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Moving beyond draft genomes

Next-generation sequencing technologies made rapid assembly of draft microbial genomes possible. But now, using SMRT Sequencing, we can go well beyond generating draft genomes to achieve the highest quality complete genomes, allowing us to truly characterize and understand microbial genomes and populations.

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

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

Spotlight: Gapless assemblies to better understand fungal genomes

A recent study highlighted the importance of complete genomes to understand effector and co-regulated genes as well as the role of centromeres and telomers in adaptive genome evolution in fungal species. Explore this research further:

Thomma, B.P.H.J. et al., 2016. Mind the gap; seven reasons to close fragmented genome assemblies. Fungal Genetics and Biology, 90, pp.24–30.

Spotlight: Resolve GC-rich microbial genomes with SMRT Sequencing

Scientists used SMRT Sequencing to resolve the genome of Burkholderia pseudomallei and compared their assembly results with hybrid and short-read assemblies. Their findings concluded that PacBio long-read sequencing generated the highest-quality, cost-effective assembly and enabled closure of a complex microbial genome. Explore this research further:

Teng, J.L. et al., 2017. PacBio but not Illumina technology can achieve fast, accurate and complete closure of the high GC, complex Burkholderia pseudomallei two-chromosome genome. Frontiers in Microbiology, 8, p.1448.

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

Selected Resources