Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes.

BACKGROUND: The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultural plants and soils. Collectively, members of FIESC can produce diverse mycotoxins. However, because the species diversity of FIESC has been recognized only recently, the potential of species to cause mycotoxin contamination of crop plants is unclear. In this study, therefore, we used comparative genomics to investigate the distribution of and variation in genes and gene clusters responsible for the synthesis of mycotoxins and other secondary metabolites (SMs) in FIESC. RESULTS: We examined genomes of 13 members of FIESC that were selected based primarily on their phylogenetic diversity and/or occurrence on crops. The presence and absence of SM biosynthetic gene clusters varied markedly among the genomes. For example, the trichothecene mycotoxin as well as the carotenoid and fusarubin pigment clusters were present in all genomes examined, whereas the enniatin, fusarin, and zearalenone mycotoxin clusters were present in only some genomes. Some clusters exhibited discontinuous patterns of distribution in that their presence and absence was not correlated with the phylogenetic relationships of species. We also found evidence that cluster loss and horizontal gene transfer have contributed to such distribution patterns. For example, a combination of multiple phylogenetic analyses suggest that five NRPS and seven PKS genes were introduced into FIESC from other Fusarium lineages. CONCLUSION: Our results suggest that although the portion of the genome devoted to SM biosynthesis has remained similar during the evolutionary diversification of FIESC, the ability to produce SMs could be affected by the different distribution of related functional and complete gene clusters.

Alternaria species associated to wheat black point identified through a multilocus sequence approach.

Black point is one of the most important wheat disease and its incidence is increasing worldwide due to climate change too. Among the fungal genera that can cause black point, Alternaria is one of the predominant genus, often associated with mycotoxin contamination. The correct identification is the baseline for prevention and control of the disease. Taxonomy of the genus Alternaria is not completely clear yet, since its species can be differentiated for few morphological traits and, in some cases, also molecular phylogeny is not very effective in establishing species boundaries. In this study, one-hundred sixty-four strains, isolated from wheat kernels affected by black point sampled worldwide, were analyzed in order to assess their identity. Sequences of elongation factor, ß-tubulin, glyceraldehyde-3-phosphate dehydrogenase and allergen alt-a1 genes were used to identify the variability of this population and their phylogenetic relationships. Isolates were grouped in two main clades: the Alternaria section, including A. alternata, A. tenuissima and A. arborescens species, and the Infectoriae section, that includes the two species A. infectoria and A. triticina. Comparison of isolates according with their area of isolation did not show a correlation between phylogeny and geographic origin. Indeed, the isolates grouped on the base of only their phylogenetic relationship. Due to the data arisen by our study, we strongly recommend a multilocus sequence approach to define Alternaria species, based on common genes and procedures to be unanimously shared by scientific community dealing with Alternaria genus. Moreover, we suggest that A. alternata, A. tenuissima, A. turkisafria and A. limoniasperae species would be merged in the defined species A. alternata. Finally we recommend to consider a taxonomic re-evaluation of the Infectoriae section that, for the morphology, sexuality, genetic and mycotoxin profile of the species included, could be defined as different fungal genus from Alternaria.