantly higher number of HTTs, unveiling ecological and genomic factors shaping HTTs. Our findings thus illuminate the dynamic landscape of HTTs in fungi, providing the framework to further study the impact of HTTs on genome evolution and the processes that mediate transposon transfers within and between eukaryotic lineages.

evolutionary biology↗

bioRxiv2025

Evolution of resistance breaking in spinach downy mildew revealed through pangenome graph analysis

BackgroundFilamentous plant pathogens secrete effectors to successfully establish host infections. In resistant crop varieties, plant immunity can be triggered by immune receptors that recognize these effectors. Resistant crop varieties are grown in large-scale monocultures imposing strong selection pressure on pathogens, driving rapid evolution of effector repertoires resulting in the frequent breakdowns of resistance within just a few growing seasons. The oomycete Peronospora effusa, responsible for downy mildew on spinach, is an example of a rapidly adapting pathogen, but it is yet unknown how P. effusa can successfully overcome resistance of spinach by genomic adaptations. ResultsTo close this knowledge gap, we here generated genome assemblies and constructed a pangenome graph for 19 isolates corresponding to 19 officially denominated resistance-breaking P. effusa races, which can cause disease on a differential set of spinach cultivars. Haplotype-resolved pangenome graph analyses revealed that many isolates emerged from recent sexual recombination, yet others evolved via prolonged asexual reproduction and loss of heterozygosity. By phasing effector candidates to determine their allelic variation, we identified effector candidates associated to resistance breaking of spinach varieties and reconstructed the evolutionary events that led to their diversification. ConclusionsThe here developed and applied computational genomics approaches offer unparalleled insights into the molecular mechanisms of the rapid evolution of P. effusa, and points to potential targets for future resistance breading.

genomics↗

bioRxiv2025

Mating Type Gene Divergence is Associated with Life Cycle Differentiation in Scots Pine Blister Rust

Reproductive systems are central to the evolutionary and ecological processes shaping population structure and adaptability. Rust fungi are a large group of obligate plant pathogens with complex life cycles and diverse reproductive modes. In the rust fungus Cronartium pini, which exists in both macrocyclic heteroecious and microcyclic autoecious forms, transitions between reproductive modes can be studied within a single species. Here, we used comparative genomics to analyse the structure, diversity, and organization of mating-type (MAT) loci across both forms of C. pini. We identified a canonical tetrapolar system in the heteroecious form, characterized by unlinked, multiallelic homeodomain (HD) and pheromone/receptor (P/R) loci, consistent with obligate outcrossing. In contrast, the autoecious form displayed distinct reproductive signatures, including MAT gene homozygosity in some samples--indicative of clonal reproduction--and MAT gene duplications in others, suggesting self-fertility or altered mating pathways. Three HD loci were detected, but only one exhibited high allelic diversity and was consistently present, indicating functional divergence. Expanded allelic diversity at the STE3.2 pheromone receptor further suggests plasticity at the P/R locus. Although allele sharing between life cycle forms was rare, isolated cases of shared MAT alleles suggest limited historical connectivity and possible trans-specific polymorphism. Together, our findings reveal flexibility in the mating system architecture of C. pini and suggest that transitions between sexual and asexual reproduction may be facilitated by retained, functionally ambiguous MAT structures. This work highlights C. pini as a powerful model for studying life cycle evolution and mating system transitions in rust fungi.

evolutionary biology↗

bioRxiv2025

From omics to enhanced fungal virulence: Overexpression of a putative secreted protein improves Beauveria bassiana biocontrol potential against the insect pests Piezodorus guildinii and Tenebrio molitor

The entomopathogenic fungus Beauveria bassiana is widely used as a biocontrol agent, but its efficacy varies depending on the target insect species. Piezodorus guildinii, a major soybean pest, exhibits low susceptibility to B. bassiana. Thus, biocontrol of this pest requires improving virulence of B. bassiana. Here, we used genomic and transcriptomic analyses to identify novel genes associated with the enhanced virulence of B. bassiana strain ILB308 when exposed to the insect epicuticular hydrocarbon n-pentadecane. Comparative analysis with the lower-virulence strain ILB205 revealed differentially expressed genes (DEGs) linked to genetic information process pathways and immune evasion. Among these DEGs, we identified BbCBM9_1, a secreted carbohydrate-binding protein, as a candidate virulence factor. Overexpression of BbCBM9_1 in ILB205 led to enhanced virulence against P. guildinii and Tenebrio molitor, as well as improved conidial germination, tolerance to oxidative and cell wall stress, and increased growth in nutrient-rich and glycerol-supplemented media. This demonstrates that the enhanced virulence observed in ILB308 grown on n-pentadecane can be replicated by overexpressing an associated gene in a low-virulence strain. Our study, highlights the potential of integrating transcriptomics and targeted genetic modifications to optimize fungal biocontrol agents for improved pest management.

