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Thursday, July 28, 2016

The Birth of a Symbiont: Epigenome Analysis Reveals Shifting Methylation Profile

A recent publication from scientists at the University of Florida and the University of Missouri used SMRT Sequencing to analyze epigenomic changes that occur when free-living bacteria associate with a host and become symbiotic instead. Published in the Frontiers in Microbiology journal, “Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis” comes from a team of collaborators including lead author Austin Davis-Richardson and senior author Eric Triplett. The scientists aimed to assess the role of epigenetics in bacterial evolution from free-living to symbiont and chose SMRT Sequencing because it generates base-specific modification information as it…

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Tuesday, July 26, 2016

Mitochondrial Genome Analysis Yields Novel Findings in Antiretroviral-Treated HIV Patients

Scientists from Yale University and Memorial Sloan Kettering Cancer Center used SMRT Sequencing to determine whether antiretroviral therapies were triggering mitochondrial genome mutations in HIV patients. The results were recently published in HIV Medicine (“High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals”). The publication, from lead author Min Li, senior author Elijah Paintsil, and collaborators, reports results from an analysis of 71 people, including 47 HIV patients who had received antiretroviral therapy (about half had mitochondrial toxicity) and 24 healthy controls. DNA was isolated from peripheral blood mononuclear cells and mitochondrial genome sequencing performed on a PacBio System.…

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Monday, July 11, 2016

First Comprehensive View of Alternative Splicing in Sorghum Powered by SMRT Sequencing

A paper from scientists at Colorado State University and the National Center for Genome Resources provides an in-depth view of the transcriptome of sorghum, a crop that’s important for human and animal food and also shows potential as a biofuel. Through this project, the team produced a new isoform analysis pipeline for community use and identified novel genes, as well as far more alternative splicing than had been expected for this plant. The publication, “A survey of the sorghum transcriptome using single-molecule long reads,” comes from lead author Salah Abdel-Ghany, senior author Anireddy Reddy, and collaborators. The researchers were particularly…

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Wednesday, July 6, 2016

In Chinese Genome Assembly, SMRT Sequencing Finds Novel Genes and Recovers Missing Sequence

A paper just out in Nature Communications reports the de novo genome assembly and transcriptome of a Chinese individual, generated from long-read SMRT Sequencing and other technologies. The effort revealed nearly 13 Mb of sequence not included in the GRCh38 reference genome as well as novel gene and alternative splicing content not annotated in GENCODE. “Long-read sequencing and de novo assembly of a Chinese genome” comes from lead author Lingling Shi at Jinan University and senior author Kai Wang from the University of Southern California, as well as many other collaborators in China and the US. The team was particularly interested in…

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Friday, June 24, 2016

Iso-Seq Study Reveals More Complexity than Expected in Maize Transcriptome

In a new publication from Cold Spring Harbor Laboratory, scientists produced a dataset for what authors call “the single largest collection of [full-length] cDNAs available in maize” and significantly improved genome annotation. The effort relied on the Iso-Seq method with SMRT Sequencing, which allows scientists to generate ultra-long reads covering full transcripts. The paper, “Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing,” comes from lead author Bo Wang and senior author Doreen Ware, who is also affiliated with the USDA Agricultural Research Service. It offers the first published results from using the Iso-Seq method on a maize…

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Wednesday, June 22, 2016

East Coast UGM: SMRT Sequencing Data for Carnivorous Plants, Hummingbirds, Mammalian Methylation, Repeat Expansions, and More

Many thanks to the nearly 200 scientists who signed up for our East Coast User Group Meeting, and to the Institute for Genome Sciences for hosting us! The event was a hit with customers and PacBio staff alike, and discussions we heard in the hallways and during breaks told us there was some great knowledge exchange that should give labs inspiration for generating and analyzing their SMRT Sequencing data. The day kicked off with a talk from our own Marty Badgett, senior product manager for the PacBio RS II System and Sequel System. He offered some historical perspective on throughput improvements…

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Wednesday, June 15, 2016

SMRTest Microbe Grant Program:
Nominate Your Favorite Microbe Now!

We’re pleased to launch the latest opportunity to have your favorite microbe sequenced on a PacBio System. The SMRTest Microbe Grant Program, kicking off at this year’s American Society for Microbiology annual meeting in Boston, will give one scientist a free genome sequence for his or her chosen microbe. For those folks unable to make it to the meeting this year, don’t worry — you do not need to attend ASM Microbe to enter the program. To enter, simply submit a short application describing your microbe or microbial community and how it would benefit from the long read lengths, high…

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Friday, June 10, 2016

Case Study: Institute for Genome Sciences Expands Long-Read Capabilities with Sequel System

