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Normalized Illumina read mapping to the SMRT assembly of Forc016 confirms horizontal transfer of chr RC in a Fo47 background. (A) Reads mapped more abundantly to the transferred chr RC sequence than the rest of the assembly. (B) HCT strains #2, #4, #9 showed a relative (compared to total # mapped reads) depth of coverage of ~4 on chr RC , whereas the relative coverage of HCT#8 sequences was ~8 along the entire chromosome. This indicates a chromosomal duplication, in accordance with the ~5Mb-sized band in the CHEF gel in Fig. 5.
Source publication
The genome of Fusarium oxysporum (Fo) consists of a set of eleven 'core' chromosomes, shared by most strains and responsible for housekeeping, and one or several accessory chromosomes. We sequenced a strain of Fo f.sp. radicis-cucumerinum (Forc) using PacBio SMRT sequencing. All but one of the core chromosomes were assembled into single contigs, an...
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... T-DNA, as well as to the wild type Forc016 strain and the two other knockout strains ( Fig. 4; pictures shown in Fig. S6). When tested at a lower ambient temperature of 18-20 °C, all strains caused quick and uniform death to all plants of the three tested species, indicating that these conditions are more favourable for Forc disease development and do not require Six6 (data not shown). Disruption of SIX9 or SMP1 did not significantly affect virulence ...
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... Illumina short-read mapping of HCT strains #2, #4, #8 and #9 on the Forc016 assembly showed that these strains indeed contain the full chr RC sequence but no other Forc016-derived sequences (the core genomes of Forc016 and Fo47 have an average SNP density of 0.4% (more towards the telomeres), reducing mapping of reads to ~85%) (Fig. 6). This confirms that chr RC now resided in a Fo47 core genome background. Remarkably, HCT#8 showed a relative depth of coverage of chr RC about two times higher than the other HCT strains, indicating that the chr RC sequences are present twice. Since a double band at the expected size of chr RC (~2.5 Mb) is missing in this strain but a ...
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... Nanopore sequencing 43 . Manual curation of the assembly improved it to the point where five chromosomes are complete (telomere-to-telomere), fifteen contigs have telomeric repeats on only one end and 20 contigs are left with no telomeric repeats on either end. The estimated chromosome count of Forc016 is 14, which is most clearly visible in Fig. 6 where the separation in the 1-1.5 Mb region shows that Forc016 possesses two small accessory chromosomes. Considering their size and accessory-like appearance (high TE and low gene content), these pos- sibly correspond to contig 53 and the non-conserved region that is probably erroneously attached to chromosome 11 in the assembly. This ...
Citations
... By contrast, individual strains typically only infect a single host plant (Edel-Hermann & Lecomte, 2019). Fusarium oxysporum evolved a two-speed genome organization where specific genomic regions are characterized by extensive presence-absence polymorphisms between strains (Ma et al., 2010;van Dam et al., 2017;Fokkens et al., 2018;Zhang et al., 2020). These variable accessory regions (ARs) can be embedded in core chromosomes or can encompass entire accessory chromosomes (Ma et al., 2010;Fokkens et al., 2018). ...
Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown.
We defined the pan‐genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs.
Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta ‐induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum .
Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum , which contribute to the evolution of virulence.
... At the proteome level, "effector" proteins have been detected that help colonization with suppression or protection against the plant's immune system. 60 Banana root exudates help stimulate the germination of F. oxysporum f sp. cubense chlamydospores in the soil. ...
Musa spp. (banana and plantain) is the most widely consumed and exported fruit globally, and it plays a crucial role in the diets of billions of people worldwide. Over the years, many diseases have threatened this crop, including the recent emergence of Fusarium wilt, caused by Fusarium oxysporum race 4. Puerto Rico is home to numerous economically significant variants of Musa spp. Due to the crop's importance in the island's economy and nutrition, research on maintaining existing varieties and developing new ones has been initiated. Although Fusarium oxysporum f.sp. cubense race 4 has not been detected in Puerto Rico, it has been detected in the Caribbean region. Therefore, it is essential to know both the plant and the pathogen to prevent and fight this disease. This review summarizes information about Musa spp, including its plant description, morphology, and genetic characteristics. Furthermore, it covers information about Fusarium sp., its pathogenicity, detection methods, and prevention of its spread. We also reviewed the few articles published for the island of Puerto Rico about Musa and Fusarium, and the guidelines suggested regarding the threat of the Fusarium wilt race 4 for the island. Finally, we underline Puerto Rico's opportunities to develop disease-resistant Musa cultivars.
... Formae speciales of F. oxysporum typically have a narrow host range, often restricted to a single plant species (Kawai et al., 1958;Kistler et al., 1998;Van Dam et al., 2017). One of the Fusarium isolates from luffa (Fsp. ...
