Accessory Chromosomes in Fusarium oxysporum

Pangenomics of flax fungal parasite Fusarium oxysporum f. sp. lini

To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.

The differential virulence of Fusarium strains causing corneal infections and plant diseases is associated with accessory chromosome composition

Fusarium oxysporum is a cross-kingdom pathogen. While some strains cause disseminated fusariosis and blinding corneal infections in humans, others are responsible for devastating vascular wilt diseases in plants. To better understand the distinct adaptations of F. oxysporum to animal or plant hosts, we conducted a comparative phenotypic and genetic analysis of two strains: MRL8996 (isolated from a keratitis patient) and Fol4287 (isolated from a wilted tomato [Solanum lycopersicum]). In vivo infection of mouse corneas and tomato plants revealed that, while both strains cause symptoms in both hosts, MRL8996 caused more severe corneal ulceration and perforation in mice, whereas Fol4287 induced more pronounced wilting symptoms in tomato. In vitro assays using abiotic stress treatments revealed that the human pathogen MRL8996 was better adapted to elevated temperatures, whereas the plant pathogen Fol4287 was more tolerant of osmotic and cell wall stresses. Both strains displayed broad resistance to antifungal treatment, with MRL8996 exhibiting the paradoxical effect of increased tolerance to higher concentrations of the antifungal caspofungin. We identified a set of accessory chromosomes (ACs) and protein-encoding genes with distinct transposon profiles and functions, respectively, between MRL8996 and Fol4287. Interestingly, ACs from both genomes also encode proteins with shared functions, such as chromatin remodeling and post-translational protein modifications. Our phenotypic assays and comparative genomics analyses lay the foundation for future studies correlating genotype with phenotype and for developing targeted antifungals for agricultural and clinical uses.

Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

The fungal pathogen, Magnaporthe oryzae Triticum pathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzae strains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole-genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini-chromosome. Genome assembly of a Zambian strain revealed that its mini-chromosome was similar to the B71 mini-chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini-chromosomes have undergone marked diversification. The maintenance of the mini-chromosome and rapid genomic changes suggest the mini-chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.

Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte

Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a ∼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.

Meiosis in an asymmetric dikaryotic genome of Tremella fuciformis Tr01 facilitates new chromosome formation

BACKGROUND

The dikaryotic stage dominates most of the life cycle in basidiomycetes, and each cell carries two different haploid nuclei. Accurate phasing of these two nuclear genomes and their interactions have long been of interest.

RESULTS

We combine PacBio HiFi reads, Nanopore ultra-long reads, and Hi-C data to generate a complete, high-quality asymmetric dikaryotic genome of Tremella fuciformis Tr01, including Haplotypes A and B genomes. We assemble a meiotic haploid DBZ04 genome and detect three recombination events in these two haplotypes. We identify several chromosomal rearrangements that lead to differences in chromosome number, length, content, and sequence arrangement between these two haplotypes. Each nucleus contains a two-speed genome, harboring three accessory chromosomes and two accessory compartments that affect horizontal chromatin transfer between nuclei. We find few basidiospores are ejected from fruiting bodies of Tr01. Most monospore isolates sequenced belong to Tr01-Haplotype A genome architecture. More than one-third of monospore isolates carry one or two extra chromosomes including Chr12B and two new chromosomes ChrN1 and ChrN2. We hypothesize that homologous regions of seven sister chromatids pair into a large complex during meiosis, followed by inter-chromosomal recombination at physical contact sites and formation of new chromosomes.

CONCLUSION

We assemble two haplotype genomes of T. fuciformis Tr01 and provide the first overview of basidiomycetous genomes with discrete genomic architecture. Meiotic activities of asymmetric dikaryotic genomes result in formation of new chromosomes, aneuploidy of some daughter cells, and inviability of most other daughter cells. We propose a new approach for breeding of sporeless mushroom.

Accessory genes in tropical race 4 contributed to the recent resurgence of the devastating disease of Fusarium wilt of banana

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most damaging plant diseases recorded. Foc race 1 (R1) decimated the Gros Michel-based banana trade. Currently, tropical race 4 (TR4) is threatening the global production of its replacement cultivar, Cavendish banana. Population genomics and phylogenetics revealed that all Cavendish banana-infecting race 4 strains shared an evolutionary origin that is distinct from R1 strains. The TR4 genome lacks accessory or pathogenicity chromosomes, reported in other F. oxysporum genomes. Accessory genes-enriched for virulence and mitochondrial-related functions-are attached to ends of some core chromosomes. Meta-transcriptomics revealed the unique induction of the entire mitochondria-localized nitric oxide (NO) biosynthesis pathway upon TR4 infection. Empirically, we confirmed the unique induction of NO burst in TR4,suggesting the involvement of nitrosative pressure in its virulence. Targeted mutagenesis demonstrated the functional importance of accessory genes SIX1 and SIX4 as virulent factors.

