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Monday, April 29, 2013

PNAS: Copy Number Analysis in Maize Sheds Light on Tolerance for Acidic Soil

A new study of maize sheds light on the importance of copy-number variation in genes related to stress tolerance with implications to boost crop yield in suboptimal soil environments. A paper published in PNAS, “Aluminum tolerance in maize is associated with higher MATE1 gene copy number,” was published by senior author Leon Kochian and a team of scientists at the US Department of Agriculture, Cold Spring Harbor Laboratory, University of Arizona, and several other institutions. The authors report on the discovery of aluminum stress-tolerance modulation through changing copy-number variation of a rare allele found in maize that has survived in…

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Tuesday, April 23, 2013

Current Opinion in Microbiology: Bacterial Methylomes in Review – ‘An Exciting Era’

A new review paper from Brigid Davis, Michael Chao, and Matthew Waldor at Harvard Medical School considers a number of recent studies and findings that have used single molecule, real-time (SMRT®) sequencing to generate epigenomic information. “Entering the era of bacterial epigenomics with single molecule real time DNA sequencing” was recently published in Current Opinion in Microbiology. In the review, the authors note the importance of fully understanding and analyzing genome-wide methylation data, but say that technologies to date have not made it feasible to generate this information. “The advent of new sequencing platforms in the last decade has allowed…

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Thursday, April 18, 2013

Guest Blog: Michael Schatz shares his perspective on the new PacBio RS II

Michael Schatz, Ph.D. Assistant Professor of Quantitative Biology at Cold Spring Harbor Laboratory, shares some thoughts about his experience with the PacBio RS and his hopes for future work with the new PacBio RS II: “For several important genomic analysis, including de novo genome assembly, mapping structural variations, and discovering alternative splicing, we are principally limited by the read lengths of sequencing technology available. When it comes to assembling a genome, for example, read length is critically important for spanning repetitive sequences, as reads shorter than those repeats fundamentally just don’t have enough information for the assembler to determine the…

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Wednesday, April 10, 2013

Rapid Genome Assembly: Salmonella Outbreak Strain Sequenced and Closed in Less Than One Week

A newly reported Salmonella genome showcases the utility of single molecule, real-time (SMRT®) sequencing for characterizing a foodborne outbreak pathogen. The outbreak strain, Salmonella enterica subsp. enterica serovar Javiana (S. Javiana), representing one of the top five most common forms of Salmonella associated with fresh-cut produce, was sequenced and analyzed late last year; its genome was published this month in Genome Announcements, a journal from the American Society for Microbiology. The study was led by the US Food & Drug Administration’s Center for Food Safety & Applied Nutrition. Scientists from Pacific Biosciences and New England BioLabs participated in the study,…

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Tuesday, April 9, 2013

It’s a Very Microbial Season

This springtime, we’ve got microbes on the brain! The annual meeting of the American Society for Microbiology is just over a month away, so we’ve been thinking a lot about microbial genomics and how we can contribute to this burgeoning field. Microbiology is a key application for customers using the PacBio® RS. With its throughput, turnaround time, cost-effectiveness, and long reads, it is the perfect tool for performing de novo sequencing of microbes and generating closed genomes — often bringing microbial genomes together in a single contig. Beyond that, the unique way in which SMRT® Sequencing produces epigenetic data together…

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