Draft genome assembly of hyper citric acid-producing Aspergillus niger mutant strain developed through gamma radiation bombardment

Abstract

Objectives

Aspergillus niger is a renowned filamentous fungus with extensive industrial and biotechnological applications. A. niger is widely used to produce diverse organic acids, enzymes, and other value-added metabolites. Although strain-specific metabolic capabilities have been widely applied in industry, the genomic foundations of these capabilities have not yet been fully characterized. Here, we have described the isolation and provided the draft genome sequence of A. niger strain AN-L103_M1 to further study the genetic determinants of primary and secondary metabolism, given its metabolic versatility and great potential in biotechnology. This A. niger strain was developed through gamma radiation bombardment, and subsequently, all the mutants were screened through various steps for hyperproduction of citric acid. This genome sequence provided valuable information for further functional genomics and strain-improvement research.

Data description

The A. niger strain was obtained through gamma radiation bombardment. After gamma radiation bombardment of the A. niger culture, it was subjected to various screening steps to achieve hyperproduction of citric acid. These experiments were performed in the Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan. The mycotoxin production potential of this mutant strain was assessed using LC-MS analysis, which detected no mycotoxins.

Objective

The Aspergillus niger strain is used to produce an extensive variety of organic acids, enzymes, and secondary metabolites [1]. This study aimed to develop and share a high-quality draft genome of the filamentous fungal developed A. niger strain (AN-L103_M1), which has strong potential for industrial-scale citric acid production. Due to its high secretion capacity, tolerance to low pH, and effective fermentation, A. niger is the leading microbial platform for commercial citric acid manufacturing. Each year, over 2.5 million tons of citric acid are produced worldwide, with growing use in food, medicine, cosmetics, and biodegradable detergents, supporting a multibillion-dollar market. Its genetic adaptability and metabolic efficiency allows A. niger to produce 80 to 90% of the global citric acid [2–4].

Citric acid serves as a metabolic intermediate in the Krebs cycle and is utilized in industry as an acidulant, buffering agent, metal chelator, excipient, and preservative (E330). The availability of a strain-specific genome assembly will simplify the identification of genes involved in carbon transport, glycolysis, TCA cycle flux, organic acid export systems, and global regulatory networks affecting acidogenesis. This analysis reports the draft genome sequence of an A. niger strain, developed via gamma radiation bombardment, which produces citric acid [5]. High-resolution genome data significantly enhance metabolic engineering efforts aimed at increasing yields and reducing by-products in industrial strains, as supported by recent genomic and systems biology research [6, 7]. Consequently, this genome assembly provides an essential genetic framework to facilitate comparative genomics, pathway reconstruction, and rational strain optimization for sustainable, commercially viable citric acid production.

Data description

The wild-type Aspergillus niger strain was sourced from Fermentation Biotechnology for Industrial Products Group, within the Industrial Biotechnology Division at the National Institute for Biotechnology and Genetic Engineering in Pakistan. The A. niger strain was cultured in Potato Dextrose Broth at 180 rpm and 30 °C. It was then exposed to different doses of gamma radiation (1.6, 1.8, 2.0, 2.2, and 2.4 KGy) [8]. Subsequently, it was passed through multiple screening steps to select the best strain for hyperproduction of citric acid [9]. The most effective strain was identified and proceeded for further research.

A. niger was grown in Potato Dextrose Broth at 30 °C and shaking (180 rpm) for 2 days [10]. Using the manufacturer’s guidelines, a high-quality and sufficient amount of DNA was extracted with the Thermo Scientific™ Gene JET Genomic DNA Purification Kit [11]. Its concentration and purity were measured with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, USA). The integrity of the genomic DNA was checked through agarose gel electrophoresis [12]. The Nextera XT Library Prep Kit (Illumina, San Diego, USA) was used to prepare genomic DNA libraries following the manufacturer’s guidelines, with two modifications: doubling the input DNA and extending the PCR elongation time (45s). Its library preparation and quantification were done using a Hamilton Microlab STAR automated liquid handling system (Hamilton Bonaduz AG, Switzerland). Sequencing was carried out on an Illumina NovaSeq 6000 using a 250 bp paired-end protocol. Applying Trimmomatic version 0.30, reads were adapter-trimmed, setting a sliding window quality cutoff of Q15 [13].

SPAdes version 3.7 is used for de novo assembly on samples [14], and Funannotate 1.8.17 was used to annotate contigs [15]. Trimmomatic was used to trim these raw Illumina reads, and internal scripts using the Samtools, BedTools, and bwa-mem software were used to assess the quality. After the fasta file was cleaned, it was assembled, and the assembly features were recorded using the QUAST online tool. Genome assembly and raw reads were submitted to NCBI, as details are written in Table 1.

Table 1.

Description of data file

Label	Name of data file/data set	File types (file extension)	Data repository and identifier (DOI or accession number)
Genome dataset II	281050_20240604Latif.fsa	Fasta contig (.fna)	NCBI GenBank Database https://identifiers.org/ncbi/insdc.gca:GCA_055944285.1 [16]
Genome dataset I	281050_20240604Latif1_1_trimmed.fastq (fastq) 281050_20240604Latif1_2_trimmed.fastq (fastq)	SRA file (.sra)	NCBI Sequence Read Archive https://identifiers.org/insdc.sra:SRR37288825 [17]

Limitations

The genome sequence presented in this article was studied for citric acid production. However, A. niger can produce a wide range of metabolites that could be subject of future studies.

Author contributions

AL contributed in performing experiments and DNA extraction. AL, HA and SH participated in executing the experiments and collection of data. AL and AA are involved in data cleaning and various in silico analysis. AL, MBKN, HA contributed in manuscript writing and final review. NH did final review and editing in manuscript. HA and SH supervised all the activities.

Funding

No funding.

Data availability

The genome assembly presented in this data note is publicly available through NCBI GenBank under accession GCA_055944285.1 and can be accessed via the persistent identifier https://identifiers.org/ncbi/insdc.gca:GCA055944285.1. The raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) under accession SRR37288825 and are available through the persistent identifier https://identifiers.org/insdc.sra:SRR37288825.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.