microbiology↗

bioRxiv2025

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution

Starships form a recently discovered superfamily of giant transposons in Pezizomycotina fungi, implicated in mediating horizontal transfer of diverse cargo genes between fungal genomes. Their elusive nature has long obscured their significance, and their impact on genome evolution remains poorly understood. Here, we reveal a surprising abundance and diversity of Starships in the phytopathogenic fungus Verticillium dahliae. Remarkably, Starships dominate the plastic genomic compartments involved in host colonization, are enriched in virulence-associated genes, and exhibit genetic and epigenetic characteristics associated with adaptive genome evolution. We further uncover extensive horizontal transfer of Starships between Verticillium species and, strikingly, from distantly related Fusarium fungi. Finally, we demonstrate how Starship activity facilitated the de novo formation of a novel virulence gene. Our findings illuminate the profound influence of Starship dynamics on fungal genome evolution and the development of virulence.

microbiology↗

bioRxiv2024

Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen

Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when chromosomes are missing from reference genomes. Pangenome variation graphs offer a reference-free alternative for studying these chromosomes. Here, we constructed a pangenome variation graph for Fusarium oxysporum, a major fungal plant pathogen with a compartmentalized genome. To study accessory chromosomes, we constructed a chromosome similarity network and identified eleven conserved core chromosomes and many highly variable accessory chromosomes. Some of these are host-specific and are likely involved in determining host range, which we corroborate by analyzing nearly 600 F. oxysporum assemblies. By a reconstruction of pangenome variation graph per homologous chromosomes, we show that these evolve due to extensive structural variation as well as the exchange of genetic material between accessory chromosomes giving rise to these mosaic accessory chromosomes. Furthermore, we show that accessory chromosomes are horizontally transferred in natural populations. We demonstrate that pangenome variation graphs are a powerful approach to elucidate the evolutionary dynamics of accessory chromosomes in F. oxysporum and provides a computational framework for similar analyses in other species that encode accessory chromosomes.

genomics↗

bioRxiv2024

Extensive intrachromosomal duplications in a virulence-associated fungal accessory chromosome

Filamentous fungi have evolved compartmentalized genomes consisting of conserved core regions and dynamic accessory regions, which aid the adaptation to changing environments including the interaction with host organisms. In the Fusarium oxysporum species complex, accessory regions play an important role during infection and it has been reported that these regions undergo extensive duplications, however, it is currently unknown how such duplications shape accessory regions. Moreover, the function of accessory regions apart from encoding virulence effectors is not completely understood. Here we determined the karyotype of F. oxysporum Tropical Race 4 (TR4), which causes the ongoing pandemic of Fusarium wilt of banana (FWB). We show that the single accessory chromosome of TR4 isolate II5 has undergone extensive intrachromosomal duplications, resulting in triplication of the chromosome size compared to other closely related TR4 strains. By obtaining mutant strains that have lost the accessory chromosome, we demonstrate that this chromosome is dispensable for vegetative growth but is required for full virulence on banana. Lastly, we found that the loss of chromosome 12 co-occurs with structural rearrangements of core chromosomes, which are generally co-linear between members of the F. oxysporum species complex. Together, our results provide new insights into the chromosome dynamics of the banana infecting TR4 lineage of the F. oxysporum species complex. SignificanceFusarium oxysporum is a major fungal plant pathogen that causes vascular wilt disease on a wide variety of agronomically important crops. A current epidemic of Fusarium wilt of banana (FWB), caused by tropical race 4 (TR4), poses a major threat to global banana production and threatens food security in tropical and subtropical regions where banana is an important staple crop. Controlling TR4 requires a better understanding of the molecular mechanisms underlying pathogenicity, including the evolution of pathogenicity-related accessory regions. Here we demonstrate that intrachromosomal duplications are a key mechanism of accessory chromosome evolution in the F. oxysporum species complex. We identified a single accessory chromosome and show that TR4 mutants that lost this accessory chromosome display significantly reduced virulence on banana plants. Our results provide insight into the evolution of accessory chromosomes in the F. oxysporum species complex, underscore their importance in pathogenicity, and provide new clues for the development of resistant banana plants.

