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Carbendazim resistance was detected using 4701 Fusarium graminearum species complex (FGSC) isolates collected from major wheat producing regions in China from 2018 to 2020. A total of 348 carbendazim-resistant isolates were identified. The majority of carbendazim-resistant isolates were detected in Jiangsu and Anhui Provinces. 227 and 88 isolates were obtained from each of Jiangsu and Anhui Provinces with the high resistance frequency of 41.12% and 20.56%. The predominant resistant isolates harboring point mutation F167Y (79.31%), followed by E198Q (16.38%) and F200Y (4.31%). Compared with F. graminearum, F. asiaticum isolates were more likely to produce carbendazim resistance. In this study, we firstly detected carbendazim-resistant isolates in Hebei, Shaanxi, Sichuan and Hunan Province. In Jiangsu, Anhui and Zhejiang, the frequency of carbendazim-resistant isolates maintained a high level resulting in stable carbendazim-resistant populations. We also found the dynamic of carbendazim-resistant frequency in most provinces showed similar trend of the epidemic of FHB. Our results facilitate the understanding of the current situation of carbendazim resistance of FHB pathogens, and will be helpful for fungicides selection in different wheat producing areas in China.

Exploiting wheat cultivars with stable resistance to Fusarium Head blight (FHB) and toxin accumulation is a cost-effective and environmentally friendly strategy to reduce the risk of yield losses and contamination with mycotoxins. To facilitate the deployment of stable cultivar resistance, we evaluated FHB resistance and resistance to mycotoxin accumulation in 410 wheat lines bred by local breeders from four major wheat growing regions in China after natural infection at three distinct locations (Hefei, Yangzhou and Nanping). Significant differences in disease index were observed among the three locations. The disease indexes (DI’s) in Nanping were the highest, followed by Yangzhou and Hefei. The distribution of DI’s in Yangzhou showed the best discrimination of FHB resistance in cultivars. Growing region and cultivar had significant effect on DI and mycotoxins. Among the climate factors, relative humidity and rainfall were the key factors resulting in the severe disease. Even though most cultivars were still susceptible to FHB under the strongly conducive conditions applied, the ratio of resistant lines increased in the Upper region of the Yangtze River (UYR) and the Middle and Lower Region of the Yangtze River (MLYR) between 2015 and 2019. Deoxynivalenol (DON) was the dominant mycotoxin found in Hefei and Yangzhou, while NIV was predominant in Nanping. Disease indexes were significantly correlated with DON content in wheat grain.

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.

Fusarium head blight (FHB) in wheat (Triticum aestivum L.) is caused by a consortium of mutually interacting Fusarium species. In the field, the weakly pathogenic F. poae often thrives on the infection sites of the virulent F. graminearum. In this ecological context, we investigated the efficacy of chemical and biocontrol agents against F. graminearum in wheat ears. For this purpose, one fungicide comprising prothioconazole + spiroxamine and two bacterial biocontrol strains, Streptomyces rimosus LMG 19352 and Rhodococcus sp. R-43120 were tested for their efficacy to reduce FHB symptoms and mycotoxin (deoxynivalenol, DON) production by F. graminearum in presence or absence of F. poae. Results showed that the fungicide and both actinobacterial strains reduced FHB symptoms and concomitant DON levels in wheat ears inoculated with F. graminearum. Where Streptomyces rimosus appeared to have direct antagonistic effects, Rhodococcus and the fungicide mediated suppression of F. graminearum was linked to the archetypal salicylic acid and jasmonic acid defense pathways that involve the activation of LOX1, LOX2 and ICS. Remarkably, this chemical- and biocontrol efficacy was significantly reduced when F. poae was co-inoculated with F. graminearum. This reduced efficacy was linked to a suppression of the plant’s intrinsic defense system and increased levels of DON. In conclusion, our study shows that control strategies against the virulent F. graminearum in the disease complex causing FHB are hampered by the presence of the weakly pathogenic F. poae. This study provides generic insights in the complexity of control strategies against plant diseases caused by multiple pathogens.

