Fusarium graminearum Species Complex: A Bibliographic Analysis and Web-Accessible Database for Global Mapping of Species and Trichothecene Toxin Chemotypes.

Fusarium graminearum is ranked among the five most destructive fungal pathogens that affect agroecosystems. It causes floral diseases in small grain cereals including wheat, barley, and oats, as well as maize and rice. We conducted a systematic review of peer-reviewed studies reporting species within the F. graminearum species complex (FGSC) and created two main data tables. The first contained summarized data from the articles including bibliographic, geographic, methodological (ID methods), host of origin and species, while the second data table contains information about the described strains such as publication, isolate code(s), host/substrate, year of isolation, geographical coordinates, species and trichothecene genotype. Analyses of the bibliographic data obtained from 123 publications from 2000 to 2021 by 498 unique authors and published in 40 journals are summarized. We describe the frequency of species and chemotypes for 16,274 strains for which geographical information was available, either provided as raw data or extracted from the publications, and sampled across six continents and 32 countries. The database and interactive interface are publicly available, allowing for searches, summarization, and mapping of strains according to several criteria including article, country, host, species and trichothecene genotype. The database will be updated as new articles are published and should be useful for guiding future surveys and exploring factors associated with species distribution such as climate and land use. Authors are encouraged to submit data at the strain level to the database, which is accessible at https://fgsc.netlify.app.

Reference Genome Resource for the Citrus Pathogen Phytophthora citrophthora.

Phytophthora citrophthora is an oomycete pathogen that infects citrus. Its occurrence in citrus-growing regions worldwide is considered a major contributor to crop losses. This study presents a high-quality genome resource for P. citrophthora, which was generated using PacBio HiFi long-read high-throughput sequencing technology. We successfully assembled a 48.5 Mb genome containing 16,409 protein-coding genes from high-quality reads. This marks the first complete genome assembly of P. citrophthora, providing a valuable resource to enhance the understanding of pathogenic behaviour and fungicide sensitivity of this destructive citrus pathogen.

Phylogenetic and Biological Characterization of Fusarium oxysporum Isolates Associated with Onion in South Africa.

Fusarium oxysporum f. sp. cepae causes Fusarium basal rot of onion, a disease of worldwide importance. Limited information is available on the phylogenetic diversity, vegetative compatibility groups (VCGs), mating type idiomorphs, and virulence of F. oxysporum isolates associated with onion. Therefore, these characteristics were investigated in 19 F. oxysporum f. sp. cepae isolates from Colorado, 27 F. oxysporum f. sp. cepae and 33 F. oxysporum isolates nonpathogenic to onion from South Africa. Six F. oxysporum f. sp. cepae VCGs (0421 to 0426) were identified, of which three were new. The dominant VCGs in Colorado and South Africa were VCG 0421 (47% of isolates) and VCG 0425 (74%), respectively. VCG 0423 was the only VCG that was shared between the two regions. Molecular phylogenies (intergenic spacer region of the rDNA, elongation factor 1α, and mitochondrial small-subunit) confirmed the polyphyletic nature of F. oxysporum f. sp. cepae and showed that some F. oxysporum f. sp. cepae and nonpathogenic F. oxysporum isolates were genetically related. Most F. oxysporum f. sp. cepae isolates clustered into two distinct, well-supported clades. The largest clade only contained highly virulent isolates, including the two main VCGs (0421 and 0425), whereas the basal clade mostly contained moderately virulent isolates. These groupings along with the VCG data provide an important basis for selection of isolates for use in breeding programs, and for the development of molecular makers to identify VCGs. Mating type genotyping revealed the distribution of both mating type (MAT1-1 and MAT1-2) idiomorphs across phylogenetic clades, and the fact that several isolates contained both idiomorphs.

The distribution and type B trichothecene chemotype of Fusarium species associated with head blight of wheat in South Africa during 2008 and 2009.

Fusarium head blight (FHB) of wheat occurs commonly in irrigation regions of South Africa and less frequently in dryland regions. Previous surveys of Fusarium species causing FHB identified isolates using morphological characters only. This study reports on a comprehensive characterisation of FHB pathogens conducted in 2008 and 2009. Symptomatic wheat heads were collected from the Northern Cape, KwaZulu-Natal (KZN), Bushveld and eastern Free State (irrigation regions), and from one field in the Western Cape (dryland region). Fusarium isolates were identified with species-specific primers or analysis of partial EF-1α sequences. A representative subset of isolates was characterized morphologically. In total, 1047 Fusarium isolates were collected, comprising 24 species from seven broad species complexes. The F. sambucinum (FSAMSC) and F. incarnatum-equiseti species complexes (FIESC) were most common (83.5% and 13.3% of isolates, respectively). The F. chlamydosporum (FCSC), F. fujikuroi (FFSC), F. oxysporum (FOSC), F. solani (FSSC), and F. tricinctum species complexes (FTSC) were also observed. Within the FSAMSC, 90.7% of isolates belonged to the F. graminearum species complex (FGSC), accounting for 75.7% of isolates. The FGSC was the dominant Fusaria in all four irrigation regions. F. pseudograminearum dominated at the dryland field in the Western Cape. The Northern Cape had the highest species diversity (16 Fusarium species from all seven species complexes). The type B trichothecene chemotype of FGSC and related species was inferred with PCR. Chemotype diversity was limited (15-ADON = 90.1%) and highly structured in relation to species differences. These results expand the known species diversity associated with FHB in South Africa and include first reports of F. acuminatum, F. armeniacum, F. avenaceum, F. temperatum, and F. pseudograminearum from wheat heads in South Africa, and of F. brachygibbosum, F. lunulosporum and F. transvaalense from wheat globally. Potentially novel species were identified within the FCSC, FFSC, FOSC, FSAMSC, FIESC and FTSC.

