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SMRT Sequencing Highlights – Top Publications of 2019

Friday, December 27, 2019

With the release of the award-winning Sequel II System, 2019 was an exciting year for the SMRT Sequencing community. We were inspired by our users’ significant contributions to science across a wide range of disciplines. As the year draws to a close, we have taken this opportunity to reflect on the many achievements made by members of our community, from newly sequenced plant and animal species to human disease breakthroughs.

 

“It has been another phenomenal year for science. The introduction of the Sequel II System will accelerate discovery even more, and I can’t wait to see what 2020 will hold.”

Jonas Korlach, Chief Scientific Officer

 

Human Biomedical Research

The year brought incredible insights into human genetics. Some researchers homed in on single mutations, while others zoomed out to explore variation on a population scale. PacBio technology was also selected for new large-scale sequencing projects, including the NHGRI Human Genome Reference Program and the All of Us program. Here are some of our favorite publications from the year:

 

  • The mystery cause of progressive myoclonic epilepsy in a family that eluded detection in standard whole-exome sequencing was revealed with PacBio whole genome sequencing, as reported in Journal of Human Genetics and on our blog.
  • New insights into specific human populations were revealed in several studies, including Melanesians, as reported in Science, and Tibetans, as reported in National Science Review.
  • Double mutations in the PIK3CA oncogene were found to influence targeted therapy, as highlighted in Science and our blog.
  • The importance of comprehensive variant detection was featured in several papers. University of Washington researchers Mitchell R. Vollger and Evan Eichler reported that “HiFi may be the most effective standalone technology for de novo assembly of human genomes” in their Annals of Human Genetics paper (read our blog), while members of the Human Genome Structural Variation Consortium reported “the most comprehensive assessment of SVs in human genomes to date” in Nature Communications. University of Michigan researchers Steve S. Ho and Ryan E. Mills shared their review entitled “Structural variation in the sequencing era.”
  • A PLoS One paper by Mayo Clinic researchers demonstrated the use of No-Amp targeted sequencing to interrogate the sequence structure of expanded repeats in Fuchs Endothelial Corneal Dystrophy.
  • The utility of the PacBio Iso-Seq method for studying disease risk genes was showcased in a Frontiers in Genetics paper by PacBio and Duke University researchers studying transcripts across synucleinopathies.

Plant & Animal Sciences

Commoner’s law of ecology states that “everything is connected to everything else,” and this was highlighted in several studies that showed the interdependence of microbes, plants, insects, and other animals. International consortia such as the Vertebrate Genomes Project, the Earth Biogenome Project, and the Sanger Institute’s 25 Genomes Project released many new reference genomes, which will only bolster our understanding of individual species as well their interactions with their ecosystem cohabitants. Here are some of our favorite publications from the year:

 

  • Korean scientists provided a great example of mutualistic interactions in their Nature Communications paper examining the relationships between Streptomyces bacteria, strawberry plants, and pollinating bees.
  • A USDA project to sequence the spotted lanternfly showcased the power of SMRT Sequencing to rapidly generate high-quality genomes from the DNA of single insects to fight invasive species.
  • The latest Nature publication from the Cantu Lab delved into a largely unexplored feature of plant genomes — structural variants — in a study of the population genetics in grapevine domestication.
  • Pathologists interested in uncovering the secrets of plant immunity used PacBio targeted sequencing to create inventories of NLR genes, which are candidates for engineering new pathogen resistance (read our blog).
  • For shrimp, which have notoriously hard genomes to sequence, an isoform-level transcriptome reference generated with the Iso-Seq method was reported on Fish and Shellfish Immunology and summarized in our blog.

Microbiology & Infectious Disease

From C. difficile to symbiotic defense systems, we were treated to new insights in the realm of microbiology. We also learned about a new way to use an old method to provide unprecedented taxonomic resolution at species and strain level and gained insight into intra-bacterial defense. Here are some of our favorite publications from the year:

 

  • Not only has the Mount Sinai Pathogen Surveillance Program adopted SMRT Sequencing for continuous monitoring and disease control, the accumulated PacBio data has also inspired new research, including a paper published in Nature Microbiology on the discovery of a conserved orphan methyltransferase that drives C. difficile infection persistence (read our blog).
  • A team of researchers at the Jackson Laboratory published a study in Nature Communications, and featured on our blog, using HiFi sequencing to unlock the full potential of 16S rRNA Sequencing to provide taxonomic resolution of the human gut microbiome at species and strain level.
  • PacBio reference genomes enabled a groundbreaking study published in Nature of intra-bacterial defense genes in the human gut microbiome by researchers at the University of Washington.
  • As published in Science, long reads were also used to reconstruct a tripartite symbiotic factory for a marine toxin, involving bacteria, algae and a sea slug.

Did we miss one of your favorite publications of 2019? Tweet your favorites to us @PacBio, using #PoweredbyPacBio. And check out our searchable publications database for more than 1300 examples of outstanding SMRT Science from 2019.

 

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