Bacterial Whole-Genome De Novo Sequencing

Absolutely. We can create a comprehensive mapping of a bacterial genome for you. Bacterial genomes possess distinctive characteristics that set them apart from other species:

• Compact Size: Bacterial genomes are typically small, often ranging from less than 10 million base pairs (Mbp) with the majority falling in the 4 to 5 Mbp range.
• Single Chromosome: Most bacterial species have a single circular chromosome as their primary genetic material. In addition to this, some bacteria may also contain plasmid sequences, which are smaller, circular pieces of DNA.
• Variable GC Content: Bacterial genomes exhibit a wide range of GC content, varying from as low as 25% to as high as 70% or more. This GC content plays a crucial role in genome stability and adaptation.
• Simplicity in Composition: Bacterial genomes are relatively straightforward in composition. Typically, over 80% of the genome consists of coding regions, which means that genes constitute a substantial portion of the genome. Moreover, bacterial genomes tend to have fewer repetitive sequences compared to more complex organisms.
• Gene Continuity: Bacterial genes are generally contiguous, lacking introns. This continuous arrangement simplifies the process of identifying genes and their functions.

These two categories are both part of genome matching, mobile elements are transposons and so on, and resistance genes are specific genes. Mobile elements refer to a type of DNA that can change its position within a genomic region, including transposons, plasmids, phage elements, etc. Resistance genes refer to genes with a particular resistance, such as antibiotic resistance genes.

Zero gaps typically entail a single contig assembly, while a high-quality finished map should ideally comprise no more than three contigs. However, successful genome completion may be compromised under the following conditions:

• Bacterial genome size exceeding 6 million base pairs.
• Presence of impurities in the sample, including but not limited to sequence contamination from other species.
• Cumulative count of chromosomal genomes and plasmids equaling or surpassing five.
• Existence of transposons or other repetitive sequences exceeding 20,000 base pairs, or an exceptionally high proportion of such sequences in the genome, exceeding 20%.
• Sample DNA quality falling below the standards required for long-read sequencing, with varying gap tolerances for different sample grades.
• A GC content greater than 70% or less than 30%.

Microbial resequencing entails variant detection through high-throughput sequencing and comparison with a closely related reference genome. This method yields a range of variant data, such as single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), structural variations (SVs), and more. These variants can be dissected to understand trait disparities between genomes or employed as markers for comprehensive evolutionary analysis.

Distinctions between fungal/bacterial framework maps, fungal/bacterial fine maps, and bacterial completion maps primarily revolve around assembly completeness and sequencing strategies. The bacterial completion map utilizes PacBio sequencing, tailoring the strategy to the specific characteristics of the bacterial strain in question. This approach aims for a fully finished genome sequence, characterized by a single scaffold with minimal gaps (ideally ≤5 gaps). It represents the highest standard for bacterial genome sequencing assembly.

This includes predictions for various genetic elements such as genes (gene, CDS, tRNA, rRNA, 23S rRNA, 16S rRNA, 5S rRNA, miscRNA, tmRNA), pseudogenes, CRISPR sequences, gene islands, prophages, repetitive sequences, and secondary metabolism gene clusters. For more customized report needs, you can contact us.

This encompasses both widely used general-purpose databases (such as Nr, KEGG, GO, Swiss-Prot, COG, CARD, CAZy) and specialized proprietary databases (including VFDB, PHI, Antismash, TCDB, ARDB, Pfam, and CYP450).

Certainly, the experimental workflow for the bacterial completion map and bacterial methylation is identical, allowing for the sharing of data. However, it's important to note that a larger data volume is necessary, and it's recommended to achieve a coverage of 300x or more.

It is advisable to conduct an initial round of strain identification to ensure the presence of a single bacterium before proceeding with subsequent experiments and analyses. In the unfortunate event of contamination being detected after completing all experiments, one possible approach is to increase the data volume to reach the desired depth for the target strain. Nonetheless, it is strongly recommended to prevent contamination from occurring at the outset of the experiment. Strain contamination typically falls into two categories: intraspecies and interspecies contamination. To clarify these concepts:

• Interspecies contamination: This involves interactions between populations of different species, indicating differences in species classification.
• Intraspecies contamination: This refers to interactions between individuals of the same species, signifying that they belong to the same species.

A plasmid is a distinct genetic unit separate from the chromosomal DNA, capable of autonomous replication. It encompasses relatively simple deoxyribonucleic acid (DNA) molecules found outside the chromosomes in various organisms, including symbiotic organisms, eukaryotic organelles, and bacterial cells. The study of plasmids encompasses vital theoretical concepts such as genetic recombination, DNA replication, and biological evolution. Furthermore, the potential for drug-resistant plasmids to disseminate among disease-causing bacteria has elevated plasmid research to an epidemiological concern.

Upon assembly, there is a noticeable disparity in size between plasmids and genomes. Additionally, when subjected to comparison against the NR (non-redundant) database, significant distinctions become apparent. Plasmids have the capacity to encode genes and consist of DNA sequences. However, plasmids, in general, do not appear to be thoroughly validated.