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Tuesday, March 12, 2019

AGBT 2019: First Look at Early Access Results from the Sequel II System

The PacBio team was honored to have the opportunity to give several talks at this year’s Advances in Genome Biology & Technology conference. If you weren’t able to be there, we’ve got you covered with videos and highlights. In a plenary session, Marty Badgett, senior director of product management, gave attendees a look at the latest results using the HiFi reads with the circular consensus sequencing (CCS) mode as well as a sneak peek at data from our soon-to-be-released Sequel II System. As he demonstrated, HiFi reads cover the same molecule many times, delivering high consensus accuracy (Q30 or 99.9%)…

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Monday, February 18, 2019

Asian Aquaculture Industry Benefits From Two New Genome Assemblies

With their large brains, sophisticated sense organs and complex nervous systems, cephalopods could teach us a thing or two about learning, memory, and adaptability. But despite their evolutionary, biological, and economic significance, their genome information is still limited to a few species. To bridge this gap, a team of Korean scientists has assembled the genome of the common long-arm octopus (Octopus minor) using PacBio technology to sequence both the DNA and RNA of the emerging model species. Found in Northeast Asia, particularly in coastal mudflats of South Korea, China, and Japan, O. minor has become a major commercial fishery product…

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Tuesday, January 8, 2019

SMRT Grant Winner: Uncovering the Metabolic Secrets of Hibernation

What has four legs, lots of fat and fur, and will possibly help uncover novel mechanisms to combat diabetes? Photo courtesy of WSU Bear Center Grizzly bears! If humans were to undergo regular, extended cycles of weight gain and inactivity, they’d likely end up with obesity, muscle atrophy, or type 2 diabetes. But grizzly bears experience no ill effects from their annual fat gain and sedentary hibernation. Somehow they are able to switch their insulin resistance between seasons, and researchers at Washington State University are hoping to figure out how, with possible therapeutic value for humans. We’re proud to support…

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Friday, December 21, 2018

The Genomic Gift Worth Giving: New Assembly Could Help Conserve Declining Turtle Dove Populations

Turtle dove. Photo by Andy Morfew You may be more likely to get five gold rings or three French hens than two Turtle doves this Christmas. The subject of the famous holiday carol is in precipitous decline across Europe, with 94 percent of Turtle doves lost since 1995, and fewer than 5,000 breeding pairs left in the UK. In an attempt to save the species, geneticists at the Wellcome Sanger Institute identified it as a priority species to be sequenced as part of a year-long 25th anniversary project. Collaborators at the University of Lincoln sent samples (collected from live birds…

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Wednesday, December 19, 2018

New Low-Input Protocol Enables High-Quality Genome Created from Single Mosquito

Anopheles coluzzii mosquito UPDATED January 18, 2019 This paper is now available at Genes. ORIGINAL POST December 19, 2018 High-quality reference and de novo genomes have been celebrated by geneticists, population biologists and conservationists alike, but it’s been a dream deferred for entomologists and others grappling with limited DNA samples, due to previous relatively high DNA input requirements (~5 μg for standard library protocol). A new low-input protocol now makes it possible to create high-quality de novo genome assemblies from just 100 ng of starting genomic DNA, without the need for time-consuming inbreeding or pooling strategies. The targeted release date for…

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Thursday, December 13, 2018

A Sweet Sequence: Sugarcane Genome Assembly After Five-Year Collaborative Effort

It took nearly 20 years until the technology was right, and five years of hard graft by more than 100 scientists from 16 institutions, but the result was worth it, according to University of Illinois plant biology professor Ray Ming. One of several authors of a paper published and featured on the cover of Nature Genetics reporting the assembly of a 3.13 Gb reference genome of the incredibly complex autopolyploid sugarcane Saccharum spontaneum L, Ming said he dreamed about having a reference genome for sugarcane while working on sugarcane genome mapping in the late 1990s. But sequencing technology was not…

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Monday, December 3, 2018

Barn Swallow Project Helps Introduce PacBio Long Read Technology to Italy

Its reliable return to the same spot year after year has made the barn swallow a beloved symbol of Spring and safe passage, for mariners and landlubbers alike. But our changing climate is altering the birds’ migratory behavior, and Italian ecologists are turning to genetics to figure out how. As reported previously in this blog, scientists at the University of Milan joined forces with researchers from the University of Pavia and California State Polytechnic University to create the first high-quality reference genome for the European barn swallow (Hirundo rustica rustica), using SMRT Sequencing and newly available Bionano Genomics optical mapping…

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Wednesday, November 28, 2018

Tracking the Tuna: How PacBio Sequencing Could Help Save the “King of the Sea”