microbiology↗

bioRxiv2024

Frequent genetic exchange shapes the pan-mitogenome of the fungal plant pathogen Fusarium oxysporum

Mitochondria are present in almost all eukaryotic lineages. The mitochondrial genomes (mitogenomes) evolve separately from nuclear genomes, and they can therefore provide relevant insights into the evolution of their host species. Fusarium oxysporum is a major fungal plant pathogen that is assumed to reproduce clonally. However, horizontal chromosome transfer between strains can occur through heterokaryon formation, and recently signs of sexual recombination have been observed. Similarly, signs of recombination in F. oxysporum mitogenomes challenged the prevailing assumption of clonal reproduction in this species. Here, we construct, to our knowledge, the first fungal pan-mitogenome graph of nearly 500 F. oxysporum mitogenome assemblies to uncover the variation and evolution. In general, the gene order of fungal mitogenomes is not well conserved, yet the mitogenome of F. oxysporum and related species are highly co-linear. We observed two strikingly contrasting regions in the Fusarium oxysporum pan-mitogenome, comprising a highly conserved core mitogenome and a long variable region (6-16 kb in size), of which we identified three distinct types. The pan-mitogenome graph reveals that only five intron insertions occurred in the core mitogenome and that the long variable regions drive the difference between mitogenomes. Moreover, we observed that their evolution is neither concurrent with the core mitogenome nor with the nuclear genome. Our large-scale analysis of long variable regions uncovers frequent recombination between mitogenomes, even between strains that belong to different taxonomic clades. This challenges the common assumption of incompatibility between genetically diverse F. oxysporum strains and provides new insights into the evolution of this fungal species. Importance statementInsights into plant pathogen evolution is essential for the understanding and management of disease. Fusarium oxysporum is a major fungal pathogen that can infect many economically important crops. Pathogenicity can be transferred between strains by the horizontal transfer of pathogenicity chromosomes. The fungus has been thought to evolve clonally, yet recent evidence suggests active sexual recombination between related isolates, which could at least partially explain the horizontal transfer of pathogenicity chromosomes. By constructing a pan-genome graph of nearly 500 mitochondrial genomes, we describe the genetic variation of mitochondria in unprecedented detail and demonstrate frequent mitochondrial recombination. Importantly, recombination can occur between genetically diverse isolates from distinct taxonomic clades and thus can shed light on genetic exchange between fungal strains.

genomics↗

bioRxiv2024

Novel genomic features in entomopathogenic fungus Beauveria bassiana: supernumerary chromosomes and putative virulence genes involved in the infection process of soybean pest Piezodorus guildinii.

Biological control methods involving entomopathogenic fungi like Beauveria bassiana have shown to be a valuable approach in integrated pest management as an environmentally friendly alternative to control pests and pathogens. Identifying genetic determinants of pathogenicity in B. bassiana is instrumental for enhancing its virulence against insects like the resistant soybean pest Piezodorus guildinii. This study focused on comparative genomics of different B. bassiana strains and gene expression analyses to identify virulence genes in the hypervirulent strain ILB308, especially in response to infection of P. guildniii and growth on hydrocarbon HC15, a known virulence enhancer. Strain ILB308 showed the highest number of virulence-related features, such as candidate virulence proteins, effectors, small secreted proteins, and biosynthetic gene clusters. ILB308 also had a high percentage of unique DNA sequences, including six putative supernumerary scaffolds. Gene expression analysis at 4 days post-inoculation revealed upregulation of known virulence factors, including Tudor domain proteins, LysM motif-containing proteins, and subtilisin-like proteases, and novel genes like secreted effectors and heat-labile enterotoxins. Growth on HC15 led to the upregulation of genes associated with oxidoreductase activity related to cuticular alkane degradation and fermentation metabolism/antioxidant responses in the hemolymph. The presence of supernumerary chromosomes and unique virulence genes in ILB308 may contribute to its higher virulence and could be considered as potential targets for enhancing fungal virulence through genetic manipulation. Author SummaryUnderstanding mechanisms of virulence and virulence enhancement in Beauveria bassiana can lay the basis for the development of improved biocontrol agents. Here we used genomic and transcriptomic approaches to study the infection process of ILB308 -an hypervirulent strain- against insect pest Piezodorus guildinii. We found that this strain has putative supernumerary chromosomes and an enriched set of presumed virulence proteins like secreted effectors. We infer that the particular assortment of strain specific genes and supernumerary chromosome/s play a role in the degree of virulence exhibited by ILB308 and could be used for future strain improvement strategies.

