Complete Plasmid DNA Sequencing

CD Genomics provides complete plasmid DNA sequencing service, and our improved bioinformatics pipelines are available to perform de novo assembly with no reference required.

What Is Complete Plasmid DNA Sequencing

Plasmids are perceived as mobile genetic elements that exist extra-chromosomally and occasionally carry accessory genes that confer an advantage to their host in its ecological niche. They are thus thought to play an important evolutionary role in microbial communities by laterally introducing genes and traits into microbial genomes. Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness towards environmental change. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens.

Despite their importance, technical obstacles still limit the plasmid study. Plasmid DNA sequencing is rapidly becoming a standard approach to increase our understanding of the genetic diversity and evolutionary history of plasmids. Complete plasmid genome sequencing refers to the process of determining the entire genetic sequence of a plasmid. It not only helps to define the molecular events that took place during the evolution of these plasmids, but also give us a more complete overview of the enormous collection of accessory genes encoded on plasmids. And comparative plasmid sequence analysis has provided insights into the evolution of plasmids and their relatedness, their modular structure and the existence of hot spots for the insertion of accessory genes.

Our Full length Plasmid DNA Sequencing Methods

Plasmids exhibit significant heterogeneity in terms of size and complexity, often featuring high GC content, intricate structures, or large repetitive segments. These characteristics have historically rendered traditional Sanger sequencing methods cost-prohibitive, prone to high failure rates, and characterized by relatively slow processing.

Whole Plasmid Sequencing vs. Sanger Sequencing

Aspect Sanger Sequencing Whole Plasmid Sequencing (NGS)
Methodology Chain-termination method Utilizes Next-Generation Sequencing (NGS)or Long Read Sequencing technologies
Sequence Length Suitable for shorter fragments (up to 1,000 bp) Can sequence entire plasmids, regardless of size or complexity
Speed Sanger Sequencing can involve extended processing times and is particularly suited for small-scale projects. In contrast, Whole Plasmid Sequencing using NGS technologies provides a swifter turnaround, making it well-suited for high-throughput applications.
Cost Can be cost-prohibitive for larger plasmids due to multiple sequencing reactions Generally more cost-effective, especially for larger plasmids, as it involves fewer sequencing reactions
Accuracy Sanger Sequencing is renowned for its exceptional precision and minimal error rates. Whole Plasmid Sequencing maintains a high degree of accuracy and incorporates enhanced error correction methods.
Applicability Sanger Sequencing is appropriate for smaller plasmids but may encounter challenges when dealing with larger, intricate, or repetitive plasmid structures. Whole Plasmid Sequencing is highly versatile and can accommodate plasmids of various sizes and complexities, rendering it suitable for comprehensive plasmid analysis.

At CD Genomics, we carry out a thorough examination of plasmid genomes using cutting-edge next-generation high-throughput sequencing technology. Our method includes both library creation and sequencing, and it integrates state-of-the-art bioinformatics tools to provide a thorough analysis of sequencing depth, GC content, and the full assembly of plasmid sequences.

Moreover, we deploy a unique long-read assembly protocol in conjunction with state-of-the-art sequencing technology. This innovative combination affords an expedient, economical, and highly efficient avenue for the singular assembly of plasmids spanning various length spectrums. This novel approach not only facilitates an all-encompassing comprehension of plasmid content but also establishes it as the foremost scientific tool in the landscape of plasmid research.

Its utility transcends scientific boundaries, finding application in a multitude of interdisciplinary fields. These encompass the domains of synthetic biology, the nuanced regulation of gene expression, the precision of genome editing, the thorough exploration of bacterial antibiotic resistance mechanisms, and the meticulous scrutiny of various trait-associated phenomena. Furthermore, this method demonstrates its prowess in the realms of cellular therapy, the advancement of pharmaceuticals, and the enhancement of medical diagnostics, underscoring its invaluable contribution to the scientific community.

Key Features and Advantages of Complete Plasmid DNA Sequencing

  • High-Quality Data & Swift Turnaround For large plasmids or plasmids lacking known reference sequences, Sanger sequencing and NGS sequencing typically entail multiple sequencing attempts, whereas complete plasmid genome sequencing can often be accomplished within a short timeframe, sometimes requiring just a few working days.
  • Cost-Effective High-Throughput Sequencing The larger and more numerous the plasmids, the lower the cost. Sequencing large plasmids exceeding 60,000 base pairs can be achieved at less than one-tenth the cost of traditional methods, significantly less than Sanger sequencing.
  • Precise Assembly Compared to standard plasmids, alignment accuracy exceeds 99.9%.
  • High Success Rate For plasmids without reference sequences, both NGS and traditional Sanger sequencing suffer from high failure rates, especially in cases involving plasmids with high GC content or extensive repetitive structural elements. Complete plasmid genome sequencing does not require reference sequences and can achieve successful assembly in a single attempt.
  • High Automation Level Automated assembly analysis eliminates the need for manual peak profile interpretation, reducing the potential for errors.
  • User-Friendly Results Assembly files can be directly aligned, while variation files resemble peak profiles, allowing for straightforward data interpretation.

Sample Requirement

Service Sample Type Recommended Quantity Minimum Quantity Minimum Concentration
Complete Plasmid DNA Sequencing (Illumina) Plasmid DNA ≥ 1 µg 500 ng 20 ng/µL
Plasmid DNA Long Read Sequencing Genomic DNA ≥ 1 µg 500 ng 10 ng/µL

Project Workflow

Project Workflow

Data analysis

  • Data quality control
  • High quality data acquisition
  • Genome de novo assembly
  • Detection of plasmid-specific sequences
  • …and more

Analysis pipeline

Analysis pipeline

CD Genomics's plasmid sequencing service utilizes the power of Illumina Platform for plasmid verification, and has developed a low-cost high-throughput approach for complete larger plasmid sequencing using nannopore technology. We are pleased to use our extensive experience and advanced platform to offer the best service and the most qualified products to satisfy each demand from our customers.

For Research Use Only. Not for use in diagnostic procedures.
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! For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment.
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