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

Abstract

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. Electronic supplementary material The online version of this article (10.1186/s12864-019-5567-7) contains supplementary material, which is available to authorized users.

Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium

“…The presence of homologous SAM clusters in the Dothideomycetes, Eurotiomycetes, Lecanoromycetes and Sordariomycetes indicate that HGT of SAM clusters could have occurred between fungal genera and even between classes of fungi. Together, the inferences of HGT of SAM clusters among fusaria reported in the current study and inferences of HGT of PKS and nonribosomal peptide synthetase genes between members of the F. incarnatumequiseti species complex and other lineages of Fusarium [49] provide evidence that HGT has significantly impacted the distribution of secondary metabolite biosynthetic genes and, therefore, production of secondary metabolites in Fusarium.…”

“…We used previously described approaches [18,49] to assess the potential contribution of HGT to the discontinuous distribution of SAM clusters among Fusarium species. The approaches were: 1) reconciliation analysis with the program NOTUNG, which infers HGT, duplication or loss of genes to reconcile branch conflicts between gene trees and species trees; 2) constraint analysis with the Shimodaira-Hasegawa and Approximately Unbiased (SH-AU) tests; and 3) estimates of synonymous site divergence.…”

Evolutionary Histories of Type III Polyketide Synthases in Fungi

“…This number is nearly the double of the reported HGT frequency of 4% for metabolic enzymes (Wisecaver et al, 2014), but is much lower than the 25-35% reported for SM gene clusters by Marcet-Houben and Gabaldón (2019). Manual inspection of inferred HGTs in our study suggests that the total number of events is actually overestimated by reconciliation software like NOTUNG, which has been recently reported (Villani et al, 2019). The weak support of certain branches is likely due to accelerated evolution in certain fungal species, as exemplified with Z. cellare (Zasce1) in clade 1 and P. niveus (Bysni1) in clade 7.…”

Fungal Diversity and Mycotoxins in Low Moisture Content Ready-To-Eat Foods in Nigeria

“…Eight Aspergillus species covering four sections were recovered in this study: Samson et al, 2007;Perrone et al, 2011;Varga et al, 2011). The Fusarium isolates comprised two species (F. chlamydosporum and F. incarnatum/equiseti species complex; O' Donnell et al, 2013;Villani et al, 2019) and one unresolvable species reported here as Fusarium sp. The Penicillia were clustered into four sections: Charlesia (P. coffeae; Visagie et al, 2014c), Citrina (P. citrinum, P. copticola, P. paxilli, and P. steckii; Visagie et al, 2014b), Lanata-Divaricata (P. rolfsii; , and Sclerotiora (P. sclerotiorum; Rivera and Seifert, 2011;Visagie et al, 2014b).…”