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The Capnodiales, which includes fungi known as the sooty moulds, represents the second largest order in Dothideomycetes, encompassing morphologically and ecologically diverse fungi with different lifestyles and modes of nutrition. They include saprobes, plant and human pathogens, mycoparasites, rock-inhabiting fungi (RIF), lichenised, epi-, ecto- and endophytes. The aim of this study was to elucidate the lifestyles and evolutionary patterns of the Capnodialesas well as to reconsider their phylogeny by including numerous new collections of sooty moulds, and using four nuclear loci, LSU, ITS, TEF-1αand RPB2. Based on the phylogenetic results, combined with morphology and ecology, Capnodiales s. lat.is shown to be polyphyletic, representing seven different orders. The sooty moulds are restricted to Capnodiales s. str., while Mycosphaerellalesis resurrected, and five new orders including Cladosporiales, Comminutisporales, Neophaeothecales, Phaeothecalesand Racodialesare introduced. Four families, three genera, 21 species and five combinations are introduced as new. Furthermore, ancestral reconstruction analysis revealed that the saprobic lifestyle is a primitive state in Capnodiales s. lat., and that several transitions have occurred to evolve lichenised, plant and human parasitic, ectophytic (sooty blotch and flyspeck) and more recently epiphytic (sooty mould) lifestyles.

In this paper we give an account of the genera and species in the Botryosphaeriaceae. We consider morphological characters alone as inadequate to define genera or identify species, given the confusion it has repeatedly introduced in the past, their variation during development, and inevitable overlap as representation grows. Thus it seems likely that all of the older taxa linked to the Botryosphaeriaceae, and for which cultures or DNA sequence data are not available, cannot be linked to the species in this family that are known from culture. Such older taxa will have to be disregarded for future use unless they are epitypified. We therefore focus this paper on the 17 genera that can now be recognised phylogenetically, which concentrates on the species that are presently known from culture. Included is a historical overview of the family, the morphological features that define the genera and species and detailed descriptions of the 17 genera and 110 species. Keys to the genera and species are also provided. Phylogenetic relationships of the genera are given in a multi-locus tree based on combined SSU, ITS, LSU, EF1-α and β-tubulin sequences. The morphological descriptions are supplemented by phylogenetic trees (ITS alone or ITS + EF1-α) for the species in each genus.

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusariumwas proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceaebased on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusariumat the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu strictoas defined by F. sambucinum(sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium.Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceaelineages proposed as members of Fusarium. Species of Fusarium s. str.are characterised by Gibberellasexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusariumpresently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusariumis blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae(e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusariumup to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium(= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum,and F. sambucinumspecies complexes, but not species of Bisifusarium[F. dimerumspecies complex (SC)], Cyanonectria(F. buxicolaSC), Geejayessia(F. staphyleaeSC), Neocosmospora(F. solaniSC) or Rectifusarium(F. ventricosumSC). The present study represents the first step to generating a new online monograph of Fusariumand allied fusarioid genera (www.fusarium.org).