Brought to the brink of extinction, the future of Hawaii’s only lineage of the crow family (Corvidae) is looking up thanks to intensive conservation genomics efforts using PacBio de novo assemblies. In Hawaiian mythology, the ‘alalā is said to lead souls to their final resting place on the cliffs of Ka Lae, the southernmost tip on the Big Island of Hawaii. As one of the largest native bird populations, it also had a vital role in the ecosystem, helping to disperse and germinate seeds of many indigenous plant species. Disease, predators and shrinking habitats led to a complete loss of…
When humans are infected with the Marburg virus, the result is often lethal, with hemorrhagic fever and other symptoms similar to Ebola. When bats are infected, the result is…. nothing. The tiny mammals remain asymptomatic. In order to crack this antiviral mystery, a multi-institutional team of scientists sequenced, assembled and analyzed the genome of the bat species Rousettus aegyptiacus, a natural reservoir of Marburg virus and the only known reservoir for any filovirus. Their findings contradicted previous hypotheses about bat antiviral immunity, which assumed that bats had enhanced antiviral defenses, controlling viral replication early in infection, and developing effective adaptive immune…
[caption id="attachment_27906" align="alignright" width="201"] Computational biologist Doreen Ware harvests maize tissue for RNA isolation. Photo by Miriam Chua c/o USDA[/caption] The first reference genome for maize variety B73, completed in 2009, was a major milestone, and an improved version released by Cold Spring Harbor Laboratory scientists in 2017 provided a deeper dive into the genetics of the complex crop. Yet even this new robust reference is not enough for Kelly Dawe, Doreen Ware and Matt Hufford, who have taken up another ambitious project: creating a 26-line pangenome reference collection in just two years. “Maize is not only an important crop,…
The PacBio team was honored to attend an excellent Keystone Symposium in Hannover, Germany recently. The event, “One Million Genomes: From Discovery to Health,” offered a rare look at large-scale human genome projects, with many top-notch speakers. The meeting featured speakers from many national genomics efforts, including China, Estonia, Israel, the UK, and the US. Each of these individual national efforts is essential to overcome the representation bias seen in human genome databases today. Underrepresented groups are currently less likely to get actionable results from clinical genetic tests, a situation that threatens to confer the benefits of precision medicine…
When German diver Joachim Kreiselmaier reached the deepest parts of the Danube-Aach cave system, he couldn’t believe his eyes: a “strange fish,” with a pale body coloration and smaller eyes and larger nares and barbels than the loaches typically spotted nearby. He had discovered the first cavefish in Europe, and the northernmost in the world. “This is spectacular, as it was believed that the Pleistocene glaciations prevented fish from colonizing subterranean habitats north of 41° latitude,” said ecologist Jasminca Behrmann-Godel of the Limnological Institute of the University of Konstanz, who examined the fish Kreiselmaier brought back to the surface. “Initial…
[caption id="attachment_26599" align="alignright" width="300"] Haemophilus influenzae, a sample of which was deposited to the NCTC collection by Alexander Fleming, from his own nose.[/caption] The genomes of 3,000 strains of bacteria, including some of the deadliest in the world, are now available to researchers as part of an ambitious project by the UK’s National Collection of Type Cultures (NCTC), in partnership with the Wellcome Sanger Institute and PacBio. Plague, cholera, streptomyces, and 250 strains of E. coli, are among the reference genomes created, as well as all ‘type strains’ of the bacteria in the collection -- the first strains that describe…
Many investigators rely on targeted sequencing approaches for deep dives into genomic regions of interest. By designing specific probes -- often using short-read sequences directed towards the exome and supported by existing reference genomes or transcriptome assemblies -- scientists can home in on exactly the area they want to explore. But what about sequences in intergenic regions not covered by short reads, which could contain crucial regulatory elements varying between populations that might be of functional and evolutionary importance? Or, what about species lacking high-quality reference genomes to guide probe design? A team of Norwegian researchers are tackling these challenges…
From wild animals to perfect pets, dogs have undergone some interesting changes during their centuries-long domestication. Intent on unraveling some of the developmental secrets of the process, a team of scientists from the University of New South Wales in Sydney, Australia, is doing deep dives into the genomes of a range of canine cousins along the evolutionary chain. A desert dingo named Sandy has already provided some insight into the process after its genome was sequenced as part of the 2017 Plant and Animal SMRT Grant. Study leader Bill Ballard described in this presentation at PAG 2018 that pure dingoes…
The Mexican salamander, or the axolotl, may have tiny feet, but the feat of decoding its genetic footprint was huge—32 billion base pairs huge, making it ten times bigger than the human genome and the largest ever sequenced. The accomplishment by an international team of scientists is significant, not only because of its sheer size, but also because of the insights it could provide into tissue regeneration. The easily recognizable critter has an astounding ability to regenerate body parts, growing lost limbs – bones, muscles, nerves and all – within weeks. It can also repair spinal cord and retinal tissue,…
Maize is amazingly diverse. A study comparing genome segments from two inbred lines, for instance, revealed that half of the sequence and one-third of the gene content was not shared – that’s more diversity within the species than between some other species, for example humans and chimpanzees, which exhibit more than 98 percent sequence similarity. So how can researchers and commercial breeders rely upon a single reference genome to represent the genetic diversity in their germplasms? More and more scientists are deciding they cannot. At DuPont Pioneer, where DNA sequencing is paramount for R&D to reveal the genetic basis for…
Scientists championed their cases, school children sifted through species, and thousands of members of the public from around the globe took to social media to weigh in. Now the results are in, and high-quality genome assemblies for 25 organisms integral to United Kingdom ecosystems can begin. As mentioned last month, we teamed up with the Wellcome Trust Sanger Institute on a project to celebrate their twenty-fifth anniversary. Sanger scientists will use the Sequel System and complementary technologies to produce reference-grade assemblies for squirrels, scallops, and sharks, as well as balsam, blackberries, bats, butterflies, bees, and many others. The final five…
Happy DNA Day, everyone! This scientific celebration has us reflecting on the many advancements the community has made in the past year. For a molecule that is sequenced thousands of times a day all over the world, there is still much to learn. Today we’d like to honor some of the remarkable science enabled by SMRT Sequencing since last year’s DNA Day. Scientists have continued to make progress exploring regions of the genome that have long been considered intractable. Two of our favorite stories this year came from the always-challenging Y chromosome. Researchers studying the mosquitoes that carry malaria…
We’re already looking forward to next month’s Personalized Medicine World Conference. Long before “precision medicine” was an industry catchphrase, PMWC was bringing together stakeholders from genomics companies and academic research, regulatory agencies, clinical groups, pharma/biotech, and more. Launched in 2009, the meeting has prompted important discussions as well as insight about how to move the field forward in a thoughtful way. From January 24th to the 27th, some 1,200 PMWC attendees will descend on the Computer History Museum in Mountain View, Calif. The event will kick off with a reception honoring the four awardees of this conference: Merck’s Roger Perlmutter…