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Build a strong foundation for research

High-quality reference genomes are critical for the development of nutritious crops, healthy livestock, and innovative biotech products. However, the complex genomes of plants and animals — often with multi-gigabase sizes, polyploidy, and difficult-to-sequence repetitive regions — have proven challenging for de novo assembly algorithms relying on short-read sequencing data1. With cost-effective, high-quality reference genomes and evidence-based annotations, you can make advances in biological, agricultural, and biomedical research.

 

Produce a comprehensive view of genetic diversity

Single Molecule, Real-Time (SMRT) Sequencing provides the longest reads with uniform coverage and the highest consensus accuracy, generating high-quality reference genomes and contiguous assemblies. These comprehensive assemblies capture undetected SNPs, fully intact genes, and regulatory regions embedded in complex structures that fragmented draft genomes often miss. With the PacBio Systems, you have the ability to:

  • Gain insight into individual gene functions and their coordination within networks
  • Obtain intact genes and gene clusters for reconstructing biosynthetic pathways
  • Differentiate and distinguish gene expansion and duplication events to understand adaptive mechanisms for selection pressure
  • Resolve transposable elements for evolutionary analysis to trace adaptive, retained, and transferred traits

 

spotlight-plant-icon

Workflow: from DNA to comprehensive genome assemblies

  • SMRT Sequencing with PacBio Systems
    • Take advantage of the Sequel System to reduce project costs and generate 7X more reads compared with the PacBio RS II
    • Achieve ~10 kb average read lengths, with some reads as long as 60 kb
    • Scale throughput based on project needs
      • 5-10X coverage for gap filling
      • 25X coverage for hybrid assembly
      • 50X coverage for high-quality de novo assembly
    • Simultaneously capture epigenetic information
  • Read more about recommendations for large-genome assembly

Featured research: SMRT Sequencing and assembly of the gorilla genome

Scientists from the University of Washington, the McDonnell Genome Institute, and other organizations present a new gorilla genome assembly, generated with PacBio long-read sequencing, with a >150-fold improvement over previous assemblies. The rectangles in the treemaps in panels B and C above are the largest contigs that cumulatively make up 300 Mb (~10%) of the assembly, representing the differences in fragmentation of the long-read and short-read gorilla genome assemblies2.

Explore this research further.

To learn more about PacBio’s true whole genome sequencing solutions for plant and animal sciences, contact us.

 

References

  1. Michael, T & Jackson, S., (2013) The First 50 Plant Genomes. The Plant Genome. 6 (2).
  2. Gordon D. et al. (2016) Long-read sequence assembly of the gorilla genome. Science. 352 (6281), aae0344.

 

Selected Resources