Establishment of a CRISPR/Cas9-Mediated Efficient Knockout System of Trichoderma hamatum T21 and Pigment Synthesis PKS Gene Knockout

Trichoderma hamatum is a filamentous fungus that serves as a biological control agent for multiple phytopathogens and as an important resource promising for fungicides. However, the lack of adequate knockout technologies has hindered gene function and biocontrol mechanism research of this species. This study obtained a genome assembly of T. hamatum T21, with a 41.4 Mb genome sequence comprising 8170 genes. Based on genomic information, we established a CRISPR/Cas9 system with dual sgRNAs targets and dual screening markers. CRISPR/Cas9 plasmid and donor DNA recombinant plasmid were constructed for disruption of the Thpyr4 and Thpks1 genes. The result indicates the consistency between phenotypic characterization and molecular identification of the knockout strains. The knockout efficiencies of Thpyr4 and Thpks1 were 100% and 89.1%, respectively. Moreover, sequencing revealed fragment deletions between dual sgRNA target sites or GFP gene insertions presented in knockout strains. The situations were caused by different DNA repair mechanisms, nonhomologous end joining (NHEJ), and homologous recombination (HR). Overall, we have successfully constructed an efficient and convenient CRISPR/Cas9 system in T. hamatum for the first time, which has important scientific significance and application value for studies on functional genomics of Trichoderma and other filamentous fungi.

Immunity to pathogenic fungi in the eye

Fusarium, Aspergillus and Candida are important fungal pathogens that cause visual impairment and blindness in the USA and worldwide. This review will summarize the epidemiology and clinical features of corneal infections and discuss the immune and inflammatory responses that play an important role in clinical disease. In addition, we describe fungal virulence factors that are required for survival in infected corneas, and the activities of neutrophils in fungal killing, tissue damage and cytokine production.

Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

Colletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site-associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I-IV). The strong population structure and high overall standardized index of association (r̅_d ) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host-pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.

Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex

The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.

The Role of the Fusarium oxysporum FTF2 Transcription Factor in Host Colonization and Virulence in Common Bean Plants (Phaseolus vulgaris L.)

The FTF (Fusarium Transcription Factor) gene family is composed of two members (FTF1 and FTF2) with high-sequence homology that encode transcription factors involved in the modulation of virulence in the F. oxysporum species complex (FOSC). While FTF1 is a multicopy gene exclusive of highly virulent strains of FOSC and is located in the accessory genome, FTF2 is a single-copy gene, located in the core genome, and well-conserved in all filamentous ascomycete fungi, except yeast. The involvement of FTF1 in the colonization of the vascular system and regulation of the expression of SIX effectors has been stablished. To address the role of FTF2, we generated and characterized mutants defective in FTF2 in a F. oxysporum f. sp. phaseoli weakly virulent strain and analyzed them together with the equivalent mutants formerly obtained in a highly virulent strain. The results obtained highlight a role for FTF2 as a negative regulator of the production of macroconidia and demonstrate that it is required for full virulence and the positive regulation of SIX effectors. In addition, gene expression analyses provided compelling evidence that FTF2 is involved in the regulation of hydrophobins likely required for plant colonization.

Palmitoyl Transferase FonPAT2-Catalyzed Palmitoylation of the FonAP-2 Complex Is Essential for Growth, Development, Stress Response, and Virulence in Fusarium oxysporum f. sp. niveum

