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Plasmid Identification - Full Length Plasmid Sequencing

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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:
  • Enhanced Efficiency: Significantly shortening experimental timelines, particularly for large plasmids and challenging plasmids without reference sequences, contributes to heightened overall efficiency.
  • Cost-Effectiveness: The cost of whole plasmid sequencing is substantially lower than Sanger sequencing, offering a cost-effective alternative with high value for money.
  • High Accuracy: Whole plasmid sequencing exhibits a matching accuracy of over 99.9% when aligned against standard quality plasmids, ensuring the reliability of experimental outcomes.
  • Increased Success Rate: For plasmids lacking reference sequences, the approach enables a one-time successful assembly, thereby elevating the overall success rate.
  • High Automation: Leveraging automated assembly analysis in whole plasmid sequencing reduces errors associated with manual peak chart interpretation, consequently enhancing sequencing accuracy.
  • User-Friendly Results: Assembly files are directly comparable, and variant files resemble peak charts, facilitating straightforward data assessment and thereby improving the efficiency of data processing.

What Is Whole Plasmid Sequencing

Plasmids are small and circular pieces of DNA presenting in bacteria (like Escherichia coli) and other organisms. It can replicate independently in host genome. Plasmids are important vehicles for microbial populations to adapt rapidly to environmental changes. Plasmid-mediated gene transfer is crucial 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 plasmid information in food or feed industry, mainly because of the transmission of antibiotic resistance traits.

Whole-plasmid sequencing refers to the technique that utilizes high-throughput sequencing technology to sequence an entire plasmid genome. This process involves library construction of the plasmid genome for sequencing. The sequencing data is subsequently subjected to bioinformatics analyses, wherein aspects such as sequencing depth, GC content, and the assembly of the full plasmid sequence are systematically examined and analyzed.

What Is The Difference Between Whole Plasmid Sequencing And Sanger Sequencing?

  Sanger Sequencing Whole Plasmid Sequencing
Data Quality Peaks, double peaks; requires manual analysis and correction Superior quality; no need for manual correction
Sequencing Length 1 kb 2.5 - 300 kb
Cost Low Lower
Sample Quantity 100 ng 1-100 ng
Accuracy 70-90% ≥97%
Sequencing Capability Requires sequencing primers; limited to sequencing primer-targeted fragment sequences No need for sequencing primers; capable of sequencing the entire plasmid length
Throughput Low High
Experimental Timeline Several tens of days A few days
Service Specifications

Introduction to Whole Plasmid Sequencing Service

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 offer 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 information are key when determining food safety & quality and controlling for antimicrobial resistance.

Plasmid Construction

At CD Genomics, we offer a comprehensive modular plasmid design approach to meet diverse requirements. Whether you require plasmids with repetitive sequences, high or low GC content, exceptionally long target sequences, or plasmids with multiple transgenes, we can assemble plasmids tailored to your specific needs. Our team of experts brings years of experience in plasmid engineering, ensuring the precision of each designed plasmid. If the desired plasmid type is not readily available, rest assured, as we will closely collaborate with you to design and construct plasmids that align with your exact specifications.

Technical Parameters:

Sequencing Platform Library Type Sequencing Depth
Illumina 150PE/250PE 400~500 bp 100X
PacBio SMRT 2 K 100X

Whole Plasmid Sequencing 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

Sample type Category Size Concentration Minimum volume
Plasmid Standard 2.5 -25 kb 30 ng/uL ≥10 uL
Big 25-125 kb 50 ng/uL ≥20 uL
Huge 125-300 kb 50 ng/uL ≥40 uL
Linear/Amplicon Standard 600 bp - 25 kb 30 ng/uL ≥10 uL
Big 25 - 125 kb 50 ng/uL ≥20 uL



Whole Plasmid Sequencing FAQ

Please feel free to reach out if you have any further inquiries or require additional information.




  1. Thomas C M, Thomson N R, Cerdeno-Tarraga A M, et al. Annotation of plasmid genes. Plasmid, 2017, 91: 61-67.
* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.

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