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Monday, January 15, 2018

When A Single Reference is Not Enough

Maize is amazingly diverse. A study comparing genome segments from two inbred lines, for instance, revealed that half of the sequence and one-third of the gene content was not shared – that’s more diversity within the species than between some other species, for example humans and chimpanzees, which exhibit more than 98 percent sequence similarity. So how can researchers and commercial breeders rely upon a single reference genome to represent the genetic diversity in their germplasms? More and more scientists are deciding they cannot. At DuPont Pioneer, where DNA sequencing is paramount for R&D to reveal the genetic basis for…

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Thursday, January 4, 2018

Collaborative Effort Results in High-Quality Mosquito Genome, Raising Hope for Infectious Disease Control

In an unprecedented crowd-sourced effort stoked by social media, 72 scientists collaborated via 25 conference calls and 3,323 emails to produce a new high-quality Aedes aegypti mosquito genome. Assembled using PacBio long-read sequencing, the resource could provide the DNA map researchers need to combat the pest and the infectious diseases it spreads, including Zika, dengue, chikungunya, and yellow fever. Eager to share the results with the scientific community, lead author Leslie B. Vosshall, first author Benjamin Matthews, both of Rockefeller University, and colleagues at several other institutions, published a pre-print of their paper, “Improved Aedes aegypti mosquito reference genome assembly…

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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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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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Wednesday, December 2, 2015

PMWC 2016: Advancing Genomics for Improved Patient Care

We’re already looking forward to next month’s Personalized Medicine World Conference. Long before “precision medicine” was an industry catchphrase, PMWC was bringing together stakeholders from genomics companies and academic research, regulatory agencies, clinical groups, pharma/biotech, and more. Launched in 2009, the meeting has prompted important discussions as well as insight about how to move the field forward in a thoughtful way. From January 24th to the 27th, some 1,200 PMWC attendees will descend on the Computer History Museum in Mountain View, Calif. The event will kick off with a reception honoring the four awardees of this conference: Merck’s Roger Perlmutter…

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