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Microbial Whole Genome Sequencing

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Microbial Whole Genome Sequencing

CD Genomics can offer complete genome de novo sequencing services for bacteria, yeast, fungi, phage and virus, by combining Illumina (short reads) and PacBio (long reads) data and also the whole genome re-sequencing, which is a very cost effective approach with only the Illumina system.

Bacteria are microscopic single-celled organisms that thrive in the soil, in the ocean, and inside the human gut, sometimes they lend a helping hand, and at other times they are destructive. The genes in bacterial genomes are usually a single continuous stretch of DNA. Microbial whole-genome sequencing (WGS) yields tons of data enabling a comprehensive evaluation of all genetic feature of an isolated bacterium, which is crucial for precise microbial identification, generating accurate reference genomes and comparative genomic studies to identify low-frequency variants and genome rearrangements. The sequencing steps do not need labor-intensive cloning, which saves tremendous time and money. Furthermore, high-throughput sequencing allows customers to sequence hundreds of bacteria at the same time with the power of multiplexing.

The individual bacterial whole-genome shotgun do novo sequencing has a variety of application including comparative genomics, which compares the sequence to that of a known reference and reveals important differences in genomic composition and organization by analyzing the diverse new bacterial genomes, and exploiting genomics, which facilitates high-throughput screening of functional genes involved in fuels bioprospecting, food fermentation and drug discovery. Bacterial WGS holds great promise for enhancing pathogen diagnostics, as well as industrial, agricultural and environmental strains exploration.

Fungi play a critical role in the environment through the decomposition of organic material and through symbiotic relationships with prokaryotes, plants, and animals. Genomic information of fungi can help researchers investigate key fungal genes and proteins to reveal their specific functions and predict metabolic pathways. The sequencing of fungal genomes has greatly expanded our understanding of the genetic, physiological, and ecological diversity of these organisms and has intensively enhanced research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Its board application areas are illustrated in Figure 1.

Fungal genome sequencing has wide applications Figure 1. Fungal genome sequencing has wide applications.

Recommend Sequencing Platform and Sequencing Depth

  • HiSeq PE150 and PacBio SMRT
  • Sequencing coverage ≥ 100X

Sample Requirements

Small number and large number of microbial samples from a wide variety of sources can be sequenced and analyzed. Customers may submit pure cultured samples for gDNA extraction services or submit extracted genomic DNA. All DNA samples are validated for purity and quantity and subject to quality control prior to processing. The recommended DNA amount for submission is 2 µg or more with a concentration of ≥ 20 ng/µl.

Experimental Workflow and Data Analysis

In the process, short-insert or long-insert libraries are generated using TruSeq or Nextera protocols and include a unique barcode sequence, followed by sequencing on Illumina HiSeq system or PacBio SMRT system.

A wide range of analyses can be conducted including de novo assembly, reference genome mapping, genome annotation (pathogenic and susceptibility genes prediction, non-coding RNA prediction CRISPRs prediction), gene function annotation, (COG/ GO/ KEGG), SNP/InDel identification and annotation and comparative genomics analysis.

We provide the comprehensive service from microbial DNA isolation, library preparation, next generation sequencing, to de novo assembly & annotation, by harnessing our unique bioinformatics analysis capabilities, up-to-date software tools and databases, and microbiology based expertise. We are able to provide draft whole-genome sequence or complete genome sequence based on your research objectives. We have sequenced and assembled significant numbers of bacteria in the medical, industrial, environmental and agricultural field. These sequencing services are useful for gene finding, characterizing antibiotic resistance, variant detection, genome comparisons and diagnostics of infectious organisms. With our annotation service, you can search easily for specific genes, enzymes and proteins in your genomes. You can choose a variety of options regarding the library construction method, the depth of coverage, and the data analysis strategies and so on based on your study's aims and the size of the genome. If you have additional requirements or questions, do not hesitate to contact us, our specialists would like to help you at the best efforts.

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CONTACT CD GENOMICS

45-1 Ramsey Road, Shirley, NY 11967, USA
Tel: 1-631-275-3058
Fax: 1-631-614-7828
Email: info@cd-genomics.com