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Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Stink bug species (Pentatomoidea superfamily) have developed an interdependence with obligate bacterial gut symbionts in specialized midgut crypts (M4 sub-region). Species of the Enterobacteriaceae family (predominantly Pantoea) are vertically transferred to their offspring and provide nutrients that cannot be obtained from plant sap food sources. However, the bacteria in the other gut compartments of stink bugs have rarely been investigated. The two-spotted stink bug, Bathycoelia distincta, is a serious pest of macadamias in South Africa. Nothing is currently known regarding its gut microbiome or how symbionts are transferred between insect generations. In this study, the consistency of B. distincta gut bacteria across geographic locations and life stages was determined with 16S rRNA metabarcoding, considering both the M4 and other gut compartments. A novel Pantoea species was found to be the primary M4 gut symbiont and is vertically transferred to the offspring. The other gut compartments had a low bacterial diversity and genera varied between stink bug populations but a Sodalis species was prominent in all populations. Sequence data of the M4 compartment were used to produce high-quality metagenome-assembled genomes (MAGs) for the Pantoea and Sodalis species. Functional analyses suggested a similar role in nutrient provision for the host, yet also unique metabolites produced by each species. The Sodalis sp. also had additional traits, such as secretion systems, that likely allowed it to establish itself in the host. The Pantoea species was described as Pantoea bathycoeliae sp. nov based on the rules of the SeqCode. [ABSTRACT FROM AUTHOR]

The primary symptoms associated withFusarium circinatuminfection in pine seedling nurseries are root and collar rot, shoot and tip die-back and seedling mortality. Management of this pathogen in nurseries usually involves the integration of various strategies relating to sanitation, insect control and fungicide treatment. The overall goal of this study was to use quantitative real-time PCR (qPCR) to detect and quantify the airborne inoculum ofF. circinatumin a commercial pine seedling nursery. For this purpose, an existing qPCR method was optimised and evaluated for its efficacy to quantify and monitor airborne conidia over a one-year period. Results showed thatF. circinatumoccurred at relatively low levels in the nursery throughout the year and that its distribution was spatially sporadic. The data suggest that standard nursery sanitation practices in the test nursery maintained the airborne inoculum ofF. circinatumat low levels. The uneven distribution of infection also suggests that airborne inoculum does not represent the primary source of inoculum for theF. circinatum-associated seedling disease. [ABSTRACT FROM AUTHOR]

Fusarium circinatumis a pathogen causing serious post-planting mortality ofPinus patulaseedlings in southern Africa. Containerised planting stock that is asymptomatic but associated withF. circinatumin the nursery is thought to be the cause of this problem. The aim of this study was to determine if re-use of seedling containers could be a source of inoculum resulting in asymptomatic planting stock and increased post-planting mortality ofP. patula. Two experiments were conducted in successive years comparing nursery cull of symptomatic seedlings, seedling growth, association ofF. circinatumwith asymptomatic seedlings and post-planting mortality for crops raised in re-used containers, with and without sanitation, and factory-new containers. Each experiment consisted of a nursery production trial followed by out-planting into pots to assess post-planting mortality. Our results show that re-use of containers without sanitation increases the cull of symptomatic seedlings, incidence ofF. circinatumassociated with asymptomatic seedlings and post-planting mortality compared with the re-use of containers after steam sanitation or factory-new containers. Growth of asymptomatic seedlings was unaffected by container treatment or association withF. circinatumand in the absence of wilt symptoms the root system did not exhibit typical discolouration. Watering frequency did not influence post-planting mortality in pots. The comparison of two open-pollinated seed mixes ofP. patulathat, based on seedling stem inoculation screening, represented susceptible and tolerant material did not show differences in nursery cull or post-planting mortality. This work demonstrated that natural contamination of re-used containers can be a primary source of inoculum producing asymptomatic seedlings associated withF. circinatumthat will succumb to the pathogen after field planting. The process of seedling infection, apparent latent infection in the seedling and expression of disease after planting needs greater understanding to improve nursery hygiene measures to control this disease. [ABSTRACT FROM AUTHOR]

Fusarium circinatumis an important fungal pathogen ofPinusspecies. In South Africa, it is the most significant pathogen ofPinus patulaseedlings in forestry nurseries where it presents a substantial constraint to productivity and can continue to cause mortality in-field for up to two years after establishment. This study describes the results from two trials whereP. patulaseedlings were inoculated withF. circinatumto determine the impact of the pathogen on nursery and field performance. Seedlings were also subjected to water stress treatments to ascertain whether this would trigger the onset of disease symptoms. Inoculum load and timing of inoculation had significant effects on seedling survival in both the nursery and field. High inoculum concentrations caused greater levels of mortality and, where seedlings were inoculated at a young age, they showed higher levels of susceptibility toF. circinatum. Temporary water-stress in the nursery produced smaller plants and improved in-field survival, but this treatment did not trigger higher mortality in inoculated treatments. On the other hand, transplant stress was a major contributor to the higher levels of mortality observed in inoculated treatments. Overall, these studies confirmed that infection in the nursery leads to the disease problems observed during early plant establishment in the field. [ABSTRACT FROM AUTHOR]