Fusarium wilt is a serious disease of cucurbit crops including cultivated Luffa species (Luffa aegyptiaca, Luffa acutangula) causing considerable amount of reduction in yield and quality. Luffa is starting to be used as rootstocks for major commercial cucurbit crops, but little is known of its resistance against soilborne diseases. Here, 63 Luffa accessions from the World Vegetable Center genebank were evaluated for resistance to an aggressive isolate of Fusarium oxysporum f. FoCu-1 (Fsp-66). According to visual screening based on disease severity rating, 14 accessions exhibited a high level of resistance against Fsp-66. These accessions were further evaluated for resistance against Fsp-66 and two more isolates FoCu-1 (isolated from infected cucumber plants) and FoM-6 (isolated from infected bitter gourd plants). Of the 14 accessions, 11 were confirmed resistant against isolate Fsp-66. In addition, 13 accessions showed high resistance against isolates FoCu-1 and FoM-6. This is the first report of Fusarium wilt resistance in Luffa and these sources will be valuable for the development of Luffa rootstocks/cultivars resistant to soil-borne pathogen to manage this serious disease.
... Pathogenic F. oxysporum species often carry dispensable chromosomes that are not required for non-pathogenic growth but are virulence-associated and carry genes coding for specific host-interacting proteins and toxins, also referred to as effectors. Horizontal transfer of these chromosomes from pathogenic to a non-pathogenic recipient lineage of F. oxysporum renders the latter pathogenic on the respective host (van Dam et al. 2017). Such dispensable chromosomes have, however, not yet been identified in H. fraxineus . ...
Tree diseases constitute a significant threat to biodiversity worldwide. Pathogen discovery in natural habitats is of vital importance to understanding current and future threats and prioritising efforts towards developing disease management strategies. Ash dieback is a fungal disease of major conservational concern that is infecting common ash trees, Fraxinus excelsior , in Europe. The disease is caused by a non-native fungal pathogen, Hymenoscyphus fraxineus . Other dieback causing-species have not previously been identified in the genus Hymenoscyphus . Here, we discover the pathogenicity potential of two newly identified related species of Asian origin, H. koreanus and H. occultus , and one Europe-native related species, H. albidus . We sequence the genomes of all three Hymenoscyphus species and compare them to that of H. fraxineus . Phylogenetic analysis of core eukaryotic genes identified H. albidus and H. koreanus as sister species, whilst H. occultus diverged prior to these and H. fraxineus . All four Hymenoscyphus genomes are of comparable size (55–62 Mbp) and GC contents (42–44%) and encode for polymorphic secretomes. Surprisingly, 1133 predicted secreted proteins are shared between the ash dieback pathogen H. fraxineus and the three related Hymenoscyphus endophytes. Amongst shared secreted proteins are cell death-inducing effector candidates, such as necrosis, and ethylene-inducing peptide 1-like proteins, Nep1-like proteins, that are upregulated during in planta growth of all Hymenoscyphus species. Indeed, pathogenicity tests showed that all four related Hymenoscyphus species develop pathogenic growth on European ash stems, with native H. albidus being the least virulent. Our results identify the threat Hymenoscypohus species pose to the survival of European ash trees, and highlight the importance of promoting pathogen surveillance in environmental landscapes. Identifying new pathogens and including them in the screening for durable immunity of common ash trees is key to the long-term survival of ash in Europe.
... Often relatively small changes in fungal genomes can result in pathogenic lifestyle, such as the SIX genes identified in Fusarium spp. (Czislowski et al., 2017); without these genes, the fungi may be commensal or mutualist (Van Dam et al., 2017). Nevertheless, taxa may also switch between being mutualist and pathogenic under certain conditions (Slippers and Wingfield, 2007;Ribeiro et al., 2020). ...
Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). To identify a list of 21 core fungal taxa, we first characterised the effects of edaphic conditions and host genotype – two factors that are likely to differ between farms – on the diversity of fungal communities in bulk soil and seven plant compartments. This experiment facilitated shortlisting of core ‘candidates’, which were then elevated to full core status if also found to frequent a wide-range of field-grown Musa spp. and exhibit hub-like characteristics in network analyses. Subsequently, we conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes , Dothideomycetes , and Mortierellomycota . Our study provides a robust list of common core fungal taxa for Musa spp. Further studies may consider how changes in the frequencies and activities of these taxa influence host fitness and whether they can be managed to improve banana production.
... During the infection process, Fusarium uses a number of secretion systems and releases a variety of virulence factors such as mycotoxins, effector proteins and CWDEs to overcome the target host cells. CWDEs such as polygalacturonases, pectate lyases, xylanases, peptidases, peptide hydrolases, ribonucleases and cutinases may contribute to pathogenesis by degrading waxes, cuticles and cell walls to promote tissue invasion and pathogen spread [50,51]. Cutinases and lipases that catalyse the hydrolysis of ester bonds from fatty acid polymers, facilitating fungal invasion through the cuticle. ...
