The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

The genus Alternaria includes both plant-pathogenic and saprophytic species, which may affect crops in the field or cause harvest and postharvest decay of plant products. The taxonomy of the genus Alternaria is not well-defined yet. A polyphasic approach based on morphological features, phylogeny and toxin profiles could be the key to a correct identification at species level and the evaluation of mycotoxin risks associated with fungal contamination. Species of Alternaria are known to produce many metabolites, mostly phytotoxins, which play an important role in the pathogenesis of plants. However, certain species, in particular the most common one A. alternata, are capable of producing several mycotoxins in infected plants and/or in agricultural commodities. The major Alternaria mycotoxins belong to three structural classes: the tetramic acid derivative, tenuazonic acid; the dibenzopyrone derivatives, alternariol, alternariol monomethyl ether and altenuene; and the perylene derivatives, the altertoxins. The toxic effects of the Alternaria toxins have not yet received the same attention as the biological activities of other mycotoxins. However, the Alternaria mycotoxins should not be underestimated since they are produced by several Alternaria species frequently associated with a wide range of diseases in many plants of a high agrifood value. The major problems associated with Alternaria mycotoxin contamination of agricultural products are illustrated by focusing on various crops and their relevant diseases, e.g. black rot of tomato, olive, and carrots; black and grey rot of citrus fruits; black point of small-grain cereals; and Alternaria diseases of apples.

In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.