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Our bacterial whole genome de novo sequencing platform leverages the power of high-throughput sequencing technology to generate accurate draft or complete genomes for microbial identification and comparative genomic studies. We provide reliable sequencing approaches and confidential bioinformatics analysis to help you gain an insight into functional elements, functional genes, and phylogeny.

Our Advantages:

• Expert Design: Offering scientifically rigorous design with multi-platform solutions to ensure high-quality bacterial genome sequencing tailored to diverse research needs.
• Rapid Turnaround: Utilizing advanced sequencing platforms for quick data acquisition and analysis, ensuring efficient project delivery.
• Accurate Assembly: Enhancing genome assembly accuracy through multiple rounds of correction, ensuring precise and reliable results.
• Comprehensive Strain Identification: Providing free strain identification to prevent misidentification and ensure data reliability.
• Extensive Experience: Drawing from numerous successfully completed bacterial genome sequencing projects to guarantee high-quality technical and service standards.
• Detailed Service: Offering meticulous attention to detail, including adjustments of starting points and accurate translation of start codons, to achieve customer satisfaction.

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What is Bacterial Whole-Genome De Novo Sequencing

With the significant reduction in sequencing costs and the exponential improvement in sequencing efficiency, whole-genome sequencing has substantially propelled research in microbial single-genome genomics. Utilizing whole-genome sequences, it is possible to construct comprehensive genome databases for various species. This serves as an efficient platform for subsequent research into critical questions related to the growth, development, evolution, and origin of the species. Furthermore, these sequences provide essential DNA information for future gene mining and functional validation.

Bacterial genome sequencing can be categorized into de novo sequencing and resequencing. Bacterial whole genome de novo sequencing refers to sequencing a species' genome for which the sequence is unknown or lacks closely related genomic information. This process involves constructing genomic libraries with different insert fragment lengths, followed by sequencing and subsequent assembly using bioinformatics methods. The end result is the acquisition of a complete bacterial genomic sequence map, including predictions of gene functions and annotations.

Applications of Bacterial Whole Genome De Novo Sequencing

• Gene function research
• Evolutionary analysis
• Pathogen identification and mechanism study
• Antibiotic, vaccine, and drug development
• Comprehensive genomic and plasmid mapping
• Pathogenic gene discovery for health, agriculture, and biocontrol
• Functional gene analysis in industrial strains for fermentation and production
• Exploration of evolutionary mechanisms and drug efficacy

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Partial results of our bacterial whole genome de novo sequencing service are shown below:

Bacterial Whole Genome De Novo Sequencing FAQ

• 1. Is it feasible to complete a bacterial genome map using only third-generation single-molecule sequencing platforms?

  • It is not feasible. Small plasmid fragments (20 kb) might be lost during library construction, and certain regions of the chromosome may not be sequenced due to sampling probabilities or sample degradation.

• 2. Given the low single-base accuracy of third-generation single-molecule sequencing platforms, how is the accuracy of assembly results ensured?

  • The single-base accuracy of sequencing data from third-generation single-molecule sequencing platforms is between 87-92%. The accuracy of assembly results is ensured through a three-step correction process: pre-assembly correction utilizing overlaps between the sequencing reads, post-assembly correction with the same sequencing data, and a final correction using high-quality second-generation high-throughput sequencing data. This multi-step correction process can achieve an accuracy of over 99.99%.

• 3. How is 0 gap ensured?

  • Currently, over 90% of strains can be directly assembled into complete genome sequences using a combination of second- and third-generation sequencing platforms. For the remaining approximately 10% of strains, gaps are typically filled using first-generation sequencing platforms.

• 4. What are the advantages of third-generation sequencing compared to second-generation sequencing for bacterial genome sequencing?

  • Third-generation sequencing offers several advantages over second-generation sequencing, primarily due to its longer read lengths and reduced sensitivity to GC content. These features enable it to effectively resolve repetitive sequences within bacterial genomes and ensure even sequencing coverage, even for GC-rich bacteria. Although third-generation sequencing is generally more expensive, the smaller size of bacterial genomes requires less sequencing effort, making the costs manageable. For highly detailed bacterial complete genome maps, third-generation sequencing can sometimes be more cost-effective than combining second- and first-generation sequencing methods. Currently, second-generation sequencing maintains a cost advantage for lower-resolution bacterial genomic frameworks. However, as the throughput of third-generation sequencing improves and costs continue to decline, its application in bacterial genomics is expected to become more widespread.

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

Case Study

Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil
Journal: Frontiers in Microbiology
Impact factor: 4.235
Published: 31 March 2020

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Backgrounds

Pseudomonas bacteria can survive in harsh environments like crude oil by producing enzymes and rhamnolipids (RLs) that help degrade alkanes. This study compared three such strains, finding they have flexible genomes and high levels of alkane-degrading enzymes, making them suitable for bioremediation and oil recovery.

Methods

Sample preparation:

• P. aeruginosa strains
• DNA extraction

Method:

• Whole-genome sequencing
• PacBio SMRT sequencing
• Illumina HiSeq sequencer

Data Analysis:

• Genome assembly
• Annotation
• Phylogenetic analysis
• Comparative genome analysis

Results

IMP66, IMP67, and IMP68 were isolated from crude oil, and their complete genomes were sequenced. Phylogenetic analysis using ten housekeeping genes confirmed that IMP67 and IMP68 are P. aeruginosa, while IMP66 was also identified as P. aeruginosa. A maximum likelihood tree of 54 Pseudomonas strains and core genome analysis of 90 P. aeruginosa isolates revealed that all three strains clustered together in the same group, indicating they are closely related within the P. aeruginosa species.

Figure 1. Phylogeny of P. aeruginosa population structure.

IMP66, IMP67, and IMP68 have similar genome sizes and GC content, with about 6,100 coding sequences (CDSs) each, which is higher than the well-studied PAO1 strain. Compared to PAO1, most crude oil isolates have larger genomes, potentially aiding their survival. Comparative analysis revealed 592 unique genes in IMP66, IMP67, and IMP68, mostly related to mobile genetic elements and gene functions such as transcription and cell wall biogenesis. Horizontal gene transfer (HGT) appears common in these strains, with conserved regions indicating potential gene acquisition and adaptation advantages, including features linked to alkane degradation.

Figure 2. Whole genome comparison of IMP66, IMP67, IMP68, and PAO1.

Conclusions

P. aeruginosa strains IMP66, IMP67, and IMP68, isolated from crude oil, are highly adaptable, excelling in alkane degradation and rhamnolipid production. They have numerous alkane hydroxylase genes and show signs of horizontal gene transfer, enhancing their survival. Their efficient QS signaling helps balance rhamnolipid production. These traits make them promising for bioremediation and industrial applications, with their CRISPR-Cas system offering potential for genetic engineering.

Reference

1. Xu A, Wang D, Ding Y, et al. Integrated comparative genomic analysis and phenotypic profiling of Pseudomonas aeruginosa isolates from crude oil. Frontiers in Microbiology. 2020, 11:519.