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Fungal complete genome


BMKGene offers versatile solutions for fungal genomes, catering to diverse research needs and desired genome completeness. Utilizing short-read Illumina sequencing alone allows the generation of a draft genome. For a more refined fungal genome with longer contigs, both short-reads and long-read sequencing using Nanopore or PacBio are combined. Moreover, the integration of Hi-C sequencing further enhances the capabilities, enabling the attainment of a complete chromosome-level genome.

Service Details


Demo Results

Featured publications

Service Features

With 3 possible options to choose from depending on the desired degree of genome completeness:

●   Draft genome option: short-read sequencing with Illumina NovaSeq PE150.

●   Fungal fine genome option:

                         Genome survey: Illumina NovaSeq PE150.

                         Genome assembly: PacBio Revio (HiFi reads) or Nanopore Promethion P48.

●    Chromosome-level fungal genome:

                        Genome survey: Illumina NovaSeq PE150.

                        Genome assembly: PacBio Revio (HiFi reads) or Nanopore Promethion P48.

                        Contig anchoring with Hi-C assembly.

Service Advantages

● Multiple sequencing strategies available: for different research goals and requirements of genome completeness

● Complete bioinformatics workflow: including not only genome assembly but also the prediction of multiple genomic elements, functional gene annotation and contig anchoring.

● Extensive Expertise: with over 10,000 microbial genomes assembled, BMKGENE brings over a decade of experience, a highly skilled analysis team, comprehensive content, and excellent post-sales support.

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

Service Specifications


Sequencing Strategy

Quality Control

Draft Genome

Illumina PE150 100x


Fine Genome

Genome survey: Illumina PE150 50 x

Assembly: PacBio HiFi 30x or Nanopore 100x

contig N50 ≥1Mb(Pacbio Unicellular)

contig N50 ≥2Mb(ONT Unicellular)

contig N50 ≥500kb(Others)

Chromosome-level genome

Genome survey: Illumina PE150 50 x

Assembly: PacBio HiFi 30x or Nanopore 100x

Hi-C Assembly 100x

Contig anchoring ratio>90%


Service Requirments


Concentration (ng/µL)

Total amount (µg)

Volume (µL)





















Unicellular fungus: ≥3.5x1010 cells

Macro fungus: ≥10 g


Service Work Flow

sample delivery

Sample delivery

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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    Includes the following analysis:

    Genome Survey:

    • Sequencing data quality control
    • Genome estimation: size, heterozygosity, repetitive elements

    Fine genome assembly:

    • Sequencing data quality control
    • De novo assembly
    • Genome component analysis: prediction of CDS and multiple genomic elements
    • Functional annotation with multiple general databases (GO, KEGG, etc) and advanced databases (CARD, VFDB, etc)

    Hi-C assembly:

    • Hi-C library assessment.
    • Contigs anchoring clustering, ordering and orienting
    • Evaluation of HI-C assembly: based on reference genome and heat map

    Genome survey: k-mer distribution


    Genome assembly: gene homologous annotation (NR database)



    Genome assembly: functional gene annotation (GO)


    Explore the advancements facilitated by BMKGene’s fungal genome assembly services through a curated collection of publications.


    Hao, J. et al. (2023) ‘Integrated omic profiling of the medicinal mushroom Inonotus obliquus under submerged conditions’, BMC Genomics, 24(1), pp. 1–12. doi: 10.1186/S12864-023-09656-Z/FIGURES/3.

    Lu, L. et al. (2023) ‘Genome sequencing reveals the evolution and pathogenic mechanisms of the wheat sharp eyespot pathogen Rhizoctonia cerealis’, The Crop Journal, 11(2), pp. 405–416. doi: 10.1016/J.CJ.2022.07.024.

    Zhang, H. et al. (2023) ‘Genome Resources for Four Clarireedia Species Causing Dollar Spot on Diverse Turfgrasses’, Plant Disease, 107(3), pp. 929–934. doi: 10.1094/PDIS-08-22-1921-A

    Zhang, S. S. et al. (2023) ‘Genetic and Molecular Evidence of a Tetrapolar Mating System in the Edible Mushroom Grifola frondosa’, Journal of Fungi, 9(10), p. 959. doi: 10.3390/JOF9100959/S1.

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