Protein palmitoylation, one of posttranslational modifications, is catalyzed by a group of palmitoyl transferases (PATs) and plays critical roles in the regulation of protein functions. However, little is known about the function and mechanism of PATs in plant pathogenic fungi. The present study reports the function and molecular mechanism of FonPATs in Fusarium oxysporum f. sp. niveum (Fon), the causal agent of watermelon Fusarium wilt. The Fon genome contains six FonPAT genes with distinct functions in vegetative growth, conidiation and conidial morphology, and stress response. FonPAT1, FonPAT2, and FonPAT4 have PAT activity and are required for Fon virulence on watermelon mainly through regulating in planta fungal growth within host plants. Comparative proteomics analysis identified a set of proteins that were palmitoylated by FonPAT2, and some of them are previously reported pathogenicity-related proteins in fungi. The FonAP-2 complex core subunits FonAP-2α, FonAP-2β, and FonAP-2μ were palmitoylated by FonPAT2 in vivo. FonPAT2-catalyzed palmitoylation contributed to the stability and interaction ability of the core subunits to ensure the formation of the FonAP-2 complex, which is essential for vegetative growth, asexual reproduction, cell wall integrity, and virulence in Fon. These findings demonstrate that FonPAT1, FonPAT2, and FonPAT4 play important roles in Fon virulence and that FonPAT2-catalyzed palmitoylation of the FonAP-2 complex is critical to Fon virulence, providing novel insights into the importance of protein palmitoylation in the virulence of plant fungal pathogens. IMPORTANCE Fusarium oxysporum f. sp. niveum (Fon), the causal agent of watermelon Fusarium wilt, is one of the most serious threats for the sustainable development of the watermelon industry worldwide. However, little is known about the underlying molecular mechanism of pathogenicity in Fon. Here, we found that the palmitoyl transferase (FonPAT) genes play distinct and diverse roles in basic biological processes and stress response and demonstrated that FonPAT1, FonPAT2, and FonPAT4 have PAT activity and are required for virulence in Fon. We also found that FonPAT2 palmitoylates the core subunits of the FonAP-2 complex to maintain the stability and the formation of the FonAP-2 complex, which is essential for basic biological processes, stress response, and virulence in Fon. Our study provides new insights into the understanding of the molecular mechanism involved in Fon virulence and will be helpful in the development of novel strategies for disease management.

The Genome of Fusarium oxysporum f. sp. phaseoli Provides Insight into the Evolution of Genomes and Effectors of Fusarium oxysporum Species

Fusarium oxysporum f. sp. phaseoli, the causal agent of cowpea fusarium wilt, is a serious threat to cowpea production in China. In this study, a sample of cowpea fusarium wilt was identified as Fusarium oxysporum f. sp. phaseoli using the methods of morphological characters and molecular detection. We further reported the first genome assembly for Fusarium oxysporum f. sp. phaseoli, with 53.7 Mb genome sequence comprising 14,694 genes. Comparative genomic analysis among five Fusarium oxysporum genomes showed that four accessory chromosomes in the five Fusarium oxysporum display similar characteristics, with low sequence similarity (55.35%, vs. overall average of 81.76%), low gene density (2.18 genes/10 kb vs. 3.02 genes/Mb) and highly transposable element density (TEs) (15.01/100 kb vs. 4.89/100 kb), indicating that variable accessory chromosomes are the main source of Fusarium oxysporum evolution. We identified a total of 100 Fusarium oxysporum f. sp. phaseoli-specific effectors in the genome and found 13 specific effector genes located in large insertion or deletion regions, suggesting that insertion or deletion events can cause the emergence of species-specific effectors in Fusarium oxysporum. Our genome assembly of Fusarium oxysporum f. sp. phaseoli provides a valuable resource for the study of cowpea fusarium wilt, and the comparative genomic study of Fusarium oxysporum could contribute to the knowledge of genome and effector-associated pathogenicity evolution in Fusarium oxysporum study.

Comprehending the dynamism of B chromosomes in their journey towards becoming unselfish

Investigated for more than a century now, B chromosomes (Bs) research has come a long way from Bs being considered parasitic or neutral to becoming unselfish and bringing benefits to their hosts. B chromosomes exist as accessory chromosomes along with the standard A chromosomes (As) across eukaryotic taxa. Represented singly or in multiple copies, B chromosomes are largely heterochromatic but also contain euchromatic and organellar segments. Although B chromosomes are derived entities, they follow their species-specific evolutionary pattern. B chromosomes fail to pair with the standard chromosomes during meiosis and vary in their number, size, composition and structure across taxa and ensure their successful transmission through non-mendelian mechanisms like mitotic, pre-meiotic, meiotic or post-meiotic drives, unique non-disjunction, self-pairing or even imparting benefits to the host when they lack drive. B chromosomes have been associated with cellular processes like sex determination, pathogenicity, resistance to pathogens, phenotypic effects, and differential gene expression. With the advancements in B-omics research, novel insights have been gleaned on their functions, some of which have been associated with the regulation of gene expression of A chromosomes through increased expression of miRNAs or differential expression of transposable elements located on them. The next-generation sequencing and emerging technologies will further likely unravel the cellular, molecular and functional behaviour of these enigmatic entities. Amidst the extensive fluidity shown by B chromosomes in their structural and functional attributes, we perceive that the existence and survival of B chromosomes in the populations most likely seem to be a trade-off between the drive efficiency and adaptive significance versus their adverse effects on reproduction.

