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Thursday, May 30, 2019

Unraveling Malaria Mysteries with Long-Read Sequencing

Plasmodium falciparum Malaria is a complicated killer, and efforts to develop effective vaccines have been hindered by gaps in our understanding of both the parasite that causes the infection, Plasmodium falciparum, and its transmitter, the mosquito. Like many virulent parasites, P. falciparum has evaded close genetic scrutiny due to its complex and changing composition. Its 23 Mb haploid genome is extremely AT rich (~80%) and contains stretches of highly repetitive sequences, especially in telomeric and subtelomeric regions. To make matters more complicated, it expands its genetic diversity during mitosis via homologous recombination, leading to the acquisition of new variants of…

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Thursday, May 23, 2019

Review: How Long-Read Sequencing Could Make a Difference in Medical Genetics

A recent review article published in Frontiers in Genetics offers a great look at the landscape of long-read sequencing. Authors Tuomo Mantere, Simone Kersten, and Alexander Hoischen from Radboud University Medical Center in the Netherlands focus on emerging applications in medical genetics for long-read technologies. “With the recently demonstrated success in identifying previously intractable DNA sequences and closing gaps in the human genome assemblies, long-read sequencing (LRS) technologies hold the promise to overcome specific limitations of NGS-based investigations of human diseases,” the scientists write. “LRS has the potential to grow into a technology that is used not only to produce…

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Tuesday, May 21, 2019

Applications and Benefits of Single-Molecule Transcriptome Sequencing

When looking to understand the functional implications of genetic variability, scientists should seek out the Iso-Seq method, according to Cold Spring Harbor researchers. In a recent paper published in Frontiers in Genetics, Doreen Ware, Bo Wang, and colleagues reviewed the state of transcript sequencing and analysis technologies, and concluded that single-molecule sequencing from PacBio provided several advantages over other methods. A major challenge in molecular biology continues to be the complex mapping of the same genome to diverse phenotypes in different tissue types, development stages and environmental conditions, the paper states. “A better understanding of the transcripts and expression of…

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Thursday, May 16, 2019

Top 10 Tools and Tips from the SMRT Leiden Informatics Developers Meeting

Hundreds of SMRT scientists came together recently in Leiden to learn about the latest updates to PacBio technology and to showcase their data analysis tools. Extremely useful information was shared, and future collaborations were sparked. For those who weren’t able to jet to the Netherlands to attend, we’ve rounded up the top tools and tips presented at the European SMRT Informatics Developers Meeting. For an in-depth report on the event, check out this blog post by PacBio Principal Scientist Elizabeth Tseng. SMRT Link – Of course our own open-source SMRT analysis software suite will be top of the list. Updates…

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Wednesday, May 15, 2019

SMRT Leiden Symposium Showcases Successes in Clinical and Conservation Genomics

What can a cute, cuddly, stingless bee from the Brazilian rainforest teach us about eusociality and mitochondrial evolution? Natalia S Araujo wants to find out, and she’s not the only one. As the only bee species in which true polygyny (multiple fertile queens in the same colony) occurs, there is great interest in Melipona bicolor, and its mitochondrial genome (mt genome) was one of the first sequenced in bees. But the sequence was incomplete and lacked information about its mitochondrial gene expression pattern. So Araujo, a postdoctoral researcher of animal genomics in the GIGA Institute of the University of Liège,…

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Tuesday, May 7, 2019

Sequencing of Historical Cholera Sample Surprises Sanger Scientists

They are the unwelcome comeback kids: Measles, mumps and other old-time diseases that were once nearly extinct are on the rise in suburban communities as well as developing nations. In order to better understand the evolution of these microbial menaces, researchers at the Wellcome Sanger Institute and Public Health England have been sequencing historical samples deposited in the UK’s National Collection of Type Cultures (NCTC). The latest is a strain of cholera-causing bacteria (Vibrio cholerae) extracted in 1916 from the stool of a British soldier who was convalescing in Egypt. Researchers at the Sanger Institute revived the WWI soldier’s bacteria…

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Monday, May 6, 2019

New Sequel II System Enables Rapid Characterization of Invasive Pests

USDA campaign poster to stop the spread of the invasive pest UPDATE October 2019 – This paper has now been published in Gigascience. Stop, Scrape, Squash… and Sequence! The latest invasive insect to hit headlines, the spotted lanternfly, has a voracious, indiscriminate appetite, with a particular taste for apples, grapes and maple — bad news for the wine, orchard and syrup industries of New England, where the Asian pest has been spotted. But there’s good news too, thanks to the expanded capacity of the new Sequel II System. USDA scientists were able to generate a high-quality, 2.3 Gb de novo…

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Wednesday, May 1, 2019

The Sequencing of the Octoploid Strawberry Genome Uncovers its Evolution

Ángel Vergara Cruces By Ángel Vergara Cruces, Universidad de Málaga Plant geneticists have achieved a sweet feat: the first assembly of the octoploid strawberry genome. As reported in Nature Genetics earlier this year, a team led by Steven J. Knapp of the University of California-Davis and Patrick P. Edger of Michigan State University, identified more than 100,000 genes in their high-quality assembly and annotation of the commercial strawberry, Fragaria x ananassa. The main challenge when assembling a polyploid genome is that similar regions in different subgenomes (so-called homeologous regions) can lead to uncertainty about where to assign a given read…

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