Fungal Genome Editing

Aspergillus niger Genome Editing Services

Accelerate your strain engineering projects with our validated CRISPR/Cas9 editing workflow tailored for Aspergillus niger.

Custom guide RNA design and synthesis
Efficient protoplast transformation
PCR and sequencing validation of edits

Why Choose Our A. niger Editing Service?

Streamlined genome editing for research and industrial strains, backed by experienced fungal biologists.

CRISPR/Cas9 ribonucleoprotein or plasmid delivery
Marker selection and recycling options
Single or multi-gene editing capabilities

Experienced fungal biologists

Custom strain background

Rapid turnaround

Our Approach

Our approach

We combine customized guide RNA design with optimized protoplast transformation protocols to achieve precise genome modifications in your Aspergillus niger strains. Our service covers both wild-type and industrial strains, with Sanger sequencing verification of all edits. Using validated CRISPR/Cas9 systems, we deliver targeted knockouts and, on a case-by-case basis, precise knock-ins or point mutations. Each project is scoped to your specific strain background and editing goals.

Guide RNA Design & Construction

We design and synthesize high-specificity guide RNAs targeting your gene of interest, using in silico off-target analysis to minimize unintended edits.

Custom gRNA design based on your target sequence
In silico off-target prediction
Synthesis of gRNA expression cassettes

Transformation & Selection

Protoplast-mediated transformation with Cas9 RNP or plasmid DNA, followed by marker-based selection of edited clones.

Efficient protoplast preparation
Selection on appropriate media
Rapid screening of primary transformants

Deliverables

What You Receive

A complete package of edited strains and supporting data.

Edited Strains & Clones

Isolated edited A. niger clones (quantity scoped per project)
Parental control strain for comparison
Glycerol stocks of confirmed edited isolates

Documentation & Data

Full sequencing data confirming the intended edit
Project report detailing design, transformation, and QC results
Genotyping PCR gel images or capillary electrophoresis traces

Service Scope

Parameter	Typical project scope
Target gene(s)	Genes per project (multi-gene on request)
Guide RNAs per target	Multiple gRNAs designed and tested (number defined during project scoping)
Transformation method	Protoplast transformation with RNP or plasmid
Selection marker	Hygromycin, nourseothricin, or auxotrophic (as scoped)
Clone screening depth	Number defined during project scoping
Validation	PCR + Sanger sequencing; optional whole-genome re-sequencing
Marker recycling	With mxr/pyrG systems when selected

Workflow

How It Works

A five-step process from design to delivery of validated edited strains.

Project Initiation & Design

We review your target gene(s) and strain background, perform in silico guide RNA design, and select appropriate transformation and selection strategies.

Guide RNA Construction

Synthesis of single guide RNAs and assembly into expression cassettes using validated promoters for A. niger.

Protoplast Transformation

Preparation of fresh protoplasts from your A. niger strain and transformation with Cas9 RNP or plasmid DNA carrying the gRNA and marker.

Selection & Clone Isolation

Recovery of transformants on selective media, picking colonies, and transferring to fresh plates for further growth.

Validation & Handover

Screening transformants by PCR for evidence of editing, followed by Sanger sequencing to confirm precise modification. Selected clones are provided as glycerol stocks with full QC report.

Applications

Improving Enzyme Production

Targeted gene editing to modify enzyme-encoding genes for improved expression, altered substrate specificity, or reduced protease background.

Knockout of repressor genes
Knock-in of enzyme variants
Multi-gene pathway optimization

Citric Acid & Organic Acid Production

Modify central carbon metabolism to increase citric acid yield or redirect flux to other organic acids.

Gene knockout in TCA cycle
Overexpression of rate-limiting enzymes
Deletion of competing pathways

Functional Gene Studies

Elucidate gene function by targeted knockout or precise point mutation in A. niger.

Knockout mutants for candidate genes
Complementation studies
Phenotypic analysis support (scope-dependent)

Frequently Asked Questions

Our standard service supports gene knockout via CRISPR/Cas9. Precise knock-in and point mutations can be performed on a case-by-case basis using repair templates; the feasibility depends on target locus and strain.
Primary screening uses diagnostic PCR to detect the edit, followed by Sanger sequencing of the target region. Optional whole-genome sequencing can be added to assess off-target changes if needed.
Yes, we can accept confidential strains under a materials transfer agreement. Our protocol is optimized for both laboratory and industrial A. niger strains, though we recommend a feasibility test for non-standard backgrounds.
Project timelines are provided during the quotation phase. Typical single-gene knockout projects require a timeline confirmed during project scoping.

Scientific Literature

References

Zheng X, Zheng P, Sun J. [CRISPR/Cas-based genome editing in Aspergillus niger]. Sheng wu gong cheng xue bao = Chinese journal of biotechnology. 2021;37(3):980-990. View on PubMed
Shen Y, Chen Z, Chen J, et al. [An efficient marker-free genome editing method for Aspergillus niger]. Sheng wu gong cheng xue bao = Chinese journal of biotechnology. 2022;38(12):4744-4755. View on PubMed
Yuan G, Deng S, Czajka JJ, et al. CRISPR-Cas9/Cas12a systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger. Frontiers in bioengineering and biotechnology. 2024;12:1452496. View on PubMed
Song L, Ouedraogo JP, Kolbusz M, et al. Efficient genome editing using tRNA promoter-driven CRISPR/Cas9 gRNA in Aspergillus niger. PloS one. 2018;13(8):e0202868. View on PubMed
Li C, Zhou J, Rao S, et al. Visualized Multigene Editing System for Aspergillus niger. ACS synthetic biology. 2021;10(10):2607-2616. View on PubMed

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