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Wednesday, August 7, 2019

SMRT Sequencing Helps Crack the Code of Elusive Centromeres

Crucial assembly sites and mitosis mediators, centromeres are central to every cell, but missing from even the most complete genome assemblies.  Until now. In a PLOS Biology paper, Amanda Larracuente and colleagues at the University of Rochester and Barbara G. Mellone of the University of Connecticut, described how they sequenced the repetitive regions of the fruit fly genome, including its centromeres, using SMRT Sequencing.  Embedded in blocks of highly repetitive satellite DNA, centromeres have eluded efforts at assembly. Only recently, long-read single molecule sequencing technologies have made it possible to obtain assemblies of highly repetitive parts of multicellular genomes such…

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Monday, July 29, 2019

HiFi Reads Add Unparalleled Accuracy to the Long-Read Sequencing Arsenal

To enable better understanding of biology, sequencing data must be accurate and complete. This is especially true when seeking out variants and determining their implications. Luckily, technical and software improvements for SMRT Sequencing are making it easier to efficiently generate genome assemblies with unparalleled accuracy. As presented in a webinar by PacBio Staff Scientist Sarah Kingan (@drsarahdoom) and GoogleAI Genomics Project Lead Andrew Carroll (@acarroll_ATG), HiFi reads enabled by circular consensus sequencing (CCS) on the new Sequel II System challenge the notion that sequencing technologies require a tradeoff between length and accuracy. Highly accurate long reads (HiFi reads) offer the…

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Wednesday, May 15, 2019

SMRT Leiden Symposium Showcases Successes in Clinical and Conservation Genomics

What can a cute, cuddly, stingless bee from the Brazilian rainforest teach us about eusociality and mitochondrial evolution? Natalia S Araujo wants to find out, and she’s not the only one. As the only bee species in which true polygyny (multiple fertile queens in the same colony) occurs, there is great interest in Melipona bicolor, and its mitochondrial genome (mt genome) was one of the first sequenced in bees. But the sequence was incomplete and lacked information about its mitochondrial gene expression pattern. So Araujo, a postdoctoral researcher of animal genomics in the GIGA Institute of the University of Liège,…

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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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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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Tuesday, September 4, 2018

Webinar Summary: Developing Benchmark Sets for Structural Variants

Justin Zook 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 few individuals, but deeply…

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Tuesday, August 7, 2018

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

Candida krusei, a form of yeast that is known to be drug-resistant and able to cause opportunistic infections in humans 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 by the US FDA…

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Wednesday, August 1, 2018

Something to Crow About: SMRT Sequencing Aids Conservation of Rare Hawaiian Bird

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…

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Tuesday, July 24, 2018

SMRT Science, Tips & Tricks Presented at Leiden Meeting

SMRT Art: Jewelry created from upcycled SMRT cells by Olga Pettersson. 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 speakers. Inge Kjaerbolling of…

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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

Haemophilus influenzae, a sample of which was deposited to the NCTC collection by Alexander Fleming, from his own nose. 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 the species and are…

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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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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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Wednesday, April 11, 2018

HudsonAlpha Chooses Sequel System for NIH-Funded Program Focused on Challenging Pediatric Cases

At the HudsonAlpha Institute for Biotechnology, scientists are building on advances in agricultural research to power a clinical pediatric research program. For this work, they’re using the Sequel System to perform whole-genome sequencing on trios of children with developmental disabilities and their parents. HudsonAlpha researchers have been using SMRT Sequencing to resolve challenging plant genomes, deploying a Sequel System and a PacBio RS II for these complex projects. The successfulness of that program led the institute to add a second Sequel System for use in sequencing human genomes. The organization is part of the NIH-funded Clinical Sequencing Exploratory Research Program,…

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Monday, April 9, 2018

Rice Revelations: Nine New Genome Assemblies Uncover Key Traits and Evolutionary Clues

Revered around the world, rice is a staple food for nearly half of the population. But as that population grows, rice breeders are faced with the challenge of producing crops that are high yielding, disease-resistant and nutritious, while at the same time being more sustainable. The International Oryza Map Alignment Project (OMAP) was initiated in 2003 to develop a set of high-quality genomic resources for the wild relatives of rice that could be used as a resource to discover and utilize novel genes, traits and/or genomic regions for crop improvement and basic research. Members of the consortium recently released new…

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