The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

Abstract

The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.

Keywords: Aspergillus; Genomic diversity; Gold standard genome; Sugar catabolism.

Fig. 1

Primary carbon metabolism pathways: summary overview of all pathways included in the A. niger NRRL 3 manually curated carbon metabolic network. Substrates are in green, reactions are depicted with an arrow, reversible reaction are indicated with double arrow. Enzyme Commission (EC) number for each reaction is indicated beside each reaction, while reactions are identified by numbers in brackets (for more information see Supplementary file 6). Proteins assigned to the reactions are indicated in black, common gene name used in A. niger is noted beside the protein ID where possible. Characterised enzymes are in red, enzymes involved in more than one reaction are indicated in lighter colour. Dash lines connect metabolites from different pathways. * The enzymes associated to that reaction form a complex. Each pathway is highlighted with a background shade, the legend for the shades is on the right.

Fig. 2

Phylogenetic tree, proteome assessment and orthology assessment. A) Phylogenetic tree inferred from 200 best bidirectional hits of 28 species. Sections are identified by colours, white indicates the section is not determined. Name of the genus and sections are indicated in the left of the figure. Bold letters indicated the species selected for further analysis. B) Protein conservation, calculated using BUSCO v.3 indicates the degree of completeness of the proteins predicted per genome against a database of conserved proteins, bars showing number of proteins being aligned to individual species to the left-hand side. Black line indicates where the value 150 is in the graph. Species with number of fragmented proteins (red bar) higher than 150 were removed from the analysis. Dark blue: complete genes (duplicated and single), light blue: complete single genes, red: fragmented, and yellow: missing. C) Total number of proteins included in the gene family orthology against the total number of proteins predicted. Bars indicates the size of the genome (Kb), number of proteins in the proteome and number of proteins included in phylogeny aligned to individual species to the left-hand side. Green, size of genome (Kb); red, total proteome predicted; and purple, total number of proteins included in the gene families.

Fig. 3

Glycolysis heatmap abundance of A. niger orthologous proteins in the glycolytic pathway. Columns are arranged according to the phylogenetic tree and rows are arranged according to the order in which the enzymatic reaction occur in A. niger metabolism. Top: The graph on the top represents growth from 0 to 10 with no carbon source (black), d-glucose (light grey) and d-fructose (dark grey). The line below represents the section to which the species belong according to the phylogenetic tree, colours match the colours in the tree. Heatmap row names: Identifiers on the right of the heatmap are according to the group name (see Materials and Methods). The name after the identifier correspond to the protein common name used in A. niger. Red: protein has been characterised in A. niger. Lighter colour: the protein is involved in more than one pathway. EC numbers column: colours correspond to EC number associated to the function they have been assigned. EC colour legend is on the right-hand of the figure. Reaction ID number are in brackets, see Supplementary file 6 for more information. Cluster column: colours correspond to clusters in which proteins have been found. Bottom legend: species abbreviation according to Table 1. Aspzo1: Penicilliopsis zonata, Aspfp1: Aspergillus luchuensis.

Fig. 4

Glyoxylate and TCA cycles heatmap abundance of A. niger orthologous proteins in the glyoxylic and TCA pathways. The legends are the same as that of Fig. 3. MdhA_P: peroxisomal MdhA and MdhA_M: mitochondrial MdhA.

Fig. 5

d-gluconate heatmap abundance of A. niger orthologous proteins in the d-gluconate catabolic pathway. The legends are the same as that of Fig. 3. Full group name: ^a NRRL3_09685_like, NRRL3_04261_like, NRRL3_02841_like, NRRL3_08917_like and ^b NRRL3_08779_like, NRRL3_06731_like and NRRL3_05649_like.

Fig. 6

Maltose heatmap abundance of A. niger orthologous proteins in the maltose catabolic pathway. The legends are the same as that of Fig. 3.

Fig. 7

Sucrose heatmap abundance of A. niger orthologous proteins in the sucrose catabolic pathway. The legends are the same as that of Fig. 3 .

Fig. 8

d-mannose heatmap abundance of A. niger orthologous proteins in the d-mannose catabolic pathway. The legends are the same as that of Fig. 3.

Fig. 9

d-galactose heatmap abundance of A. niger orthologous proteins in the d-galactose catabolic pathways. The legends are the same as that of Fig. 3.

Fig. 10

d-galacturonic and glycerol heatmap abundance of A. niger orthologous proteins in the d-galacturonic and glycerol catabolic pathways. The legends are the same as that of Fig. 3.

Fig. 11

l-rhamnose heatmap abundance of A. niger orthologous proteins in the l-rhamnose catabolic pathways. The legends are the same as that of Fig. 3.

Fig. 12

Pentose metabolism heatmap abundance of A. niger orthologous proteins in the pentose metabolic pathways. The legends are the same as that of Fig. 3.