The pitch canker pathogen,Fusarium circinatum, has major impacts on production in pine nurseries and plantations in South Africa. Thus far, efforts to reduce local spread have focused on rouging of infected pines and sanitation to eliminate local sources of inoculum. Although the host range ofF. circinatumwas thought to be limited to pines and Douglas-fir, recent studies in California indicate that this fungus is capable of infecting grasses as a symptomless endophyte. Consequently, it is possible that grasses represent a reservoir of inoculum that influences the occurrence of disease in South African pine nurseries and plantations. The objectives of this study were to survey a wide range of grass species in both nurseries and plantations in South Africa for the presence ofF. circinatum. In all, 22 species of grass were sampled at a nursery in Mpumulanga and in a plantation on the Western Cape. Isolates obtained from grasses were identified based on morphological criteria and DNA sequence data.Fusarium circinatumwas recovered from vegetative tissues of four grass species includingBriza maxima, Ehrharta erectavar.erecta, Pentameris pallidaand one species that could not be identified. All isolates were pathogenic to pines and comparable in virulence to a knownF. circinatumisolate that was included as a positive control. These studies indicate that grasses may constitute inoculum reservoirs that could facilitate persistence and dissemination of the pathogen in nurseries, and provide a means for the pathogen to move between widely separated pine stands, where grass hosts occur in intervening areas. [ABSTRACT FROM AUTHOR]

Fusarium circinatum Nirenberg & O'Donnel is listed among the species recommended for regulation as quarantine pests in Europe. Over 60 Pinus species are susceptible to the pathogen and it also causes disease on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and species in genera such as Picea and Larix. The European Food Safety Authority considers the probability of new introductions—via contaminated seeds, wood material, soil and growing substrates, natural means and human activities—into the EU very likely. Due to early detection, constant surveillance and control measures, F. circinatum outbreaks have officially been eradicated in Italy and France. However, the global spread of F. circinatum suggests that the pathogen will continue to be encountered in new environments in the future. Therefore, continuous surveillance of reproductive material, nurseries and plantations, prompt control measures and realistic contingency plans will be important in Europe and elsewhere to limit disease spread and the "bridgehead effect", where new introductions of a tree pathogen become increasingly likely as new environments are invaded, must be considered. Therefore, survey programs already implemented to limit the spread in Europe and that could be helpful for other EU countries are summarized in this review. These surveys include not only countries where pitch canker is present, such as Portugal and Spain, but also several other EU countries where F. circinatum is not present. Sampling protocols for seeds, seedlings, twigs, branches, shoots, soil samples, spore traps and insects from different studies are collated and compiled in this review. Likewise, methodology for morphological and molecular identification is herein presented. These include conventional PCR with a target-specific region located in the intergenic spacer region, as well as several real-time PCR protocols, with different levels of specificity and sensitivity. Finally, the global situation and future perspectives are addressed. [ABSTRACT FROM AUTHOR]

Removal of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs) have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspects of intron structure and diversity are taxon-specific, which can complicate the accuracy of in silico gene prediction methods. Using core genes, we evaluated the distribution and architecture of Fusarium circinatum spliceosomal introns, and linked these characteristics to the accuracy of the predicted gene models of the genome of this fungus. We also evaluated intron distribution and architecture in F. verticillioides , F. oxysporum , and F. graminearum , and made comparisons with F. circinatum Results indicated that F. circinatum and the three other Fusarium species have canonical 5' and 3' splice sites, but with subtle differences that are apparently not shared with those of other fungal genera. The polypyrimidine tract of Fusarium introns was also found to be highly divergent among species and genes. Furthermore, the conserved adenosine nucleoside required during the first step of splicing is contained within unique branch site motifs in certain Fusarium introns. Data generated here show that introns of F. circinatum , as well as F. verticillioides , F. oxysporum , and F. graminearum , are characterized by a number of unique features such as the CTHAH and ACCAT motifs of the branch site. Incorporation of such information into genome annotation software will undoubtedly improve the accuracy of gene prediction methods used for Fusarium species and related fungi., (Copyright © 2017 Phasha et al.)

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.