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Thursday, December 28, 2017

New Nematode Assembly Simplifies Search for Evolutionary Clues

Nematodes are both simple and complex, making them one of the most attractive animal taxa to study basic biological processes, including genome evolution. Studies in the nematode Caenorhabditis elegans, for instance, have provided invaluable insights into almost all aspects of biology, from developmental to neurobiology and human diseases. However, the high degree of fragmentation of current genome assemblies for many organisms complicates almost all types of genomic analysis. As the authors of a recent Cell Reports paper, Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus, point out, “general questions of chromosome evolution cannot be…

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Thursday, December 21, 2017

New Assembly of Wheat Progenitor Offers Clues to Genome Evolution

Following on the heels of the first nearly complete assembly of the hexaploid bread wheat genome, scientists from the University of California, Davis, the USDA Agricultural Research Service, Johns Hopkins University, and many other institutions recently published a high-quality genome assembly for one of wheat’s diploid ancestors. Both efforts incorporated SMRT Sequencing to improve contiguity of the assemblies. The new publication reveals that the ancestral plant’s genome has evolved more quickly than usual, driven largely by repeats. The paper, “Genome sequence of the progenitor of the wheat D genome Aegilops tauschii,” comes from senior author Jan Dvořák; lead authors Ming-Cheng Luo, Yong…

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Wednesday, December 20, 2017

Lucky Winners: Five More Species to Receive SMRT Sequencing at Sanger Institute

Scientists championed their cases, school children sifted through species, and thousands of members of the public from around the globe took to social media to weigh in. Now the results are in, and high-quality genome assemblies for 25 organisms integral to United Kingdom ecosystems can begin. As mentioned last month, we teamed up with the Wellcome Trust Sanger Institute on a project to celebrate their twenty-fifth anniversary. Sanger scientists will use the Sequel System and complementary technologies to produce reference-grade assemblies for squirrels, scallops, and sharks, as well as balsam, blackberries, bats, butterflies, bees, and many others. The final five…

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Thursday, December 14, 2017

A Fish Tale: Centromeres Prove Central to the Divergence of a Species

The ability to study the speciation of an animal in real-time is a dream come true for evolutionary and developmental biologists. A group of Japanese researchers has gotten that opportunity, thanks in part to SMRT Sequencing. Scientists at the University of Tokyo were the first to create a reference genome for an inbred strain of the medaka fish (Oryzias latipes), genome size ~800 Mb, in 2007. The genome assembly was created using Sanger sequencing, but contained low-quality regions and 97,933 sequence gaps. So, the team started from scratch with long-read sequencing to generate genome assemblies with far less missing sequence.…

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Tuesday, December 12, 2017

Creating an Epigenetic Barcode to Accurately Characterize Microbial Communities

Unraveling the role of the microbiome in human health and environmental samples is an emerging priority in scientific study. But despite the best advances in sequencing technology, identifying the bacteria, fungi, and other organisms present in complex samples remains a huge challenge. Metagenomic shotgun sequencing can read chromosomes, plasmids, and bacteriophages, and comparison to reference genome sequences can be used to place them into putative taxa and species bins, but these methods fail to sufficiently distinguish between genomes that are very similar. A team of scientists from the Icahn School of Medicine at Mount Sinai, Sema4, and other institutions has…

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Monday, December 11, 2017

Full-Length HLA Sequencing Improves Accuracy and Resolution for Community Resource

In a new publication, scientists from Anthony Nolan Research Institute and the UCL Cancer Institute present an in-depth analysis of the utility of SMRT Sequencing for Human Leukocyte Antigen (HLA) typing. They assessed more than 100 cell lines and found that PacBio long-read sequencing significantly improves the accuracy of HLA typing. “Single molecule real-time (SMRT®) DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines” comes from lead author Thomas Turner, senior author Steven Marsh, and collaborators. The scientists implemented SMRT Sequencing to perform high-resolution HLA typing for 126 B-lymphoblastoid cell lines, including…

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Thursday, December 7, 2017

Long-read Koala Assembly Provides Insight into Ongoing Retroviral Invasion

What can one koala tell us about an endemic that threatens the survival of its species? A great deal, it turns out. While doing a deep dive into the genome of a wild female koala, a team of Australian scientists led by Matthew Hobbs and Andrew King of the Australian Museum Research Institute were able to unravel some of the complexity of the species-specific gammaretrovirus KoRV. The results, published recently in Nature, paint a picture of a rapidly evolving and diversifying virus, with implications for the long-term survival of the koala, as well as our understanding of retroviral-host species interactions.…

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Tuesday, December 5, 2017

The Antibiotic Arms Race: Tracking K. pneumoniae in a Hospital Setting

Courtesy of NIAID In a recent paper, scientists in Germany call for a genomic database of Klebsiella pneumoniae strains to accelerate strain identification as well as drug-resistance status. To that end, they used SMRT Sequencing to generate high-quality assemblies for 16 isolates collected in German hospitals. “Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing” comes from lead authors Andreas Zautner and Boyke Bunk, senior authors Jorg Overmann and Wolfgang Bohne, and collaborators at University Medical Center and other institutes in Germany. The urgency to characterize K. pneumoniae strains comes from the rapid rise of…

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