Abstract
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 carbohydrate-active 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.
Highlights
Species in the genus Aspergillus are of broad interest to medical[1], applied[2,3], and basic research[4]
Additional A. niger isolates, which in combination with the other analyses allows for inter- and intraspecies comparison of 32 isolates
We present 23 whole-genome draft sequences: 20 genomes of section Nigri species previously unsequenced and 3 additional A. niger genomes for assessment of intraspecies diversity
Summary
Species in the genus Aspergillus are of broad interest to medical[1], applied[2,3], and basic research[4]. Members of Aspergillus section Nigri (‘black aspergilli’) are prolific producers of native and heterologous proteins[5,6], organic acids (in particular citric acid2,7,8), and secondary metabolites (including biopharmaceuticals and mycotoxins like ochratoxin A). Members of Aspergillus section Nigri are known as destructive degraders of foods and feeds, and some isolates produce the potent mycotoxins ochratoxin A16 and fumonisins[17,18,19]. We have de novo-sequenced the genomes of 20 species of section Nigri, completing a genome compendium of 26 described species in the section. The high resolution in genome sequences allows us to characterize both species diversification and variation within species
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