A comparative genomics study of 23 Aspergillus species from section Flavi

Abstract

Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.

Comparative genome and transcriptome analyses revealing interspecies variations in the expression of fungal biosynthetic gene clusters

“…Since the first fungal genomes were published, the potential of fungi to produce a wide variety of secondary metabolites has become generally accepted. Comparative genomics studies regarding fungal SMs have been intensively conducted during this decade, revealing the genetic diversity, universality, and plasticity of SM gene clusters in fungal genomes (5,6,9,10,38,39). Variations in SMs produced by fungi allow their metabolites to be used for medical and biotechnological applications.…”

“…A bootstrap was conducted with 1,000 replications (47). A genome synteny analysis was conducted as described previously (6).…”

“…Comprehensive genomic studies in Aspergillus sections Nigri and Flavi also showed overlaps of SM genes at specific rates. These reports provide an evolutionary insight into how secondary metabolic pathways evolve and degenerate in filamentous fungi (5,6).…”

“…The backbone gene and additional genes encoding a tailor enzyme, transcriptional regulator, and efflux pump are often arrayed in a biosynthetic gene cluster (BGC). Fungi, including phytopathogens and human pathogens, possess large numbers of SM gene cluster in their genomes, which indicates a potent ability to produce a myriad of metabolites that could be used to impact humans (4–6).…”

Characterization of two family AA9 LPMOs from Aspergillus tamarii with distinct activities on xyloglucan reveals structural differences linked to cleavage specificity

“…The genome of A. tamarii CBS 117626 has only recently been published, and it contains nine predicted proteins annotated as AA9 LPMOs [54]. Previous analysis of the transcriptome of A. tamarii BLU37 during cultivation on steam-exploded sugarcane bagasse as exclusive lignocellulosic carbon source [39] revealed seven expressed genes encoding putative AA9 enzymes, which we named AtAA9A, AtAA9B, AtAA9C, AtAA9D, AtAA9E, AtAA9F, and AtAA9G (see S1 Table for the predicted sequences, S2 Table for related LPMOs, including AA9s found in the A. tamarii CBS 117626 genome, as well as the closest related characterized LPMOs from aspergilli, and S3 Table for predicted properties in S1 Appendix).…”