Northern Bluefin Tuna Their bodies are big, bony and… warm? Unique among bony fish, Atlantic, Pacific and Southern bluefin tuna have a rare endothermic physiology that has garnered great interest among scientists. Like birds, mammals and some sharks, these kings of the sea are capable of conserving internally generated metabolic heat produced from their swimming muscles and viscera, and maintaining tissue temperatures above that of the environment. The fish are also renowned among sushi enthusiasts for their delectable, fat-laden muscle, and prized by fisherman because of the high prices they command. So the preservation of these species is paramount to…

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Thursday, November 15, 2018

At ASHG 2018, Workshop Speakers Discuss SMRT Sequencing Applications for Human Disease

Last month’s annual meeting of the American Society of Human Genetics in San Diego was a terrific reminder of how much progress is being made in this field — both in our basic understanding of human biology and in our ability to rapidly translate discoveries into clinical utility. ASHG 2018 attendees packed into the PacBio workshop. The PacBio team had the privilege of hosting an educational workshop about the value of long-read SMRT Sequencing for human genetic applications. Customers from Mount Sinai and Stanford University offered their perspectives, while PacBio scientists presented data and the technology roadmap. Here, we recap…

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Thursday, November 1, 2018

Genetic Code of All Plants, Animals, Protozoa, and Fungi to be Sequenced with Help of PacBio

It’s one of the most ambitious sequencing projects ever attempted — the assembly of all 1.5 million known species of animals, plants, protozoa and fungi on Earth — and SMRT Sequencing will play a major part. The global Earth BioGenome Project and its UK arm, the Darwin Tree of Life Project, were launched in London today in a gathering of the key scientific partners and funders from around the globe. A greater understanding of Earth’s biodiversity and the responsible stewarding of its resources are among the most crucial scientific and social challenges of the new millennium, and overcoming these challenges…

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Wednesday, October 31, 2018

Smell of Success: Garlic Study Validates New Approach to Transcriptome Association

Genome-wide association studies (GWAS) may be powerful tools for the identification of genes underlying complex traits, but what if you have an incredibly complex, uncharacterized genome, with no sequenced progenitor or related species? A team of scientists from the Chinese Academy of Agricultural Sciences in Changsha, China came up with a solution: a transcriptome-referenced association study (TRAS), powered by our Iso-Seq method. The approach, outlined in this DNA Research paper, utilized a transcriptome generated by SMRT Sequencing as a reference to score population variation at both transcript sequence and expression levels. The team, led by Touming Liu and first author Xiaojun…

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Monday, October 22, 2018

SMRT Sequencing and a Bit of Luck Help Swiss Microbiologists Solve Decades-Old Mystery

It’s a murder mystery of massive proportion, albeit on a miniature scale: Male-killing among several species of insects, caused by selfish symbiotic bacteria. Swiss researchers believe they have finally solved a question that has stumped scientists for decades, with potential implications for pest and infection control. Researchers have identified the toxin responsible for selective killing of male fruit flies (left) using PacBio sequencing. In a recent Nature publication, Toshiyuki Harumoto and Bruno Lemaitre of the Global Health Institute at the École Polytechnique Fédérale de Lausanne (EPFL) in Lausanne, Switzerland, have reported their findings regarding a toxin in Spiroplasma poulsonii, one…

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Wednesday, October 10, 2018

Sequel System 6.0 Release Offers a New Paradigm in DNA Sequencing: Highly Accurate Single-Molecule Long Reads

Today we’re pleased to announce the release of Sequel System 6.0, including new software, consumable reagents and a new SMRT Cell. Combined, the enhancements in the release improve the performance and affordability of Single Molecule, Real-Time (SMRT) Sequencing by providing individual long reads with greater than 99% accuracy, increasing the throughput up to 50 Gb per SMRT Cell, and delivering average read lengths up to 100,000 base pairs, depending on insert size. These improvements are expected to greatly enhance the accuracy and cost effectiveness of applications such as whole genome sequencing, human structural variant detection, targeted sequencing and RNA transcript isoform sequencing (Iso-Seq method). Estimated…

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Wednesday, October 3, 2018

Beloved Barn Swallow Gets SMRT Sequencing “Platinum Genome” Treatment

UPDATED Dec. 3, 2018 Congratulations to the Italian team on the publication of their European barn swallow genome! The paper is now available at GigaScience. ORIGINAL POST Oct. 3, 2018 With its bold blue plumage, russet throat and chipper chirps, the barn swallow is beloved by many avian enthusiasts. It’s also a favorite of scientists, becoming a flagship species for conservation biology. Numerous evolutionary and ecological studies have focused on its biology, life history, sexual selection, response to climate change, and the divergence between its eight subspecies in Europe, Asia and North America. But the full potential of such studies has…

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Thursday, September 13, 2018

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

The duck-billed platypus genome is one of 15 high-quality assemblies released by the Vertebrate Genome Project 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, and SMRT Sequencing was…

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