The genus Fusarium comprises more than 300 species, and many of them are pathogens that cause severe diseases in agricultural, horticultural and forestry plants in both antropogenic and natural ecosystems. Because of their importance as plant pathogens, the genomes of several Fusarium spp. have been sequenced. Within this genus, Fusarium circinatum is one of the most harmful pathogens of pine trees attacking up to 60 Pinus species. Till now, the genomes of 13 strains of F.
circinatum have been sequenced. The strain GL1327 we studied lacks a twelfth chromosome, which allows the study of virulence genes on this chromosome. Although the genome of several strains of F. circinatum has been sequenced, it is still almost completely unannotated, which severely limits the possibilities to further investigate the molecular mechanisms of virulence of Fusarium. Therefore, this study aimed to annotate the 12th chromosome of F. circinatum and integrate currently available resources. In silico annotation of the 12th chromosome of F. circinatum revealed the presence of 118 open reading frames (ORFs) encoding 141 proteins which were predicted using an ab initio gene prediction tool. The InterProScan and SMART analyses identified known domains in 30 proteins and
eggNOG additionally in 12 of them. Among them, four groups can be distinguished: genes possibly related to heterokaryon incompatibility (4 genes), regulation of transcription (5 genes), plant cell wall degrading enzymes (7 genes) and
richothecene synthesis (3 genes). This study also integrated data of F.circinatum reference strain CMWF1803 assembled to chromosome level but not annotated with currently best annotated but assembled only to scaffold level strain NRRL 25331.
... Many of the genes that determine pathogenicity among formae speciales, i.e., effector genes, are encoded on accessory chromosomes that are transferable among isolates (Li et al. 2020a, b;Ma et al. 2010;Schmidt et al. 2013;van Dam et al. 2017). This explains, in part, the complicated evolutionary relationships among isolates of many formae speciales (Henry et al. 2021;O'Donnell et al. 2009;van Dam et al. 2016). ...
Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is a significant limitation for producers of vegetative spinach and spinach seed crops during warm temperatures and/or on acid soils. Identification of isolates of F. oxysporum f. sp. spinaciae, and distinction of isolates of the two known races entails time-intensive pathogenicity tests. In this study, two real-time PCR assays were developed: one for a candidate effector gene common to both races of F. oxysporum f. sp. spinaciae, and another for a candidate effector gene unique to isolates of race 2. The assays were specific to isolates of F. oxysporum f. sp. spinaciae (n = 44) and isolates of race 2 (n = 23), respectively. Neither assay amplified DNA from 10 avirulent isolates of F. oxysporum associated with spinach, 57 isolates of other formae speciales and Fusarium spp., or 7 isolates of other spinach pathogens. When the assays were used to detect DNA extracted from spinach plants infected with an isolate of race 1, race 2, or a 1:1 mixture of both races, the amount of target-DNA detected increased with increasing severity of wilt. Plants infected with one or both isolates could be distinguished based on the ratio in copy number for each target locus. The real-time PCR assays enable rapid diagnosis of Fusarium wilt of spinach and will facilitate research on the epidemiology and management of this disease, as well as surveys on the prevalence of this understudied pathogen in regions of spinach and/or spinach seed production.
... These accessory chromosomes (AC) are generally small and are not considered essential for survival. In some pathogenic fungi, they are characterized by the presence of genes encoding virulence factors [69][70][71]. The B. cinerea genes on ACs display little or no similarity to genes in other organisms, including fungi [39]. ...
For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.
... Fusarium oxysporum is the major shared pathogen in various Fusarium wilt diseases and is ranked fifth in a survey of the Top 10 fungal plant pathogens [47]. Forma specialis of F. oxysporum typically has a narrow host range among species, but a few forma specialis show an extended host range among genera [48]. Expanding the host range by horizontal chromosome transfer between different forma specialis of F. oxysporum makes the pathogen more deadly [16,48]. ...
... Forma specialis of F. oxysporum typically has a narrow host range among species, but a few forma specialis show an extended host range among genera [48]. Expanding the host range by horizontal chromosome transfer between different forma specialis of F. oxysporum makes the pathogen more deadly [16,48]. In this study, Fo-4 displayed much broader host ranges among families from Solanaceae, Vitaceae, Musaceae, Cucurbitaceae to Dioscoreaceae than other forma specialis of F. oxysporum. ...
... Variability was most evident when comparisons of inversions were investigated. Inversions closer to the ends of chromosomes were previously reported in fungi [36,88,89]. Inversions were most noticeable for Chromosome 8, especially when considering the host-range-associated genes on this chromosome. ...
The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.