Differential Colonization of the Plant Vasculature Between Endophytic Versus Pathogenic Fusarium oxysporum Strains

Plant xylem colonization is the hallmark of vascular wilt diseases caused by phytopathogens within the Fusarium oxysporum species complex. Recently, xylem colonization has also been reported among endophytic F. oxysporum strains, resulting in some uncertainty. This study compares xylem colonization processes by pathogenic versus endophytic strains in Arabidopsis thaliana and Solanum lycopersicum, using Arabidopsis pathogen Fo5176, tomato pathogen Fol4287, and the endophyte Fo47, which can colonize both plant hosts. We observed that all strains were able to advance from epidermis to endodermis within 3 days postinoculation (dpi) and reached the root xylem at 4 dpi. However, this shared progression was restricted to lateral roots and the elongation zone of the primary root. Only pathogens reached the xylem above the primary-root maturation zone (PMZ). Related to the distinct colonization patterns, we also observed stronger induction of callose at the PMZ and lignin deposition at primary-lateral root junctions by the endophyte in both plants. This observation was further supported by stronger induction of Arabidopsis genes involved in callose and lignin biosynthesis during the endophytic colonization (Fo47) compared with the pathogenic interaction (Fo5176). Moreover, both pathogens encode more plant cell wall-degrading enzymes than the endophyte Fo47. Therefore, observed differences in callose and lignin deposition could be the combination of host production and the subsequent fungal degradation. In summary, this study demonstrates spatial differences between endophytic and pathogenic colonization, strongly suggesting that further investigations of molecular arm-races are needed to understand how plants differentiate friend from foe. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Background

The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host.

Results

Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain.

Conclusions

The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01436-7.

Genetic Diversity and Population Structure of Fusarium oxysporum f. sp. conglutinans Race 1 in Northern China Samples

Fusarium oxysporum f. sp. conglutinans (FOC), the causal agent of cabbage fusarium wilt, is a serious threat to cabbage production in northern China, and most Chinese FOC isolates were identified as FOC race 1 (FOC1). To better understand the genetic diversity of FOC1 in northern China, we collected FOC isolates from five provinces in northern China and identified them as FOC1 through pathogenicity and race test. To evaluate the genome-level diversity of FOC1, we performed a genome assembly for a FOC1 isolate (FoYQ-1) collected from Yanqing, Beijing, where cabbage fusarium wilt was first reported in China. Using resequencing data of FOC1 isolates, we conducted a genome-wide SNP (single nucleotide polymorphism) analysis to investigate the genetic diversity and population structure of FOC1 isolates in northern China. Our study indicated that Chinese FOC1 can be grouped into four populations and revealed that the genetic diversity of FOC1 were closely associated with geographical locations. Our study further suggests that genetic differentiation occurred when FOC1 spread to the northwest provinces from Beijing Province in China. The FOC1 genetic diversity based on whole-genome SNPs could deepen our understanding of FOC1 variation and provide clues for the control of cabbage fusarium wilt in China.

Genome editing using a versatile vector-based CRISPR/Cas9 system in Fusarium species

Fusarium species include important filamentous fungal pathogens that can infect plants, animals, and humans. Meanwhile, some nonpathogenic Fusarium species are promising biocontrol agents against plant pathogens. Here, we developed a genome editing technology using a vector-based CRISPR/Cas9 system for Fusarium oxysporum f. sp. lycopersici (Fol). This optimized CRISPR/Cas9 system, harboring an endogenous U6 small nuclear RNA promoter for the expression of single-guide RNA and an endogenous H2B nuclear localization signal for the localization of Cas9, enabled efficient targeted gene knock-out, including in the accessory chromosomal regions in Fol. We further demonstrated single crossover-mediated targeted base editing and endogenous gene tagging. This system was also applicable for genome editing in F. oxysporum f. sp. spinaciae and F. commune without any modifications, suggesting that this CRISPR/Cas9 vector has a potential application for a broad range of researches on other Fusarium species.

