Apiospora arundinis, a panoply of carbohydrate-active enzymes and secondary metabolites

Abstract

The Apiospora genus comprises filamentous fungi with promising potential, though its full capabilities remain undiscovered. In this study, we present the first genome assembly of an Apiospora arundinis isolate, demonstrating a highly complete and contiguous assembly estimated to 48.8 Mb, with an N99 of 3.0 Mb. Our analysis predicted a total of 15,725 genes, with functional annotations for 13,619 of them, revealing a fungus capable of producing very high amounts of carbohydrate-active enzymes (CAZymes) and secondary metabolites. Through transcriptomic analysis, we observed differential gene expression in response to varying growth media, with several genes related to carbohydrate metabolism showing significant upregulation when the fungus was cultivated on a hay-based medium. Finally, our metabolomic analysis unveiled a fungus capable of producing a diverse array of metabolites.

Keywords: Apiospora; Arthrinium; CAZymes; Oxford Nanopore sequencing; Secondary metabolites.

Fig. 1

A circular representation of the genome of A. arundinis AAU 773. Gene density and repeat density were calculated using bins of 10,000 kbp. Circles from the outside to the inside show the position of the telomeric regions, the gene density, the repeat density, the placement of the secondary metabolite genes, the placement of the CAZyme genes, the position of the rRNA genes, the placement of the tRNA genes, coverages of Illumina reads, and coverages of Nanopore reads

Fig. 2

Phylogenic tree of Apiospora and Arthrinium based on sequences of ITS regions. Dots on branches represent bootstrap values (1,000). The tree was rooted with the ITS region from Fusarium graminearum (CBS:131778)

Fig. 3

Transcriptomic analysis of A. arundinis AAU 773 cultivated on different media. A Principal component analysis of the gene expression in fungus cultivated on different media. Arrows represent the eight highest loadings of PC1 and PC2. Red arrows represent genes associated with CAZymes and blue arrows represent genes with GO terms associated with transport. B Hierarchal clustering heatmap of upregulated and downregulated DEGs. Colors show the z-score of the transformed gene expression. C. CAZymes observed to be expressed by the fungus cultivated on different media. Only CAZymes with at least one z-score above 1.6 were included. The numbers represent the amount of CAZymes expressed by the fungus cultivated on this medium. Lower panel presents the sum of gene expression level observed in all samples

Fig. 4

Enrichment analysis of DEGs calculated between the transcriptome of A. arundinis AAU 773 cultivated on different media as a response to growth media. Only significantly enriched terms were included (FDR < 0.01). The GO terms were reduced to a higher term if such a term was observed. For full data, see Additional file 2, Figure S1. BP: biological process, MF: molecular function, CC: cellular component

Fig. 5

Principal component analysis of the A. arundinis AAU 773 metabolomes when cultivated on different media

Fig. 6

Feature-based molecular network of A. arundinis AAU 773 cultivated on different media. Four clusters are highlighted, ID of each node is presented on the side of the node. Color of lower circles in the nodes represent features that are overproduced (green) or underproduced (red) in the metabolomes of fungus cultivated on HTM. Color of upper circles in the nodes represent features that are overproduced (green) or underproduced (red) in the metabolomes of fungus cultivated on YES. Dotted edges represent MS1 feature shape correlation, straight lines represent MS2 similarity

Fig. 7

Gene synteny plot. A Synteny analysis between NRPS2 (ferricrocin) gene cluster in Fusarium pseudograminearum CS3096 (Tobiasen et al. 2007) and an NRPS gene cluster in A. arundinis AAU 773. B Synteny analysis between an NR-PKS (norlichexanthone) gene cluster in Penicillium aethiopicum IBT 5753 (Cacho et al. 2013) and an NR-PKS gene cluster in A. arundinis AAU 773. C Synteny analysis between a fatty acid synthases (alkylcitric acids) gene cluster in Aspergillius niger NRRL3 (Palys et al. 2020) and a fatty acid synthases gene cluster in A. arundinis AAU 773. Arrows represent the different genes in the gene clusters