An updated case study about the Genomics Resource Center (GRC) at the University of Maryland’s Institute for Genome Sciences (IGS) reports that SMRT Sequencing has become an integral tool for generating complete microbial genomes, improving plant and animal genome assemblies, and exploring human genome variation. The GRC has a scientific pedigree and a sample-to-interpretation service commitment that place it in a league of its own. The team operates under a simple mantra: ‘If it can be sequenced, we can do it.’ Both the GRC and IGS were founded in 2007 when a high-powered team of investigators formerly at The Institute…

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Tuesday, May 31, 2016

AACR Recap: Cancer Transcriptomes and a Moonshot Initiative

The PacBio team headed to New Orleans this past April to take in all the exciting new research presented at the American Association for Cancer Research Annual Meeting, show off our new Sequel instrument, and of course enjoy some crawfish and beignets! On the first day of the conference, we had the pleasure of hearing a talk from last year’s AACR “What Will You Discover About Cancer?” SMRT Grant winners, Malgorzata Komor and Remond Fijneman from the Netherlands Cancer Institute. Malgorzata discussed her work to identify novel biomarkers to identify precursor lesions in colorectal cancer, which can be integrated into…

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Thursday, May 26, 2016

Save the Spuds: UK Team Identifies Blight-Resistance Genes with SMRT Sequencing

Potato with late blight disease Scientists from the UK published new work detailing important advances in protecting potatoes from the disease that caused the Irish potato famine in the 1800s. It’s not just of historical interest; the team points out that late blight disease is once again endangering the food supply, with global yields of potatoes shrinking in recent years. “Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing,” published in Nature Biotechnology, comes from lead authors Kamil Witek and Florian Jupe, senior author Jonathan Jones, and collaborators at The Sainsbury Laboratory and The Genome Analysis…

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Wednesday, May 18, 2016

Discover New Insights into Human Genetic Variation at ESHG in Barcelona

The PacBio team is looking forward to joining 3,000 other scientists in Barcelona May 21-24 for the European Human Genetics Conference, better known as ESHG.  Organized by the European Society of Human Genetics, this is the 49th year of a high-quality meeting where the latest developments in human and medical genetics are discussed. This year, we’ll be showcasing our new Sequel System at booth #260 in the exhibit hall. Come visit us and learn more about it! With higher throughput than our previous instrument, we think the Sequel System will be a great fit for the genomics community on projects…

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Tuesday, May 17, 2016

Arizona Scientists Deploy BAC Expertise and SMRT Sequencing for Crop Genomes

At the University of Arizona, a leading genomics research facility benefits from decades of BAC-based sequencing expertise, original studies of crop genomes, and a unique emphasis on high molecular weight DNA. Rod Wing, founding director of the Arizona Genomics Institute (AGI) and a professor in the School of Plant Sciences, Ecology & Evolutionary Biology at the university, was a pioneer in building BAC-based reference genomes in the ’90s. Today, that carefully honed expertise in isolating large DNA fragments gives him and his lab a real advantage for making the most of long-read sequencing. Wing’s efforts primarily focus on plant genomes,…

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Thursday, May 12, 2016

From Seabass to Salmon:
Swimming in High-Quality Genomes

Asian seabass A global collaboration of researchers has produced what is likely the most contiguous assembly of a fish genome to date. “Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding,” published in PLoS Genetics, comes from lead author Shubha Vij and senior author László Orbán with collaborators at nearly two dozen labs. The team set out to sequence Lates calcarifer, the Asian seabass, which has a genome of about 670 Mb grouped into 24 A chromosomes and as many as 10 B chromosomes. They used SMRT Sequencing from PacBio to overcome the fragmented and incomplete…

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Wednesday, May 4, 2016

Eco-friendly Soil Remediation Gets a Boost with the Latest SMRT Grant Program Winner

Congratulations to the winner of the first-ever SMRT Grant program decided by the community: Renying Zhuo of the Chinese Academy of Forestry! We ran polling through our Genome Galaxy Initiative on the Experiment crowdfunding platform and were amazed to see much how it galvanized the genomics community. There were 30,000+ responses to the competition across the five finalists for our “Explore Your Most Interesting Genome” grant opportunity. Zhuo garnered the most support for his project to sequence two highly related strains of Sedum alfredii for a comparative genomics investigation to identify key genes important for remediating soil contaminated by heavy…

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Monday, May 2, 2016

Join the SMRT Community: User Meetings in Europe, Asia, and the US

There are several PacBio user meetings coming up, and with locations around the world we hope you’ll be able to attend one of them. These meetings are a great way to meet fellow customers, exchange tips, and learn about new applications. If you are interested, please register as soon as possible to reserve your seat.   The Netherlands: SMRT Leiden Symposium & Informatics Developers Meeting, June 6-8 This meeting, organized and hosted by Leiden University Medical Center’s human genetics department, includes a scientific symposium and the first SMRT Informatics Developers meeting in Europe. There’s an impressive agenda for the two-day…

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