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Thursday, September 13, 2018

Building a Digital Genome Ark: Vertebrate Genome Project Releases 15 New Reference Genomes

[caption id="attachment_29874" align="alignright" width="300"] The duck-billed platypus genome is one of 15 high-quality assemblies released by the Vertebrate Genome Project[/caption] When creating a global genomic ark of creatures great and small, scientists are turning to the comprehensive coverage and quality of PacBio sequencing. The Vertebrate Genomes Project (VGP), an international consortium of more than 150 scientists from 50 academic, industry and government institutions in 12 countries, recently released the first 15 of an anticipated 66,000 high-quality reference genomes representing all vertebrate species on Earth. The VGP consortium spent three years selecting technologies and workflows to produce higher quality, “platinum-level” genomes,…

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Tuesday, September 4, 2018

Webinar Summary: Developing Benchmark Sets for Structural Variants

[caption id="attachment_29573" align="alignright" width="200"] Justin Zook[/caption] A map of every individual’s genome will soon be possible, but how will we know if it is correct? Benchmarks are needed in order to check the performance of sequencing, and any genomes used for such a purpose should be comprehensive and well characterized. Enter the Genome in a Bottle Project (GIAB), a consortium of geneticists and bioinformaticians committed to the creation and sharing of high-quality reference genomes. Unlike other initiatives, such as the 1000 Genomes Project, that are seeking to sequence many representatives of different populations, GIAB is interested in sequencing just a…

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Wednesday, August 1, 2018

Something to Crow About: SMRT Sequencing Aids Conservation of Rare Hawaiian Bird

Brought to the brink of extinction, the future of Hawaii’s only lineage of the crow family (Corvidae) is looking up thanks to intensive conservation genomics efforts using PacBio de novo assemblies. In Hawaiian mythology, the ‘alalā is said to lead souls to their final resting place on the cliffs of Ka Lae, the southernmost tip on the Big Island of Hawaii. As one of the largest native bird populations, it also had a vital role in the ecosystem, helping to disperse and germinate seeds of many indigenous plant species. Disease, predators and shrinking habitats led to a complete loss of…

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Tuesday, July 24, 2018

SMRT Science, Tips & Tricks Presented at Leiden Meeting

[caption id="attachment_28544" align="alignright" width="300"] SMRT Art: Jewelry created from upcycled SMRT cells by Olga Pettersson.[/caption] When was the last time you sent your DNA off to a day at the spa? Olga Pettersson of the SciLifeLab at Uppsala University lets her molecules relax for up to a week at room temperature to enable them to untangle, achieve better chemical purity, and better sequencing output. It was one of many practical pointers shared by presenters at the popular three-day gathering of PacBio users in Leiden, Netherlands last month. SMRT Leiden featured the scientific discoveries and analytical achievements of more than 30…

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Tuesday, July 17, 2018

Long Look Into Ant Brains Provides Epigenetic Insights

To understand the epigenetic regulation of brain function and behavior, scientists are turning to ants. To understand the ants, they are applying the accurate, long reads of SMRT Sequencing. While the genetic code of many types of ant have been combed through thanks to several genomes assembled through whole-genome shotgun sequencing, there have only been brief glimpses and guesses regarding gene regulation. Existing assemblies are highly fragmented drafts, making epigenetic studies nearly impossible. Eager to determine the epigenetic changes responsible for phenotypic and behavioral plasticity in Camponotus floridanus and Harpegnathos saltator ant species, a team of researchers from the Epigenetics…

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Wednesday, July 11, 2018

Maize Collaborators Embark on Ambitious 26-line Pangenome Project

[caption id="attachment_27906" align="alignright" width="201"] Computational biologist Doreen Ware harvests maize tissue for RNA isolation. Photo by Miriam Chua c/o USDA[/caption] The first reference genome for maize variety B73, completed in 2009, was a major milestone, and an improved version released by Cold Spring Harbor Laboratory scientists in 2017 provided a deeper dive into the genetics of the complex crop. Yet even this new robust reference is not enough for Kelly Dawe, Doreen Ware and Matt Hufford, who have taken up another ambitious project: creating a 26-line pangenome reference collection in just two years. “Maize is not only an important crop,…

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Monday, June 11, 2018

New High-Resolution Genome Assemblies Expand Our Understanding of Human-Ape Differences

Ever since researchers sequenced the chimpanzee genome in 2005, they have known that humans share the vast majority of our DNA sequence with chimps, making them our closest living relatives. So what, exactly, sets us apart? While prior ape genome assemblies were helpful in finding single nucleotide changes, many researchers speculate that a variation type that is more difficult to resolve, structural differences in regulatory DNA or in the copy number of gene families, play important roles in species adaptation. Large-scale efforts to sequence and assemble more ape genomes over the last 13 years have expanded our knowledge, but many…

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Wednesday, June 6, 2018

New Resource for Microbiologists: Collection of 3,000 Bacteria Genomes Released

[caption id="attachment_26599" align="alignright" width="300"] Haemophilus influenzae, a sample of which was deposited to the NCTC collection by Alexander Fleming, from his own nose.[/caption] The genomes of 3,000 strains of bacteria, including some of the deadliest in the world, are now available to researchers as part of an ambitious project by the UK’s National Collection of Type Cultures (NCTC), in partnership with the Wellcome Sanger Institute and PacBio. Plague, cholera, streptomyces, and 250 strains of E. coli, are among the reference genomes created, as well as all ‘type strains’ of the bacteria in the collection -- the first strains that describe…

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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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