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Fungal Whole Genome Sequencing


Fungi, a large group of eukaryotes, consist of microorganisms such as yeast and mold, as well as well-known mushrooms. Many beneficial fungi have important nutritional and medicinal value. Meanwhile, a large number of pathogenic fungi can cause disease in humans, animals, or plants. With the maturity of high-throughput sequencing technologies, the cost of genome sequencing has been greatly reduced, making it possible to sequence fungal genomes quickly and economically. Fungal whole genome sequencing allows us to obtain the genome sequence of fungi and study their structure and function.

Our Advantages:
  • Advanced sequencing platforms: Illumina HiSeq, Nanopore MinION, and PacBio SMRT platforms.
  • Cloud-based platform for bioinformatics analysis.
  • Rapid, efficient, flexible workflow for sequencing and data analysis.
  • Extensive experience in the industry of genomic service.
  • Keep up with the frontiers of microbial genomics and bioinformatics analysis.
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Introduction to our fungal whole genome sequencing platform

We provide next generation sequencing (NGS) and long-read sequencing technologies for fungal whole genome sequencing. Our sequencing platforms include the advanced Illumina HiSeq/MiSeq (PE150/251), Nanopore, and PacBio SMRT instruments, which can quickly, efficiently produce high-quality sequencing data. Fungal whole genome sequencing includes two categories: fungal genome de novo sequencing and fungal genome resequencing. The workflow for fungal genome de novo sequencing includes the following steps: (1) the chromosomal DNA is randomly interrupted; (2) different lengths of sequences are selected to construct a library; (3) large-scale sequencing; (4) genomic assembly without any prior genome information; (5) fill the gaps on the draft genomes. The genome sequence of fungal individuals or populations can also be determined through alignment to reference genome sequences using the homogeny of sequences as an index. Such a method, called fungal whole genome resequencing, is a quick and accurate method for detection of variants and other uses.

Fungal whole genome sequencing can be used to identify pathogenic fungi, genes related to pathogen and host interaction, and the evolutionary relationships among closely related species. For edible and medicinal fungi, it can be used to discover complex metabolic pathways and to identify metabolites which are beneficial to human health. And some fungi have implications for biological control or industrial applications. Our platform provides a wealth of data on the fungal genome sequence, thereby enhancing research in medical science, agriculture science, ecology, bioremediation, bioenergy, and biotech industries.

Microbial diversity analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis includes: genomic assembly, genomic structure studies, functional annotation, pathogenic microbiology, and comparative genomic analysis.

Genomic Assembly Genomic assembly and outcome evaluation
Coding/noncoding gene prediction
Repetitive sequence analysis
Genomic Structure Analysis Genomic island prediction
Prophage prediction
Detection of CRISPRs
LncRNA prediction
Functional Annotation NR, GO, COG, KEGG, SwissProt, Pfam, TCDB, SignalP, CAZy
Pathogenic Microbiology Drug resistance gene database (ARDB)
Virulence factor database (VFDB)
The comprehensive antibiotic resistance database (CARD)
Comparative Genomic Analysis Synteny analysis
Analysis of gene family evolution
Phylogenetic analysis
ANI analysis

Sample Requirement

Sampling kits: We provide a complete range of microbial sampling kits for clients, including microbial collection products, DNA/RNA isolation kits, and accessories for storage and mailing.

Deliverables: Raw sequencing data, assembled and annotated sequences, quality-control dashboard, and the bioinformatics report.

References

  1. Martinez D, Larrondo L F, Putnam N, et al. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature biotechnology, 2004, 22(6): 695.
  2. Quail M A, Smith M, Coupland P, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC genomics, 2012, 13(1): 341.

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