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

Abstract

pecies 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 acid 2,7,8), and secondary metabolites (including biopharmaceuticals and mycotoxins like ochratoxin A). Furthermore, the section members are generally very efficient producers of extracellular enzymes 9,10 ; they are the production organisms for 49 out of 260 industrial enzymes 11,12. Among the most important of these, in addition to A. niger, are A. tubingensis, A. aculeatus, and A. luchuensis (previously A. acidus, A. kawachii, and A. awamori 13-15 , respectively). Members of Aspergillus section Nigri are also known as destructive degraders of foods and feeds, and some isolates produce the potent mycotoxins ochratoxin A 16 and fumonisins 17-19. In addition, some species in this section have been proposed to be pathogenic to humans and other animals 20. It is thus of interest to further examine section Nigri for industrial exploitation, as well as prevention of food spoilage, toxin production, and pathogenicity caused by these fungi. A combined phylogenetic and phenotypic approach has shown that section Nigri contains at least 27 species 21-25. Recent results have shown that the section contains species with high diversity and may consist of two separate clades: the biseriate species and the uniseriate species 26 , which show differences in sexual states 27 , sclerotium formation 28 , and secondary metabolite production 29. In the section, only six species have had their genome sequenced: A. niger 2,8 , A. luchuensis 15,30 , A. carbonarius 31 , A. aculeatus 31 , A. tubingensis 31 , and A. brasiliensis 31. This section, with its combination of species richness and fungal species with a diverse impact on humanity, is thus particularly interesting for studying the diversification of fungi into species. In this study, we have de novo-sequenced the genomes of 20 species of section Nigri, thus completing a genome compendium of 26 described species in the section. Further, we have genome-sequenced three

Resistance Gene-Directed Genome Mining of 50 Aspergillus species

“…This pattern and the resulting resistance mechanism 96 has previously been described in two different cases in fungi (13,16). 97 We have used complete and draft quality whole genome sequences, mainly from 98 the 300 Aspergillus sequencing project (5,6). The input for the pipeline was chosen to 99 consists of three different types of data derived from the whole genome sequence data: 100 1) predicted genes/proteins and functionally annotated proteins, for the functional 101 annotation we used InterPro (19,20).…”

“…The input for the pipeline was chosen to 99 consists of three different types of data derived from the whole genome sequence data: 100 1) predicted genes/proteins and functionally annotated proteins, for the functional 101 annotation we used InterPro (19,20). 2) Predictions of secondary metabolite gene 102 clusters, for this purpose we used a re-implementation of SMURF (21) as described 103 in Vesth et al (6). 3) Groups of homologous protein sequences.…”

“…469 A few of the data files were too big for Github and can be found in this repository 470 instead https://files.dtu.dk/u/ox6SPjaekiyxHpI8/Data_tables_FRIGG?l. The data includes 471 predicted secondary metabolite gene clusters based on an implementation of the 472 SMURF (21) pipeline described elsewhere (6). Homologous protein families were 473 created with Aspergillus optimized parameters based on single linkage of bidirectional 474 BLASTp hits with identity ≥ 50% and sum of query and hit coverage ≥ 130% as described 475 in (6).…”

“…The data includes 471 predicted secondary metabolite gene clusters based on an implementation of the 472 SMURF (21) pipeline described elsewhere (6). Homologous protein families were 473 created with Aspergillus optimized parameters based on single linkage of bidirectional 474 BLASTp hits with identity ≥ 50% and sum of query and hit coverage ≥ 130% as described 475 in (6). InterPro annotations of the proteins were also used (19,20) and gff information.…”

Profiling of chromatin accessibility across Aspergillus species and identification of transcription factor binding sites in the Aspergillus genome using filamentous fungi ATAC-seq

“…There have been 339 species identified in the Aspergilli genus (Samson et al 2014), and they are of broad interest because of their industrial applications, importance as pathogens for animals and crops, and relevance for basic research. Aspergillus section Nigri is the fungal genus with the most sequenced genomes, as genomes from 27 species are already publicly available (Vesth et al 2018), and genomic analyses have led to a better understanding of fungal biology and improvements in the industrial use of these organisms (Pel et al 2007; Andersen et al 2011; Yin et al 2014). Gene regulation is of major way by which fungi physiologically act in environmental circumstances and respond to changing conditions (Todd et al 2014; Schape et al 2019).…”