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The limitations of draft genomes

While the adoption of next-generation sequencing technologies has dramatically reduced microbial genome sequencing costs, scientists are often limited to producing draft genomes. These assemblies lack resolution of structural and mobile elements, such as plasmids, which are needed for characterizing antibiotic resistance and tracking transmission events. Additionally, draft genomes often contain gene fragments split across multiple assembly pieces, challenging gene-prediction algorithms.

Characterize complete microbial genomes with confidence

With Single Molecule, Real-Time (SMRT) Sequencing, you can affordably characterize complete microbial genomes. For most microbes, closed genomes and accessory plasmids can be assembled using PacBio data from a single library in a single run — with turn-around times as short as one day. These technologies offer enhanced sequencing capabilities, allowing you to:

  • Generate gold-standard reference genomes
  • Reconstruct intact genes and gene clusters
  • Clarify the role of mobile elements in drug resistance and transmission
  • Assess the contribution of DNA modification on pathogenesis

 

spotlight-microbiology-icon

Workflow: from DNA to characterized microbial genome in a single experiment

  • SMRT Sequencing with the PacBio Systems
    • Take advantage of the Sequel System to reduce project costs and generate 7X more reads compared to the PacBio RS II
    • Achieve ~10 kb average read lengths, with some reads as long as 60 kb
    • Scale throughput based on project needs; recommended 50X coverage for high-quality de novo assemblies
    • Simultaneously capture epigenetic information

Featured research: Streptomyces mining



Microbial_Whole_Genome_Sequencing.Streptomyces_mining

A PacBio de novo assembly putatively detects an intact NRPS gene cluster in a single contig. Short-read based assembly contains two incomplete fragments of the gene cluster, lying on two different contigs, with part of the cluster apparently absent1.

Explore this research further.

Featured research: resolve complex genome architectures of plant fungal pathogens

Microbial_Whole_Genome_Sequencing.Resolve_complex_genomes_of_plant_fungal_pathogensPacBio whole genome sequencing was used to create a near-finished genome of Microbotryum lychnidis-dioicae, the pathogenic fungus causing anther-smut disease of Silene latifoli. With chromosome-level resolution of the repeat-rich mating-type chromosomes and centromeres, scientists can begin investigating fundamental evolutionary questions2.

Explore this research further.

To learn more about PacBio’s true whole genome sequencing for microbiology and infectious disease research, contact us.

 

References

  1. Harrison, J. & Studholme, D. J. (2014) Recently published Streptomyces genome sequences. Microbial Biotechnology. 7 (5), 373–380.
  2. Badouin, H. et al. (2015) Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae. Genetics. Early online.

Selected Resources