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Tuesday, April 24, 2018

Nature Webinar and SMRT Grant Winner Explore Structural Variation for Disease Gene Discovery

Structural variants account for most of the base pairs that differ between human genomes, and are known to cause more than 1,000 genetic disorders, including ALS, schizophrenia, and hereditary cancer. Yet they remain overlooked in human genetic research studies due to inherent challenges of short-read sequencing methods to resolve complex variants, which often involve repetitive DNA.   At a recent webinar co-hosted by Nature Research, Professor Alexander Hoischen joined Principal Scientist Aaron Wenger to discuss how advances in long-read sequencing and structural variant calling algorithms have made it possible to affordably detect the more than 20,000 such variants that are…

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Tuesday, April 17, 2018

Scientists Aim to Develop “Genomic Ark” of High-Quality Bat Genomes

Pop quiz: Which animal accounts for around 20% of all living mammals, harbors (yet survives) some of the world’s deadliest diseases, lives proportionately longer than humans given its body size, and helps make tequila possible? Answer: Bats. From the tiniest bumblebee bat (Craseonycteris thonglongyai) to the large (1kg) golden-capped fruitbat (Acerodon jubatus), the diversity and rare adaptations in bats have both fascinated and terrified people for centuries. Now, an international consortium of bat biologists, computational scientists, conservation organizations, and genome technologists has set out to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies.…

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Monday, April 9, 2018

Rice Revelations: Nine New Genome Assemblies Uncover Key Traits and Evolutionary Clues

Revered around the world, rice is a staple food for nearly half of the population. But as that population grows, rice breeders are faced with the challenge of producing crops that are high yielding, disease-resistant and nutritious, while at the same time being more sustainable. The International Oryza Map Alignment Project (OMAP) was initiated in 2003 to develop a set of high-quality genomic resources for the wild relatives of rice that could be used as a resource to discover and utilize novel genes, traits and/or genomic regions for crop improvement and basic research. Members of the consortium recently released new…

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Tuesday, March 20, 2018

New Cattle Genome Overcomes Challenges of Haplotype Assembly

Genetic knowledge is powerful when it comes to breeding. The ability to trace desirable traits to the gene level can help create plants and animals that are adapted to existing and emerging challenges, such as temperature tolerance, productivity, or disease resistance.   By crossing two breeds of cattle, Angus (Bos taurus taurus) and Brahman (Bos taurus indicus), from opposite ends of the species spectrum, breeders can benefit from the Angus’s high productivity in cool environments and the Brahman’s tolerance for harsh, hot climates and the diseases and parasites found there. Genetically and phenotypically, the two subspecies are very different. And,…

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Friday, March 9, 2018

Coral Microbiome Project Wins 2017 Microbial SMRT Grant

[caption id="attachment_24073" align="alignright" width="300"] Rice coral (Montipora capitata) growing over Porites lobata. Credit: Dr. Dwayne Meadows, NOAA/NMFS/OPR[/caption] Corals are critical to sustaining sea life in many parts of the world, contributing to an elaborate ecosystem that lives in and around their mineralized calcium carbonate skeletons. In addition to hosting photosynthetic endosymbionts in exchange for energy, corals harbor a diverse microbial community. What role does this microbial metagenome play in the health of the coral reef, especially during thermal challenges induced by climate change? Alexander Shumaker of Rutgers University will get a chance to investigate this question, thanks to long-read sequencing…

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Monday, March 5, 2018

Dog Meet Dog World: Exploring Canine Genomes

From wild animals to perfect pets, dogs have undergone some interesting changes during their centuries-long domestication. Intent on unraveling some of the developmental secrets of the process, a team of scientists from the University of New South Wales in Sydney, Australia, is doing deep dives into the genomes of a range of canine cousins along the evolutionary chain. A desert dingo named Sandy has already provided some insight into the process after its genome was sequenced as part of the 2017 Plant and Animal SMRT Grant. Study leader Bill Ballard described in this presentation at PAG 2018 that pure dingoes…

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Friday, February 9, 2018

JGI Sequencing Fungus for Clues to Better Biofuel Production

[caption id="attachment_23152" align="alignright" width="300"] Aspergillus ochraceus[/caption] The Department of Energy has its eyes on an unassuming solution to our bioenergy needs: Aspergillus. The fungal genus contains hundreds of variations, which include powerful pathogens, industrial cell factories, and prolific producers of bioactive secondary metabolites. The DOE’s Joint Genome Institute (JGI) has embarked on an ambitious plan to sequence, annotate and analyze the genomes of 300 Aspergillus fungi, and the first results are in. In a study published in the Proceedings of the National Academy of Sciences, “Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species,” a team…

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Wednesday, February 7, 2018

Review: SMRT Sequencing ‘Is Revolutionizing’ Clinical Applications

A new review in Nucleic Acids Research offers a sweeping look at clinical uses for SMRT Sequencing, concluding: “The myth that SMRT sequencing is too error prone to be diagnostically useful is being expunged and replaced by evidence that it offers advantages over short-read sequencers.” The authors continued, “Just as second-generation platforms stepped beyond Sanger sequencing and enabled a revolution in genomics medicine, third-generation single molecule sequencing platforms will likely be the next genetic diagnostic revolution.” “Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics” written by Simon Ardui, Joris Vermeesch, and Matthew Hestand at KU Leuven…

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Monday, January 29, 2018

Small Creature, Massive Genome: Axolotl Offers Insights Into Regeneration

The Mexican salamander, or the axolotl, may have tiny feet, but the feat of decoding its genetic footprint was huge—32 billion base pairs huge, making it ten times bigger than the human genome and the largest ever sequenced. The accomplishment by an international team of scientists is significant, not only because of its sheer size, but also because of the insights it could provide into tissue regeneration. The easily recognizable critter has an astounding ability to regenerate body parts, growing lost limbs – bones, muscles, nerves and all – within weeks. It can also repair spinal cord and retinal tissue,…

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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 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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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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Thursday, August 24, 2017

Software Tools Optimized for Long Reads Improve Detection of Complex Structural Variants

Sniffles and NGMLR, structural variant detection and alignment algorithms developed in the Schatz lab for long-read sequence data, are already familiar to many in the PacBio community. Now, a preprint is available so users can see how these open-source tools perform in a variety of conditions. “Accurate detection of complex structural variations using single molecule sequencing” comes from lead author Fritz Sedlazeck at Baylor College of Medicine, senior author Michael Schatz at Johns Hopkins University, and collaborators. The team notes that long-read sequencing has introduced a much more comprehensive means of discovering structural variants, many of which are missed by…

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Wednesday, November 9, 2016

More than Halfway There: Richard Gibbs Talks Clinical Genetics with Mendelspod

Many scientists who participated in the original Human Genome Project shared a grand vision that individual genomes would one day be part of routine medical care. Genomics veteran Richard Gibbs, founder and Director of the Genome Sequencing Center at Baylor College of Medicine, tells Mendelspod host Theral Timpson in a new podcast interview that “we are more than halfway [there].” In the podcast, Gibbs shares his perspective on the complementary roles that genomics and genetics approaches have in driving our understanding of human biology.  He noted that long before the Human Genome Project gained momentum, the discovery of human single…

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