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.

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

“…Generated MS/MS spectra were searched using the mass spectral generating function plus (MSGF+) algorithm (Kim et al ., ; Kim and Pevzner, ) against the A. niger translated genome sequence available from Aspni_NRRL3_1 (Aguilar‐Pontes et al ., ). Identified peptides of at least six amino acids in length having MSGF scores ≤1E −10 , which corresponds to an estimated false discovery rate (FDR) < 1% at the peptide level, were used to generate an accurate mass and time (AMT) tag database (Zimmer et al ., ).…”

“…Data quality was assessed with htseq‐qa (Kim et al ., ). Reads were aligned to the A. niger NRRL3 genome (Aguilar‐Pontes et al ., ) using TMAP 3.0.1, with the – g parameter set to 0 and the – a parameter set to 1. The RNAseq data set was deposited at the GEO (Barrett et al ., ) database under the accession number GSE118894.…”

A seven-membered cell wall related transglycosylase gene family in Aspergillus niger is relevant for cell wall integrity in cell wall mutants with reduced α-glucan or galactomannan

“…Raw RNA-seq read sets were retrieved from the Génome Québec’s Nanuq portal, and pre-processed with BBDuk from the BBTools package ( https://sourceforge.net/projects/bbmap ) to trim sequencing adapters and remove reads derived from PhiX and ribosomal RNA. The transcriptome of A. niger NRRL3 (v. 20140311) was retrieved from the jgi Genome portal ( Aguilar-Pontes et al, 2018 ), and the libraries were mapped to the transcriptome using Salmon v0.14.1 ( Patro et al, 2017 ). The libraries were imported in RStudio 1.2.5001 ( RStudio: Integrated Development for R. RStudio, Inc., Boston, 2016 ) running R 3.6.1 ( R Development Core Team 3.6.1., 2019 ) using txtimport v.1.12.3 ( Soneson et al, 2016 ).…”

Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation

“…This is due to the recently established methods such as CRISPR/Cas9 genome editing and the potential of implementing epigenetics. These tools are still being further developed to higher efficiency and are accompanied by improved fungal genome sequences, exemplified by the gold-standard genome for A. niger (Aguilar-Pontes et al, 2018) and the recently initiated genome sequencing project of the Joint Genome Institute of the Department of Energy of the USA (https://jgi.doe.gov/csp-2019-finishing-genomes/). This diversity of possibilities for strain engineering will facilitate a more strategic choice in the best approach for a certain ultimate aim also keeping in mind legislation/public acceptance with respect to GMO methodology.…”