Microbial Whole Genome Sequencing

Bio Basic Asia Pacific is providing PacBio Single Molecular RealTime (SMRT) sequencing for microbial whole genome sequencing to get a comprehensive view of the microbial genome.

SMRT Sequencing has long reads (average >15,000 bp, some reads >100,000 bp) and the highest consensus accuracy. It is especially helpful for genome de novo assembly. As we know, repetitive stretches of DNA are abundant and are one of the main technical challenges that hinder accurate sequencing and genome assembly efforts.

In the case of bacteria, the rRNA gene operon is often the largest region of repetitive sequence and range in size between 5 and 7 kb. Microbial whole genome sequencing by illumina HiSeq platforms utilizes sequencing by synthesis technology which islimited by its read length (50 to 300 bp), and as it requires PCR amplification of multiple DNA templates before sequencing which potentially increase base-composition bias.

With SMRT Sequencing on the Sequel System, there is no need to sacrifice quality for affordability when assembling bacterial genomes. Go well beyond draft-quality to achieve reference-quality assemblies, closing even the most repeat-dense and GC-rich genomes and resolving plasmids.

The advantage of SMRT long reads, which can overcome the problem of abnormal GC and high duplication of microbial genomes, often assembled into a single contig.

Among all assemblies, the PacBio assembly recovered the highest number of core and virulence proteins, and housekeeping genes based on whole-genome multi locus sequence typing.

Bioinformatics Analysis

  • Data quality control
  • Assembly
  • Genome Annotation
  • Functional Annotation
  • Comparative Genomics
  • Evolutionary Analysis

(More upon request)

Advantages

  • Generate platinum-standard, closed reference genomes
  • Affordably assemble gold-standard genomes
  • Clarify the role of transposons, phage insertions, and other structural variants in the evolution of virulence.
  • Recover plasmids to track drug resistance and transmission paths

Image source: Shi, C., Liu, Y., Huang, H., Xia, E.-H., Zhang, H.-B., & Gao, L.-Z.. (2015). Circular plot of transcriptome reads mapping of the C. sinensis var. assamica chloroplast genome. (Version 1). PLOS ONE. https://doi.org/10.1371/journal.pone.0059620.g005

Analysis Workflow

For more information, feel free to contact us via NGS@biobasic-asia.com or +65 6928 9042.