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Thursday, September 13, 2018

Building a Digital Genome Ark: Vertebrate Genome Project Releases 15 New Reference Genomes

[caption id="attachment_29874" align="alignright" width="300"] The duck-billed platypus genome is one of 15 high-quality assemblies released by the Vertebrate Genome Project[/caption] When creating a global genomic ark of creatures great and small, scientists are turning to the comprehensive coverage and quality of PacBio sequencing. The Vertebrate Genomes Project (VGP), an international consortium of more than 150 scientists from 50 academic, industry and government institutions in 12 countries, recently released the first 15 of an anticipated 66,000 high-quality reference genomes representing all vertebrate species on Earth. The VGP consortium spent three years selecting technologies and workflows to produce higher quality, “platinum-level” genomes,…

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Tuesday, September 4, 2018

Webinar Summary: Developing Benchmark Sets for Structural Variants

[caption id="attachment_29573" align="alignright" width="200"] Justin Zook[/caption] A map of every individual’s genome will soon be possible, but how will we know if it is correct? Benchmarks are needed in order to check the performance of sequencing, and any genomes used for such a purpose should be comprehensive and well characterized. Enter the Genome in a Bottle Project (GIAB), a consortium of geneticists and bioinformaticians committed to the creation and sharing of high-quality reference genomes. Unlike other initiatives, such as the 1000 Genomes Project, that are seeking to sequence many representatives of different populations, GIAB is interested in sequencing just a…

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Friday, August 31, 2018

International Eagle Conservation Efforts Bolstered By New Genome Release

Genetics is not only key to discovering and tracing new traits in an organism, but also conserving old ones -- and in some cases, the species itself. A deep understanding of genetic variation within and among species can be used to reconstruct their evolutionary history, to examine their contemporary status, and to predict the future effects of management strategies. With this in mind, scientists at the UK’s Wellcome Sanger Institute were keen to incorporate endangered species among 25 genomes to be sequenced as part of a project to mark its 25-year anniversary, and the first assembly to be released is…

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Tuesday, August 7, 2018

PacBio Sequencing Reveals Food Processing & Pathogenic Strains of Yeast are the Same Species

[caption id="attachment_28852" align="alignright" width="300"] Candida krusei, a form of yeast that is known to be drug-resistant and able to cause opportunistic infections in humans[/caption] What’s in a name? Too much, when it comes to the taxology of yeast, it turns out. Scientists from University College of Dublin have found that two distinctly named species of yeast are in fact 99.6% identical at the base pair level, and collinear. In other words, they are the same species. It was a bit of a shock, especially considering one of the yeast species, Pichia kudriavzevii, is commonly used in food production and classified…

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Tuesday, July 24, 2018

SMRT Science, Tips & Tricks Presented at Leiden Meeting

[caption id="attachment_28544" align="alignright" width="300"] SMRT Art: Jewelry created from upcycled SMRT cells by Olga Pettersson.[/caption] When was the last time you sent your DNA off to a day at the spa? Olga Pettersson of the SciLifeLab at Uppsala University lets her molecules relax for up to a week at room temperature to enable them to untangle, achieve better chemical purity, and better sequencing output. It was one of many practical pointers shared by presenters at the popular three-day gathering of PacBio users in Leiden, Netherlands last month. SMRT Leiden featured the scientific discoveries and analytical achievements of more than 30…

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Tuesday, July 17, 2018

Long Look Into Ant Brains Provides Epigenetic Insights

To understand the epigenetic regulation of brain function and behavior, scientists are turning to ants. To understand the ants, they are applying the accurate, long reads of SMRT Sequencing. While the genetic code of many types of ant have been combed through thanks to several genomes assembled through whole-genome shotgun sequencing, there have only been brief glimpses and guesses regarding gene regulation. Existing assemblies are highly fragmented drafts, making epigenetic studies nearly impossible. Eager to determine the epigenetic changes responsible for phenotypic and behavioral plasticity in Camponotus floridanus and Harpegnathos saltator ant species, a team of researchers from the Epigenetics…

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Friday, July 13, 2018

Egyptian Rousette Bat Genome Provides Clues to Antiviral Mystery

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…

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Tuesday, July 10, 2018

One Million Genomes Meeting Discusses Progress and Promise of Population-Scale Genomics

  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…

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Wednesday, June 27, 2018

Plant and Animal SMRT Grant Will Enable Insight Into Sightless Fish

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…

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Monday, June 11, 2018

New High-Resolution Genome Assemblies Expand Our Understanding of Human-Ape Differences

Ever since researchers sequenced the chimpanzee genome in 2005, they have known that humans share the vast majority of our DNA sequence with chimps, making them our closest living relatives. So what, exactly, sets us apart? While prior ape genome assemblies were helpful in finding single nucleotide changes, many researchers speculate that a variation type that is more difficult to resolve, structural differences in regulatory DNA or in the copy number of gene families, play important roles in species adaptation. Large-scale efforts to sequence and assemble more ape genomes over the last 13 years have expanded our knowledge, but many…

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Wednesday, June 6, 2018

New Resource for Microbiologists: Collection of 3,000 Bacteria Genomes Released

[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…

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Monday, May 14, 2018

Codfish Study Employs Target Capture and SMRT Sequencing to Explore Evolution

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…

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Tuesday, April 24, 2018

Nature Webinar and SMRT Grant Winner Explore Structural Variation for Disease Gene Discovery

Structural variants account for most of the base pairs that differ between human genomes, and are known to cause more than 1,000 genetic disorders, including ALS, schizophrenia, and hereditary cancer. Yet they remain overlooked in human genetic research studies due to inherent challenges of short-read sequencing methods to resolve complex variants, which often involve repetitive DNA.   At a recent webinar co-hosted by Nature Research, Professor Alexander Hoischen joined Principal Scientist Aaron Wenger to discuss how advances in long-read sequencing and structural variant calling algorithms have made it possible to affordably detect the more than 20,000 such variants that are…

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Tuesday, April 17, 2018

Scientists Aim to Develop “Genomic Ark” of High-Quality Bat Genomes

Pop quiz: Which animal accounts for around 20% of all living mammals, harbors (yet survives) some of the world’s deadliest diseases, lives proportionately longer than humans given its body size, and helps make tequila possible? Answer: Bats. From the tiniest bumblebee bat (Craseonycteris thonglongyai) to the large (1kg) golden-capped fruitbat (Acerodon jubatus), the diversity and rare adaptations in bats have both fascinated and terrified people for centuries. Now, an international consortium of bat biologists, computational scientists, conservation organizations, and genome technologists has set out to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies.…

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Thursday, April 12, 2018

SMRT Sequencing Enables Characterization of Cavities-Causing Bacteria in Children

We’re told to avoid sugar and refined carbohydrates if we want our teeth to remain strong and cavity-free. But what is the role of microbiota in our oral health? Cavities – or caries – actually occur as the result of bacterial infection that leads to sustained decalcification of tooth enamel and the layer beneath it, the dentin. Left unchecked, it can reach the tooth’s inner layer, with its soft pulp and sensitive nerve fibers, and, in some cases, can cause serious complications such as phylogenetic osteomyelitis and the life-threatening bacterial endocarditis. In addition to diet and host factors, the occurrence…

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