A comparative genomics study of 23 Aspergillus species from section Flavi

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.Peer reviewe

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter-and intraspecies genomic variation. We further predicted 17,903 carbohydrateactive enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.Peer reviewe

RNA guided induced DNA DSBs efficiently stimulate gene targeting in <i>A</i>. <i>nidulans</i> and <i>A</i>. <i>aculeatus</i>.

<p><i>A</i>. <i>nidulans</i> and <i>A</i>. <i>aculeatus</i> were co-transformed with a CRISPR-Cas9 plasmid in combination with a gene targeting substrate. <i>yA</i> of <i>A</i>. <i>nidulans</i> was targeted by a linear gene targeting substrate; and <i>albA</i> of <i>A</i>. <i>aculeatus</i> was targeted by a linear as well as by a circular gene targeting substrate as indicated to the left of panels. The presence of an sgRNA gene (<i>yA</i> specific for <i>A</i>. <i>nidulans</i> and <i>albA</i> for <i>A</i>. <i>aculeatus</i>) gene in the CRISPR-Cas9-vector is indicated above panels. Selection conditions for each experiment are indicated above panels. Single selection refers to selection for the gene substrate alone; and double selection refers to selection for both the gene targeting substrate and the CRISPR-Cas9 vector.</p

Strains used in this study to implement functional CRISPR.

<p>Strains used in this study to implement functional CRISPR.</p