The Emergence of Fusarium oxysporum f. sp. apii Race 4 and Fusarium oxysporum f. sp. coriandrii Highlights Major Obstacles Facing Agricultural Production in Coastal California in a Warming Climate: A Case Study

Currently, Fusarium oxysporum f. sp. apii (Foa) race 4 in celery and F. oxysporum f. sp. coriandrii (Foci) in coriander have the characteristics of emerging infectious plant diseases in coastal southern California: the pathogens are spreading, yield losses can be severe, and there are currently no economical solutions for their control. Celery, and possibly coriander, production in these regions is are likely to have more severe disease from projected warmer conditions in the historically cool, coastal regions. Experimental evidence shows that Foa race 4 causes much higher disease severity when temperatures exceed 21°C. A phylogenomic analysis indicated that Foa race 4, an older, less virulent, and uncommon Foa race 3, and two Foci are closely related in their conserved genomes. These closely related genotypes are somatically compatible. Foa race 4 can also cause disease in coriander and the two organisms readily form "hetero" conidial anastomosis tubes (CAT), further increasing the likelihood of parasexual recombination and the generation of novel pathotypes. A horizontal chromosome transfer event likely accounts for the difference in host range between Foci versus Foa races 4 and 3 because they differ primarily in one or two accessory chromosomes. How Foa race 4 evolved its hyper-virulence is unknown. Although the accessory chromosomes of Foa races 3 and 4 are highly similar, there is no evidence that Foa race 4 evolved directly from race 3, and races 3 and 4 probably only have a common ancestor. Foa race 2, which is in a different clade within the Fusarium oxysporum species complex (FOSC) than the other Foa, did not contribute to the evolution of race 4, and does not form CATs with Foa race 4; consequently, while inter-isolate CAT formation is genetically less restrictive than somatic compatibility, it might be more restricted between FOSC clades than currently known. Other relatively new F. oxysporum in coastal California include F. oxysporum f. sp. fragariae on strawberry (Fof). Curiously, Fof "yellows-fragariae" isolates also have similar core genomes to Foa races 4 and 3 and Foci, perhaps suggesting that there may be core genome factors in this lineage that favor establishment in these soils.

Determinants of endophytic and pathogenic lifestyle in root colonizing fungi

Plant-fungal interactions in the soil crucially impact crop productivity and can range from highly beneficial to detrimental. Accumulating evidence suggests that some root-colonizing fungi shift between endophytic and pathogenic behaviour depending on the host species and that combinations of effector proteins collectively shape the fungal lifestyle on a given plant. In this review we discuss recent advances in our understanding of how fungal infection strategies on roots can lead to contrasting outcomes for the host. We highlight functional similarities and differences in compatibility determinants that control the colonization of specific-cell layers within plant roots, ultimately shaping the continuum between endophytic and pathogenic lifestyle.

Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager's activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome

Cladosporium fulvum is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of C. fulvum. The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of C. fulvum, indicating that Chr14 is dispensable. Thus, C. fulvum is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of C. fulvum Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the C. fulvum Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in C. fulvum Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the 'two-speed genome' model of evolution. Overall, the new reference genome of C. fulvum presents several notable features and is a valuable resource for studies in plant pathogens.

Evolution of B Chromosomes: From Dispensable Parasitic Chromosomes to Essential Genomic Players

B chromosomes represent additional chromosomes found in many eukaryotic organisms. Their origin is not completely understood but recent genomic studies suggest that they mostly arise through rearrangements and duplications from standard chromosomes. They can occur in single or multiple copies in a cell and are usually present only in a subset of individuals in the population. Because B chromosomes frequently show unstable inheritance, their maintenance in a population is often associated with meiotic drive or other mechanisms that increase the probability of their transmission to the next generation. For all these reasons, B chromosomes have been commonly considered to be nonessential, selfish, parasitic elements. Although it was originally believed that B chromosomes had little or no effect on an organism's biology and fitness, a growing number of studies have shown that B chromosomes can play a significant role in processes such as sex determination, pathogenicity and resistance to pathogens. In some cases, B chromosomes became an essential part of the genome, turning into new sex chromosomes or germline-restricted chromosomes with important roles in the organism's fertility. Here, we review such cases of "cellular domestication" of B chromosomes and show that B chromosomes can be important genomic players with significant evolutionary impact.

