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Tuesday, April 8, 2014

GC-Rich Genome of Pandoraea Bacterium Assembled with SMRT Sequencing

Scientists from the Institute of Biological Sciences at the University of Malaya recently published a description of Pandoraea sp. strain RB-44 in Genome Announcements, a journal from the American Society for Microbiology. The genome sequence was completed using Single Molecule, Real-Time (SMRT®) Sequencing. Pandoraea is a soil bacterium; this particular strain was collected from the site of a former landfill. Some strains of Pandoraea have been suggested as cystic fibrosis clinical pathogens, the authors report, though “their role in pathogenicity is still largely unknown.” Corresponding author Kok-Gan Chan and colleagues may have a new lead in that mystery. Their Pandoraea…

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Wednesday, March 26, 2014

Importance of Finished Microbial Genome Highlighted for Ethanol-Generating Clostridium

A paper in BioMed Central’s Biotechnology for Biofuels journal demonstrates how finished microbial genomes using Single Molecule, Real-Time (SMRT®) Sequencing are having an impact on the biotechnology industry. The publication, “Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia,” comes from scientists at Oak Ridge National Laboratory, the University of Tennessee, and New Zealand-based biofuels company LanzaTech. Lead authors Steven Brown and Shilpa Nagaraju and their colleagues used PacBio® sequencing to generate a finished genome sequence for a complex class III microbe that previously could not…

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Wednesday, January 29, 2014

At Plant & Animal Genome Workshop, Users Showcase Projects Enabled by SMRT Sequencing

Earlier this month, we hosted a workshop at the International Plant & Animal Genome (PAG) conference in San Diego entitled “A SMRT® Sequencing Approach to Reference Genomes, Annotation, and Haplotyping.” PacBio users presented data on various projects that have benefited from long-read sequence data, including several that had previously been attempted with short-read technologies without success. We were delighted to see reports on newer features of SMRT Sequencing, including full-length isoforms, automated haplotyping, and more. Here’s a recap, as well as links to video recordings of the presentations: Chongyuan Luo, a scientist from Joe Ecker’s lab at the Salk Institute…

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Wednesday, January 8, 2014

SMRT Sequencing for Plant and Animal Genomes: Learn More at PAG 2014

Many recent studies have demonstrated the use of Single Molecule, Real-Time (SMRT®) Sequencing for larger genomes, from complete reference genomes to de novo discovery of transcript isoforms. These advances include understanding genome complexity and variation and enabling improved leverage of haplotype information for biotechnology. Some of these efforts will be presented at the workshop we’re hosting at this year’s International Plant & Animal Genome (PAG) conference in San Diego. Sign up now to reserve your seat or receive the recording after the event.  Workshop details: A SMRT® Sequencing Approach to Reference Genomes, Annotation, and Haplotyping Tuesday, January 15 1:30 –…

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Tuesday, August 27, 2013

Oklahoma Scientists Use SMRT Sequencing to Rescue Fungal Genome Assembly

Orpinomyces is found in cattle rumen. Scientists from Oklahoma State University and the University of Oklahoma teamed up with a sequencing service provider to study the genome of an anaerobic fungus found in the rumen of cows that may have implications for effective plant biomass degradation. What made this particular species so tricky to sequence were its extreme GC content — just 17 percent — and unusually high number of repeats.The study was reported in “The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader,” a paper published in…

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