genomics↗

bioRxiv2024

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage and expand on an innovative, multi-genome method to construct, annotate, and analyse the first pangenome graph of an oomycete plant pathogen. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, pathogenicity related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens. Author SummaryPlant pathogens are known to evolve rapidly and overcome disease resistance of newly introduced crop varieties. This swift adaptation is visible in the genomes of these pathogens, which can be highly variable. Such genomic variation cannot be captured with contemporary comparative genomic methods that rely on a single reference genome or focus solely on protein coding genes. To overcome these limitations and compare multiple genomes in a robust and scalable method, we constructed the first pangenome graph for an oomycete filamentous plant pathogen with six telomere-to-telomere genome assemblies of Peronospora effusa. This high-resolution pangenomic framework enabled detailed comparisons of the genomes at any level, from the nucleotide to the chromosome, and for any subset of protein-coding genes or transposable elements, to discover novel biology and potential mechanisms for the rapid evolution of this devastating pathogen.

genomics↗

bioRxiv2024

Secondary metabolite biosynthetic gene clusters and their genomic localization in the fungal genus Aspergillus

Fungi are well-known producers of bioactive secondary metabolites (SMs), which have been exploited for decades by humankind for various medical applications like therapeutics and antibiotics. SMs are synthesized by biosynthetic gene clusters (BGCs) - physically co-localized and co-regulated genes. Because BGCs are often regulated by histone post-translational modifications (PTMs), it was suggested that their chromosomal location is important for their expression. Studies in a few fungal species indicated an enrichment of BGCs in sub-telomeric regions; however, there is no evidence that BGCs with distinct genomic localization are regulated by different histone PTMs. Here, we used 174 Aspergillus species covering 22 sections to determine the correlation between BGC genomic localization, gene expression and histone PTMs. We found a high abundance and diversity of SM backbone genes across the Aspergillus genus, with notable unique genes within sections. Being unique or conserved in many species, BGCs showed a strong bias for being localized in low-synteny regions, regardless of their position in chromosomes. Using chromosome-level assemblies, we also confirmed a significantly biased localization in sub-telomeric regions. Notably, SM backbone genes in sub-telomeric regions and about half of those in low-synteny regions exhibit higher gene expression variability, likely due to the similar higher variability in H3K4me3 and H3K36me3 histone PTMs; while variations in histone H3 acetylation and H3K9me3 are not correlated to genomic localization and expression variation, as analyzed in two Aspergillus species. Expression variability across four Aspergillus species further supports that BGCs tend to be located in low-synteny regions and that regulation of expression in those regions likely involves different histone PTMs than the most commonly studied modifications. SignificanceFungi are known for producing an array of bioactive compounds with medical benefits, yet our understanding of how the production of these compounds is regulated remains limited. Here, we focused on the fungal genus Aspergillus, containing many species known to be prolific producers of bioactive compounds, to systematically uncover the diversity and genomic localization of biosynthetic pathways. By expanding our knowledge beyond the few commonly studied fungal species, this research offers novel insights into how the genomic localization of biosynthetic pathways matters for the regulation of their expression. Thanks to a new view on BGC localization and expression in relation to histone modifications, our results are expected to stimulate functional research on neglected histone modifications that will support the discovery and harnessing of new fungal metabolites for medical and industrial applications.

bioinformatics↗

bioRxiv2023

A deep genetic analysis of banana Fusarium wilt pathogens of Cuba in a Latin American and Caribbean diversity landscape

O_LIFusarium wilt of bananas (FWB) is a devastating plant disease that causes significant economic losses in banana production worldwide and is one of the major concerns for Cuban banana cultivation. The disease is caused by members of the soil-borne Fusarium oxysporum species complex. However, the genetic diversity among Fusarium species infecting bananas in Cuba is currently unknown. C_LIO_LIWe conducted a comprehensive survey of symptomatic banana plants across all production zones of the country and assembled a collection of 170 Fusarium isolates. Using genotyping- by-sequencing and whole-genome comparisons, we investigated the genetic diversity across this suite of isolates and compared it with the genetic diversity of a global Fusarium panel. C_LIO_LITypical FWB symptoms were observed in varieties of the Bluggoe cooking banana and Pisang Awak subgroups in 14 provinces. Phylogenetic analysis revealed that F. purpurascens, F. phialophorum, and F. tardichlamydosporum cause FWB in Cuba, with the latter dominating the population. Furthermore, we identified between five and seven genetic clusters, with F. tardichlamydosporum isolates divided into at least two distinct subgroups, indicating a high genetic diversity of Fusarium spp. causing FWB in the Americas. C_LIO_LIOur study provides unprecedented insights into the population genetic structure and diversity of the FWB pathogen in Cuba and the Latin American and Caribbean regions. C_LI

microbiology↗

bioRxiv2023

A chromosome-level genome assembly of Zasmidium syzygii isolated from banana leaves

