Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus

Abstract

Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch’s postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the “narrow” generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus.

An evolutionary view of the Fusarium genome

“…The depicted phylogeny also aligns with more recent studies, supporting the concept of the 'broad' Fusarium clade, which encompasses 17 species complexes and 11 allied genera (32). The tree topology also gives support to the 'narrow' concept of the genus Fusarium sensu stricto, which includes only the 17 species complexes, often referred to as the F3 hypothesis (32)(33)(34)(35). The branch lengths observed in the phylogenomic tree further indicate a wider evolutionary divergence between the 'allied' genera and the species at the F3 node.…”

Fusarium amaranthuense sp. nov. from amaranth is an emergent species closely related to Fusarium circinatum

“…Fusarium is a genus of lamentous fungi and is distributed worldwide [1][2][3]. The genus includes more than 300 species, many of them are pathogenic to plants, animals, and humans [2].…”

“…Accurate identi cation of Fusarium species is crucial for managing and diagnosing Fusarium diseases [3,8]. However, different taxonomic frameworks (dominant by morphology or phylogenetic inference) of Fusarium have created inconsistencies in species diversity inferences [3,[9][10][11].…”

“…Accurate identi cation of Fusarium species is crucial for managing and diagnosing Fusarium diseases [3,8]. However, different taxonomic frameworks (dominant by morphology or phylogenetic inference) of Fusarium have created inconsistencies in species diversity inferences [3,[9][10][11]. For instance, the F. graminearum clade was considered a single species based on morphology until the genealogical concordance phylogenetic species recognition was applied [12].…”

“…Furthermore, many current Fusarium sequences in public databases are still under the wrong species or genus names [2.3] .To address these issues, multigene sequence analysis coupled with morphological approach has been adopted, and several online databases (FUSARIUM-ID; Fusarium MLST) have been established [8,10,14]. Evolutionary relationships of key Fusarium species complexes have also been published [2,3]. Amaranthus spp.…”