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Monday, December 12, 2016

New Genome Assembly and Analysis of Grape Pathogen Elucidate Virulence Mechanisms

A new publication from scientists at the University of California, Davis, and the USDA Agricultural Research Service presents important findings about a fungus that threatens global grape production. As part of the project, the team used SMRT Sequencing to generate a new assembly of the fungal genome, resulting in a more complete assembly than a previous short-read attempt. “Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum,” published in Molecular Plant Pathology, comes from lead author Mélanie Massonnet, senior author Dario Cantu, and collaborators. The team was eager to determine why the wood-infecting Neofusicoccum…

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Monday, October 17, 2016

New FALCON Tools Enable Diploid Assemblies from SMRT Sequencing Data

In a Nature Methods paper released today, scientists describe the new bioinformatics tools to produce diploid genome assemblies from SMRT Sequencing reads. FALCON (Fast ALignment and CONsensus for assembly) and FALCON-Unzip were developed by PacBio scientists in collaboration with researchers at Johns Hopkins University, Cold Spring Harbor Laboratory, the Joint Genome Institute, and other institutions. “Phased diploid genome assembly with single-molecule real-time sequencing” comes from lead authors Chen-Shan Chin and Paul Peluso, senior author Michael Schatz, and collaborators. In the publication, the team details how FALCON and FALCON-Unzip work and presents data from several validation studies of organisms including Arabidopsis,…

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Wednesday, October 5, 2016

Diploid Assembly of Korean Genome Reveals Population-Specific Variation and Novel Sequence

In a paper published today in Nature, scientists from Seoul National University, Macrogen, and other institutions present the de novo genome assembly for a Korean individual. The effort used SMRT Sequencing and other technologies to generate the assembly, fully phase all chromosomes, and perform detailed analyses of structural variation and other elements. In the process, the team generated novel sequence data that helps fill gaps in the human reference genome and continues the trend of developing important new population-specific resources. The work, reported in “De novo assembly and phasing of a Korean human genome,” was contributed by lead authors Jeong-Sun…

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Thursday, August 25, 2016

Precision Medicine Review Highlights Need for Accuracy & Comprehensiveness in Genome Sequencing

Stanford’s Euan Ashley wrote a terrific review about the clinical use of genome sequencing for Nature Reviews Genetics. “Towards Precision Medicine” is well worth a read, covering topics from the ethnic background of the human reference genome to public interest in precision medicine.  He also covers technical angles such as mapping of sequence reads for variant calling across challenging regions of the genome with known clinical significance. Ashley’s premise is that many of the current standards in genomics — from sequencers to analysis tools and more — were developed for use in basic research, where the consequences of inaccurate information…

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Tuesday, August 2, 2016

SMRT Sequencing Accurately Detects Gene Copy Numbers in Complex Maize Genome

Scientists from Rutgers University and the University of California, Davis, used SMRT Sequencing to study structural variation in maize. They found that this approach delivered more complete information at lower cost than standard methods and generated new findings that could be important for crop breeding. From lead author Jiaqiang Dong, senior author Jo Messing, and collaborators, “Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads” was published in PNAS recently. They chose to evaluate SMRT Sequencing for copy number detection as an alternative to short-read sequencing, which doesn’t span long repeats, and BAC cloning, which…

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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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Thursday, May 26, 2016

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

[caption id="attachment_12102" align="alignright" width="300"] Potato with late blight disease[/caption] 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…

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Thursday, May 12, 2016

From Seabass to Salmon:
Swimming in High-Quality Genomes

[caption id="attachment_12027" align="alignright" width="300"] Asian seabass[/caption] 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…

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Wednesday, April 20, 2016

Benchmarking Study:
Full-Length 16S Sequencing Offers Better Phylogenetic Resolution

Scientists from the Joint Genome Institute and other institutions recently reported a new SMRT Sequencing approach to microbial profiling using full-length sequencing of the 16S rRNA gene. In a benchmarking study, they demonstrate that this method allows for more accurate taxonomic classification than is possible with typical short-read sequencing methods. Lead author Esther Singer, senior author Tanja Woyke, and collaborators at USDA-ARS, the University of British Columbia, and other research groups published “High-resolution phylogenetic microbial community profiling” in The ISME Journal earlier this year. The scientists note that while 16S phylogenetic analysis has traditionally been performed with gold-quality Sanger sequencing,…

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Monday, April 18, 2016

First Comprehensive Analysis of Mosquito Y Chromosome Offers Clues for Vector Control

A new PNAS paper offers the first detailed analysis of the Anopheles gambiae Y chromosome, which could prove critical for biological and infectious disease research. The report uncovered extensive remodeling of the Y chromosome, which consists almost entirely of highly repetitive sequence. The authors say this study “provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.” “Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes” comes from lead authors Andrew Brantley Hall, Philippos-Aris Papathanos, Atashi Sharma, and Changde Cheng, along with senior…

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Friday, April 15, 2016

Japanese Scientists Find Gene Fusion Driving B Cell Leukemia

In a new Nature Genetics paper, scientists from the University of Tokyo and several other Japanese institutes and hospitals present results of a sweeping study of gene fusions driving a form of leukemia in teenagers and young adults. They used SMRT Sequencing to validate the gene fusion. “Recurrent DUX4 fusions in B cell acute lymphoblastic leukemia of adolescents and young adults” comes from lead author Takahiko Yasuda and senior author Hiroyuki Mano, along with many collaborators. The team embarked on the search for new oncogenes responsible for acute lymphoblastic leukemia (ALL) in subjects from 15 to 39 years of age…

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