Quantitative detection of economically important Fusarium oxysporum f. sp. cubense strains in Africa in plants, soil and water.

Banana is an important food crop and source of income in Africa. Sustainable production of banana, however, is at risk because of pests and diseases such as Fusarium wilt, caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). Foc can be disseminated from infested to disease-free fields in plant material, water and soil. Early detection of Foc using DNA technologies is thus required to accurately identify the fungus and prevent its further dissemination with plants, soil and water. In this study, quantitative (q)PCR assays were developed for the detection of Foc Lineage VI strains found in central and eastern Africa (Foc races 1 and 2), Foc TR4 (vegetative compatibility groups (VCG) 01213/16) that is present in Mozambique, and Foc STR4 (VCG 0120/15) that occurs in South Africa. A collection of 127 fungal isolates were selected for specificity testing, including endophytic Fusarium isolates from banana pseudostems, non-pathogenic F. oxysporum strains and Foc isolates representing the 24 VCGs in Foc. Primer sets that proved to be specific to Foc Lineage VI, Foc TR4 and Foc STR4 were used to produce standard curves for absolute quantification, and the qPCR assays were evaluated based on the quality of standard curves, repeatability and reproducibility, and limits of quantification (LOQ) and detection (LOD). The qPCR assays for Foc Lineage VI, TR4 and STR4 were repeatable and reproducible, with LOQ values of 10-3-10-4 ng/µL and a LOD of 10-4-10-5 ng/µL. The quantitative detection of Foc strains in Africa could reduce the time and improve the accuracy for identifying the Fusarium wilt pathogen from plants, water and soil on the continent.

Diversity and Toxigenicity of Fungi that Cause Pineapple Fruitlet Core Rot.

The identity of the fungi responsible for fruitlet core rot (FCR) disease in pineapple has been the subject of investigation for some time. This study describes the diversity and toxigenic potential of fungal species causing FCR in La Reunion, an island in the Indian Ocean. One-hundred-and-fifty fungal isolates were obtained from infected and healthy fruitlets on Reunion Island and exclusively correspond to two genera of fungi: Fusarium and Talaromyces. The genus Fusarium made up 79% of the isolates, including 108 F. ananatum, 10 F. oxysporum, and one F. proliferatum. The genus Talaromyces accounted for 21% of the isolated fungi, which were all Talaromyces stollii. As the isolated fungal strains are potentially mycotoxigenic, identification and quantification of mycotoxins were carried out on naturally or artificially infected diseased fruits and under in vitro cultures of potential toxigenic isolates. Fumonisins B1 and B2 (FB1-FB2) and beauvericin (BEA) were found in infected fruitlets of pineapple and in the culture media of Fusarium species. Regarding the induction of mycotoxin in vitro, F.proliferatum produced 182 mg kg⁻1 of FB1 and F. oxysporum produced 192 mg kg⁻1 of BEA. These results provide a better understanding of the causal agents of FCR and their potential risk to pineapple consumers.

Germline Missense Changes in the APC Gene and Their Relationship to Disease.

Familial adenomatous polyposis (FAP) is characterized by the presence of hundreds to thousands of adenomas that carpet the entire colon and rectum. Nonsense and frameshift mutations in the adenomatous polyposis coli (APC) gene account for the majority of mutations identified to date and predispose primarily to the typical disease phenotype. Some APC mutations are associated with a milder form of the disease known as attenuated FAP. Virtually all mutations that have been described in the APC gene result in the formation of a premature stop codon and very little is known about missense mutations apart from a common Ashkenazi Jewish mutation (1307 K) and a British E1317Q missense change. The incidence of missense mutations in the APC gene has been underreported since the APC gene lends itself to analysis using an artificial transcription and translation assay known as the Protein Truncation Test (PTT) or the In Vitro Synthetic Protein assay (IVSP).In this report we have used denaturing high performance liquid chromatography to analyse the entire coding sequence of the APC gene to determine if a cohort of patients adhering to the diagnostic criteria of FAP to assess the frequency of missense mutations in the APC gene. Altogether 112 patients were studied and 22 missense mutations were identified. From the total of 22 missense changes, 13 were silent changes and the remaining 9 resulted in amino acid substitutions. One or more of these changes were identified multiple times in 62.5% of the population under study.The results reveal that missense mutations in the APC gene appear not to radically alter protein function but may be associated with more subtle processing of RNA transcripts which in turn could result in the expression of differentially spliced forms of the APC gene which may interfere with the functional activity of the APC protein.