Fungal Whole-Genome Resequencing

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Fungal Whole-Genome Resequencing

Fungal whole-genome resequencing is a critical tool to complete the genomes of known fungi and to perform comparative genome analysis or map genomes of new organisms. CD Genomics is proud to offer fungal whole-genome resequencing using long-read sequencing technologies, including ONT and PacBio SMRT sequencing. We have extensive experience in fungal whole-genome resequencing projects and are committed to providing comprehensive and accurate genome resolution results.

Fungal Whole-Genome Resequencing using Third-Generation Sequencing Technology

Oxford Nanopor minION with flow cell.

With the significant increase in the availability of the complete genome of the fungus, there has been an exponential growth of various genes encoding organic acids, antibiotics, enzymes, and their pathways. The study of fungal genomics provides a broad and accurate perspective on mycology, which plays an important and positive role in human health and environmental health, among others. Genome sequencing and assembly of fungi based on third-generation sequencing technologies is capable of spanning complex repetitive regions to generate a high-quality complete genome sequence. In particular, Oxford Nanopore Sequencing Technology (ONT) takes full advantage of the ultra-long read length to easily span these complex structures in the fungal genome. This technology provides an affordable and powerful tool for the generation of high-quality genome assemblies and has been widely applied to the study of prokaryotes and eukaryotes, including fungi.

Workflow of Our Fungal Whole-Genome Resequencing

Workflow of Our Bacterial Whole Genome Resequencing - CD Genomics

Sample Requirements

  1. Sample Type: Genomic DNA, OD260/280=1.8~2.0, no degradation and no contamination
  2. Fungal DNA amount:
    -Illumina HiSeq platform: ≥ 2 μg,
    -PacBio Sequel ll platform: ≥ 10 μg,
    -Nanopore PromethION platform: ≥ 10 μg.
  3. Read length:
    -PacBio Sequel II platform: average > 15 kb.
    -Nanopore PromethION platform: average > 17 kb.
  4. Sequencing strategy:
    -Illumina HiSeq platform: recommend sequencing coverage of ≥50×.
    -PacBio Sequel ll platform: 20Kb SMRTbell library, CLR sequencing, ≥100X genome coverage depth.
    -Nanopore PromethION platform: ONT Library preparation, ≥100X genome coverage depth.

Data Analysis Contents

Data Analysis Contents -CD Genomics

Application of Our Service

Saccharomyces cerevisiae yeast.
  • Study of plant pathogenic fungi.

Identification of genes related to the interaction between pathogenic fungi and crops and pathogenicity, the study of evolutionary relationships with their relatives, comparative genomic studies, and so on.

  • Investigation of edible and medicinal fungi, such as industrial yeast research

Identification and mining of beneficial functional genes for humans, the study of species evolutionary relationships, and so on.

  • Biological control fungal research.

Discovery of complex metabolic pathways of fungi and analysis of pathogenic factors of pathogenic fungi.

CD Genomics focuses on innovative applications of long-read sequencing technologies, genomics analysis methods, and internet concepts in the pharmaceutical and biotechnology industries, science, and agricultural research. Thank you for your interest in our services. We'd love to work with you. Please send us your questions or comments via the form below.


  1. Sharma, K. K. (2016). "Fungal genome sequencing: basic biology to biotechnology." Critical reviews in biotechnology, 36(4), 743-759.
  2. Massonnet, M., et al. (2018). "Whole-genome resequencing and pan-transcriptome reconstruction highlight the impact of genomic structural variation on secondary metabolite gene clusters in the grapevine esca pathogen Phaeoacremonium minimum." Frontiers in microbiology, 9, 1784.
  3. Hao, Z., et al. (2021). "Genome Sequence Analysis of the Fungal Pathogen Fusarium graminearum Using Oxford Nanopore Technology." Journal of Fungi, 7(9), 699.
For Research Use Only. Not for use in diagnostic procedures.

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