Accurate taxonomic classification of samples from infected host material is essential for disease diagnostics and genome analyses. Despite the importance, diagnosis of fungal pathogens causing banana leaf diseases remains challenging. Foliar diseases of bananas are mainly caused by three Pseudocercospora species, of which the most predominant causal agent is P. fijiensis. Here, we sequenced and assembled four fungal isolates obtained from necrotic banana leaves in Bohol (Philippines) and obtained a high-quality genome assembly for one of these isolates. The samples were initially identified as P. fijiensis using PCR diagnostics, however, the assembly size was consistently 30 Mb smaller than expected. Based on the ITS sequences, we identified the samples as Zasmidium syzygii (98.7% identity). The high-quality Zasmidium syzygii assembly is 42.5 Mb in size, comprising 16 contigs, of which 11 are complete. The genome contains 98.6% of the expected single-copy BUSCO genes and contains 14,789 genes and 10.3% repeats. The three short-read assemblies are less continuous but have similar genome sizes (40.4 - 42.4 Mb) and contain between 96.5% and 98.4% BUSCO genes. All four isolates have identical ITS sequences and are distinct from Zasmidium isolates that were previously sampled from banana leaves. We thus report the first continuous genome assembly of a member of the Zasmidium genus, forming an essential resource for further analysis to enhance our understanding of the diversity of pathogenic fungal isolates as well as fungal diversity.

microbiology↗

bioRxiv2023

Receptor-like cytoplasmic kinases belonging to different subfamilies mediate immune responses downstream of the Cf-4 resistance protein in Nicotiana benthamiana

Cell-surface receptors, which are either receptor-like proteins (RLPs) or receptor-like kinases (RLKs), form the first layer of the plant innate immune system. The LRR-RLKs SUPPRESSOR OF BIR1-1 (SOBIR1) and BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) are the common regulatory co-receptors of LRR-RLPs. The tomato LRR-RLP Cf-4, which specifically detects the apoplastic effector Avr4 that is secreted by the pathogenic intercellular fungus Cladosporium fulvum, requires SOBIR1 and BAK1 to mediate resistance against this fungus. It is proposed that phosphorylation events take place between the cytoplasmic kinase domains of SOBIR1 and BAK1, which lead to the initiation of various downstream signaling outputs such as the rapid phosphorylation of receptor-like cytoplasmic kinases (RLCKs), the accumulation of reactive oxygen species (ROS), the activation of mitogen-activated protein kinase (MAPK) cascades, and in some cases, the hypersensitive response (HR). Here, by performing in vitro phosphorylation assays, we show that SOBIR1 directly phosphorylates BAK1, whereas BAK1, in its turn, directly phosphorylates SOBIR1, which results in the full activation of the Cf-4-containing immune complex. We found that threonine 522, present in the activation segment of the SOBIR1 kinase domain of Nicotiana benthamiana (Nb), is required for its intrinsic kinase activity, and is essential for the Avr4/Cf-4/SOBIR1/BAK1-triggered ROS burst, MAPK activation and the HR. Tyrosine residue Y469 was found to be crucial for the Avr4/Cf-4- triggered activation of MAPKs and the HR, but not for ROS production and NbSOBIR1 intrinsic kinase activity. RLCKs are well-recognized to act as the initial cytoplasmic transducers, bridging cell-surface receptor complexes with their downstream signaling partners. By knocking out multiple genes belonging to different RLCK-VII subfamilies in N. benthamiana plants stably expressing Cf-4, we show that members of the RLCK-VII subfamilies 6, 7 and 8 are required for the Avr4/Cf-4-triggered ROS production. Typically, the Avr4 protein triggers a biphasic ROS burst in leaf discs obtained from N. benthamiana:Cf-4 plants, in which the first transitory response is followed by a second, sustained ROS burst. Interestingly, the intensities of the first and second phase of the ROS burst are affected in different ways in the various rlck-vii knock-out plants, indicating that there are different downstream ROS regulatory mechanisms, involving different RLCKs in N. benthamiana. Further studies show that members from RLCK-VII-6, 7 and 8 also play an essential role in regulating the ROS production triggered by flg22, chitin, and the nlp20/RLP23 and the pg13/RLP42 combinations.

plant biology↗