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Thursday, July 27, 2017

At SMBE 2017, SMRT Sequencing Fuels Genome Assemblies for Evolution Studies

We enjoyed attending the annual meeting of the Society for Molecular Biology and Evolution in Austin earlier this month. Some 1,500 people attend SMBE, which this year offered cutting-edge sessions on evolutionary genomics, microbiome dynamics, epigenetics, and much more. There were several posters and presentations featuring SMRT Sequencing data, most focused on using highly accurate, long-read data to generate or improve reference genomes. The high-quality assemblies we saw are enabling evolutionary biologists to investigate genomic structure and function in a variety of organisms as well as characterize structural variants and other complex polymorphisms that are difficult to detect with conventional…

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Thursday, July 20, 2017

‘A Quiet Revolution’: SMRT Sequencing Powers Increasing Genome Assembly Quality

A news article in Science magazine nicely captures the improvements in the quality of genome assemblies made possible by long-read sequencing and other methods. “New technologies boost genome quality” was written by Elizabeth Pennisi and includes interviews with a number of leading scientists. One of those is Erich Jarvis, the neuroscientist at Rockefeller University who is best known in the genomics community for his work on vocal learning with songbirds and has been instrumental in both the G10K and B10K programs. As he told Pennisi, “The genome quality makes a huge difference in the type of science we can do.”…

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Wednesday, July 19, 2017

New Assembly for Complex Bread Wheat Genome: 10 Times Higher Contiguity

Photo by Max Ronnersjö UPDATE: This preprint is now published! Check it out in the November 2017 issue of GigaScience. In a new bioRxiv preprint, scientists from Johns Hopkins present a major step forward in accuracy and completeness for the wheat genome. Their new assembly, generated largely from PacBio data, demonstrates the importance of using long, highly-accurate reads for resolving extremely complex, repetitive genomes. “The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum,” comes from lead author Aleksey Zimin, senior author Steven Salzberg, and collaborators. In launching this project, the team aimed to overcome a longstanding challenge for the…

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Tuesday, July 18, 2017

Novogene to Build Database of Structural Variants in 1,000 Chinese Genomes Using SMRT Sequencing

In an effort to improve precision medicine in Chinese populations, Novogene announced plans to build a database of structural variants in 1,000 Chinese individuals using PacBio SMRT Sequencing. Databases which catalog SNVs and small indels have proven invaluable for precision medicine, serving as population controls for rare disease research and providing a list of variants for genetic association studies. Yet, most of the base pairs that differ between two human genomes are in structural variants which are not adequately represented in current databases. Furthermore, current databases do not represent the genetic background of all ethnic populations, particularly the Chinese who…

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Tuesday, July 11, 2017

Population Genomics Study Shows Faster Evolution in Domesticated Yeast

Photo from Rising Damp (Flickr) In a Nature Genetics paper, scientists used SMRT Sequencing to detect and compare structural variations in several yeast strains in order to understand evolutionary genome dynamics. They found different rates of evolution among domesticated and wild strains, and suggest that “the influence of human activities” could explain this. “Contrasting evolutionary genome dynamics between domesticated and wild yeasts” comes from lead author Jia-Xing Yue, senior author Gianni Liti, and collaborators at the Université Côte d’Azur, the Wellcome Trust Sanger Institute, and other institutes. Choosing long reads to facilitate accurate detection of structural variants, they used PacBio…

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Thursday, July 6, 2017

For High-Quality Ant Genomes, Scientific Alliance Chooses SMRT Sequencing

Photo by Luke Elstad The Global Ant Genomics Alliance (GAGA) recently announced that it has adopted SMRT Sequencing as its technology of choice for generating high-quality genome assemblies. The alliance, made up of more than 50 scientists at dozens of institutions around the world, aims to sequence 200 ant species to provide a comprehensive look at genomic diversity across ant genera and to provide the scientific community with a foundation of data to enable decades worth of research. GAGA teamed up with genomic service provider Novogene, which agreed to purchase 10 Sequel Systems earlier this year. In the announcement, GAGA noted…

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