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Genome sequencing and assembly

Plant diseases are often caused by a consortium of pathogens competing with one another to gain a foothold in the infection niche. Nevertheless, studies are often limited to a single pathogen on its host. In Europe, fusarium head blight (FHB) of wheat is caused by multiple Fusarium species, including Fusarium graminearum and F. poae. Here, we combined a time series of (co)inoculations, monitored by multispectral imaging, transcriptional, and mycotoxin analyses, to study the temporal interaction between both species and wheat. Our results showed coinoculation of F. graminearum and F. poae inhibited symptom development but did not alter mycotoxin accumulation compared to a single inoculation with F. graminearum. In contrast, preinoculation of F. poae reduced both FHB symptoms and mycotoxin levels compared to a single F. graminearum infection. Interestingly, F. poae exhibited increased growth in dual infections, demonstrating that this weak pathogen takes advantage of its co-occurrence with F. graminearum. Quantitative reverse transcription PCR revealed that F. poae induces LOX and ICS gene expression in wheat. We hypothesize that the early induction of salicylic and jasmonic acid-related defences by F. poae hampers a subsequent F. graminearum infection. This study is the first to report on the defence mechanisms of the plant involved in a tripartite interaction between two species of a disease complex and their host.

In total, 23 Fusarium fujikuroi species complex member species and 3 outgroup species were whole genome sequenced. FFSC: Fusarium sacchari CBS:147.25, Fusarium concentricum CBS:450.97, Fusarium annulatum CBS:258.54, Fusarium globosum CBS:428.97, Fusarium acutatum CBS:402.97, Fusarium verticillioides CBS:576.78, Fusarium musae CBS:624.87, Fusarium andiyazi CBS:119857, Fusarium napiforme CBS:748.97, Fusarium ramigenum CBS:418.97, Fusarium pseudocircinatum CBS:449.97, Fusarium lactis CBS:411.97, Fusarium ficicrescens CBS:125178, Fusarium brevicatenulatum CBS:404.97, Fusarium pseudoanthophilum CBS:414.97, Fusarium pseudonygamai CBS:417.97, Fusarium nygamai CBS:749.97, Fusarium bactridioides CBS:100057, Fusarium anthophilum CBS:119858, Fusarium begoniae CBS:452.97, Fusarium ananatum CBS:118516, Fusarium guttiforme CBS:409.97, Fusarium denticulatum CBS:407.97. Outgroup: Fusarium foetens CBS:110286, Fusarium oxysporum CBS:130302, and Fusarium redolens CBS:743.97

The Fusarium fujikuroi species complex (FFSC) and F. oxysporum species complex (FOSC) are two related groups of plant pathogens causing a wide diversity of diseases in agricultural crops world wide. The aims of this study are (1) to clarify the phylogeny of the FFSC, (2) to identify potential deviation from tree-like evolution, (3) to explore the value of using mitogenomes for these kinds of analyses, and (4) to better understand mitogenome evolution. In total, we have sequenced 24 species from the FFSC and a representative set of recently analyzed FOSC strains was chosen, while F. redolens was used as outgroup for the two species complexes. A species tree was constructed based on the concatenated alignment of seven nuclear genes and the mitogenome, which was contrasted to individual gene trees to identify potential conflicts. These comparisons indicated conflicts especially within the previously described African clade of the FFSC. Furthermore, the analysis of the mitogenomes revealed the presence of a variant of the large variable (LV) region in FFSC which was previously only reported for FOSC. The distribution of this variant and the results of sequence comparisons indicate horizontal genetic transfer between members of the two species complexes, most probably through introgression. In addition, a duplication of atp9 was found inside an intron of cob, which suggests that even highly conserved mitochondrial genes can have paralogs. Paralogization in turn may lead to inaccurate single gene phylogenies. In conclusion, mitochondrial genomes provide a robust basis for phylogeny. Comparative phylogenetic analysis indicated that gene flow among and between members of FFSC and FOSC has played an important role in the evolutionary history of these two groups. Since mitogenomes show greater levels of conservation and synteny than nuclear regions, they are more likely to be compatible for recombination than nuclear regions. Therefore, mitogenomes can be used as indicators t