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Plasmid Identification


Plasmid-mediated horizontal gene transfer is considered a major driving force for rapid bacterial adaptation and diversification. Identification of unknown or known plasmids was once difficult due to repeat regions. CD Genomics employs next generation sequencing (NGS) or long-read sequencing technology to accurately obtain all genomic knowledge of plasmid. Coupled with powerful bioinformatics algorithms and tools, we can help you identify antibiotic resistance genes (ARGs), mobile genetic elements and any other genes of interest.

Our Advantages:
  • Standardized laboratory methods and quality assurance processes.
  • Advanced genomics solutions and genome-based analysis.
  • Stand at the frontiers of microbial genomics and bioinformatics analyses.
  • Next-generation sequencing and long-read sequencing platforms.
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We are dedicated to providing outstanding customer service, listening to customer requests and being reachable at all times.

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Introduction to our plasmid identification service

Plasmids are small and circular pieces of DNA presenting in bacteria (like Escherichia coli) or other organisms. It can replicate independently from the host genome. Plasmids are important vehicles for rapid adaptation of microbial populations to environmental changes. Plasmid-mediated gene transfer is very important in the dissemination of ARGs. Plasmids are transmissible between host cells, leading to the quick spread of their accessory genes within a bacterial community. The Food Safety Authority (EFSA or FDA) requires critical information of plasmids in food or feed industry, mainly because of the transmission of antibiotic resistance traits. CD Genomics developed a unique and sequencing-based platform to help researchers quickly identify and characterize plasmids.

NGS and long-read sequencing technologies offer a strong potential for plasmid identification, diversity, characterization and evolution studies. Based on Illumina HiSeq, PacBio or Oxford nanopore sequencing platforms, we are dedicated to offering full-length plasmid sequencing service, to detect and identify plasmids. Long-read sequencing can span complex repetitive regions to ensure complete and accurate sequence data. We help you discover mobile genetic elements, screen ARGs, annotate other accessory genes. Good annotation of plasmid genomes is necessary to maximize the value of the rapidly increasing volume of bacterial strains. These informations are very important to ensure food safety & quality and control antimicrobial resistance.

Plasmid identification workflow

Bioinformatics Analysis

Our bioinformatics analysis includes data quality control, genome assembly, functional annotation and comparative genomic analysis, which is flexible to your needs. Please feel free to contact us to discuss your project.

Bioinformatics Analysis Details
Data QC Data resource: Illumina (PE 75/250, 100X) or PacBio (4 Kb library, 100X)
Read quality assessment, trimming and filtering
Sequence assembly De novo assembly and outcome evaluation
Functional Annotation NCBI GenBank, SwissProt, ARDB (Antibiotic Resistance Genes Database), COMBREX, Snapgene, PlasMapper, etc.

Sample requirement

Sampling kits: we provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

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

Reference

  1. Thomas C M, Thomson N R, Cerdeno-Tarraga A M, et al. Annotation of plasmid genes. Plasmid, 2017, 91: 61-67.

Areas of Interest

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