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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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Thursday, April 12, 2018

SMRT Sequencing Enables Characterization of Cavities-Causing Bacteria in Children

We’re told to avoid sugar and refined carbohydrates if we want our teeth to remain strong and cavity-free. But what is the role of microbiota in our oral health? Cavities – or caries – actually occur as the result of bacterial infection that leads to sustained decalcification of tooth enamel and the layer beneath it, the dentin. Left unchecked, it can reach the tooth’s inner layer, with its soft pulp and sensitive nerve fibers, and, in some cases, can cause serious complications such as phylogenetic osteomyelitis and the life-threatening bacterial endocarditis. In addition to diet and host factors, the occurrence…

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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, February 5, 2018

Illuminating the Origin and Evolution of Bioluminescence

A project that sparked widespread interest and a successful science crowdsourcing campaign has inspired an international collaboration that produced two high-quality reference genomes, as well as a draft genome of a related beetle. And the results have shed light on the evolution of bioluminescence. We’ve been following the progress of Team Firefly since the team of scientists from MIT, University of Rochester, Brigham Young University, Indiana University, Cornell University, and Tufts University narrowly lost our 2016 SMRT Grant competition. The project to sequence the genome of the Big Dipper Firefly, Photinus pyralis, was ultimately crowdfunded through the Experiment site and…

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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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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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