Metatranscriptomic Comparison of Endophytic and Pathogenic Fusarium-Arabidopsis Interactions Reveals Plant Transcriptional Plasticity

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two F. oxysporum strains share a core genome of about 46 Mb, in addition to 1,229 and 5,415 unique accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (about 80%) in responding to both fungal inoculums at all timepoints from 12 to 96 h postinoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses functions related to plant growth and development, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest timepoint sampled, and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Transcription factor control of virulence in phytopathogenic fungi

Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.

Accessory Chromosome-Acquired Secondary Metabolism in Plant Pathogenic Fungi: The Evolution of Biotrophs Into Host-Specific Pathogens

Accessory chromosomes are strain- or pathotype-specific chromosomes that exist in addition to the core chromosomes of a species and are generally not considered essential to the survival of the organism. Among pathogenic fungal species, accessory chromosomes harbor pathogenicity or virulence factor genes, several of which are known to encode for secondary metabolites that are involved in plant tissue invasion. Accessory chromosomes are of particular interest due to their capacity for horizontal transfer between strains and their dynamic "crosstalk" with core chromosomes. This review focuses exclusively on secondary metabolism (including mycotoxin biosynthesis) associated with accessory chromosomes in filamentous fungi and the role accessory chromosomes play in the evolution of secondary metabolite gene clusters. Untargeted metabolomics profiling in conjunction with genome sequencing provides an effective means of linking secondary metabolite products with their respective biosynthetic gene clusters that reside on accessory chromosomes. While the majority of literature describing accessory chromosome-associated toxin biosynthesis comes from studies of Alternaria pathotypes, the recent discovery of accessory chromosome-associated biosynthetic genes in Fusarium species offer fresh insights into the evolution of biosynthetic enzymes such as non-ribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and regulatory mechanisms governing their expression.

A Genomic Blueprint of Flax Fungal Parasite Fusarium oxysporum f. sp. lini

Fusarium wilt of flax is an aggressive disease caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini. It is a challenging pathogen presenting a constant threat to flax production industry worldwide. Previously, we reported chromosome-level assemblies of 5 highly pathogenic F. oxysporum f. sp. lini strains. We sought to characterize the genomic architecture of the fungus and outline evolutionary mechanisms shaping the pathogen genome. Here, we reveal the complex multi-compartmentalized genome organization and uncover its diverse evolutionary dynamics, which boosts genetic diversity and facilitates host adaptation. In addition, our results suggest that host of functions implicated in the life cycle of mobile genetic elements are main contributors to dissimilarity between proteomes of different Fusaria. Finally, our experiments demonstrate that mobile genetics elements are expressed in planta upon infection, alluding to their role in pathogenicity. On the whole, these results pave the way for further in-depth studies of evolutionary forces shaping the host–pathogen interaction.

The Genome of Banana Leaf Blight Pathogen Fusarium sacchari str. FS66 Harbors Widespread Gene Transfer From Fusarium oxysporum

Fusarium species have been identified as pathogens causing many different plant diseases, and here we report an emerging banana leaf blight (BLB) caused by F. sacchari (Fs) discovered in Guangdong, China. From the symptomatic tissues collected in the field, a fungal isolate was obtained, which induced similar symptoms on healthy banana seedlings after inoculation. Koch's postulates were fulfilled after the re-isolation of the pathogen. Phylogenetic analysis on two gene segments and the whole genome sequence identified the pathogen belonging to Fs and named as Fs str. FS66. A 45.74 Mb genome of FS66 was acquired through de novo assembly using long-read sequencing data, and its contig N50 (1.97 Mb) is more than 10-fold larger than the previously available genome in the species. Based on transcriptome sequencing and ab initio gene annotation, a total of 14,486 protein-encoding genes and 418 non-coding RNAs were predicted. A total of 48 metabolite biosynthetic gene clusters including the fusaric acid biosynthesis gene cluster were predicted in silico in the FS66 genome. Comparison between FS66 and other 11 Fusarium genomes identified tens to hundreds of genes specifically gained and lost in FS66, including some previously correlated with Fusarium pathogenicity. The FS66 genome also harbors widespread gene transfer on the core chromosomes putatively from F. oxysporum species complex (FOSC), including 30 involved in Fusarium pathogenicity/virulence. This study not only reports the BLB caused by Fs, but also provides important information and clues for further understanding of the genome evolution among pathogenic Fusarium species.