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Tuesday, March 21, 2017

New Goat Genome Assembly Breaks Continuity Record, Expands Breeding Tools

[caption id="attachment_14004" align="alignright" width="300"] Photo of San Clemente Island goat kids by Cliff, courtesy of Wikimedia Commons[/caption] Efforts to produce a reference-grade goat genome assembly for improved breeding programs have paid off. A new Nature Genetics publication reports a high-quality, highly contiguous assembly that can be used to develop genotyping tools for quick, reliable analysis of traits such as milk and meat quality or adaptation to harsh environments. The program also offers a look at how different scaffolding approaches perform with SMRT Sequencing data. “Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome” comes from…

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Tuesday, March 7, 2017

High-Quality, Chromosome-Scale Quinoa Genome Valuable for Breeding Better Crops

A new genome assembly has remarkable promise to boost the global food supply. Scientists from King Abdullah University of Science and Technology and other institutions sequenced quinoa, a nutritious grain that can grow in marginal lands and other suboptimal environments. Their assembly offers new clues that could help improve breeding efforts to make the plant more accessible worldwide. “The genome of Chenopodium quinoa” was published recently in Nature by lead author David Jarvis, senior author Mark Tester, and a large group of collaborators. They focused on this plant, which is believed to have been domesticated more than 7,000 years ago in…

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Friday, March 3, 2017

‘Mobilome’ Study of Antibiotic Resistance Implicates Transposon Activity

[caption id="attachment_13900" align="alignright" width="300"] Klebsiella pneumoniae[/caption] A recent effort to understand the genetic mechanisms behind swappable elements of drug-resistance among bacteria built on previous studies of Enterobacteriaceae isolates collected at the National Institutes of Health Clinical Center. The work was made possible by high-quality genome assemblies of these organisms generated earlier with SMRT Sequencing technology. In this project, scientists from the U.S., France, and Brazil teamed up to learn precisely how drug-resistance plasmids are spread from one species to another. They report the results of that investigation in mBio with the publication “Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids” from…

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Wednesday, March 1, 2017

Scientists Explore Extremophile Genome with SMRT Sequencing

[caption id="attachment_13897" align="alignright" width="300"] Photo by Liam Quinn[/caption] A recent Nature publication from a large team of scientists in Europe, Canada, and the US reports the use of SMRT Sequencing to elucidate the genome of Fragilariopsis cylindrus, a single-celled eukaryotic diatom adapted to living in polar waters of the Antarctic Ocean. The work has implications for the biotechnology industry, which looks to extremophiles as a potential source of important enzymes. “Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus” comes from lead author Thomas Mock, senior author Igor Grigoriev, and many collaborators at the University of East Anglia, Earlham Institute, Joint…

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Thursday, February 2, 2017

Toward a Gold Standard for Human Structural Variation

Scientists from the University of Washington and McDonnell Genome Institute recently reported in Genome Research the results of an in-depth assessment of structural variation in the human genome using SMRT Sequencing technology. They found far more variation than expected and suggest using this approach to establish a comprehensive database of structural variants that would aid future studies. “Discovery and genotyping of structural variation from long-read haploid genome sequence data” comes from lead author John Huddleston, senior author Evan Eichler, and collaborators. The team fully sequenced two haploid human cell lines (CHM1 and CHM13) with SMRT Sequencing to greater than 60-fold…

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Wednesday, February 1, 2017

Scientists Produce Reference Genome for Plasmodium, Update Phylogeny

A new Nature paper from scientists at the Wellcome Trust Sanger Institute and other institutions delves into two Plasmodium genomes and reveals novel information about how these parasites have evolved. SMRT Sequencing was used to generate a reference genome and high-quality draft assembly for the organisms, providing a clear picture of species that have previously been difficult to characterize. From lead author Gavin Rutledge, senior author Thomas Otto, and collaborators, “Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution” reports that prior studies have “been hampered by a lack of genetic information” for species responsible for many malaria infections. The scientists deployed…

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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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