A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. It has recently become apparent how important it is to sequence more than one individual to characterize the genomic variation within a species. This makes sense if you consider that sexually reproducing organisms are a mix of their parents and, therefore, not identical. This is just as true in crops as it is in humans. So, it’s not surprising that when a group of researchers from several institutions in China embarked on de novo genome assemblies of several accessions of…
It’s well known that finding the genetic cause of rare diseases can be complex — that’s why so many remain unsolved. But researchers are beginning to get a grasp on just how complex these conditions can be, thanks to the heightened power of PacBio. PacBio principal scientist Aaron Wenger kicked off a recent webinar with a quote from University of Washington scientist Evan Eichler, who said “there are three key aspects to genetic disease associations: comprehensive variant discovery, accurate allele-frequency determination, and an understanding of the pattern of normal variation and its effect on expression.” Wenger explained how HiFi reads…
Welcome to the Sequencing 101 blog series – where we will provide introductions to sequencing technology, genomics, and much more! If you’re not immersed in the field of DNA sequencing, it can be challenging to keep up with the rapid evolution among all the platforms and technologies on the market. Let’s start with a quick overview of how these different technologies came about — and how each is used today. The evolution of sequencing technology. First Generation Sequencing – Starting the Era of Genomics The process of Sanger sequencing. DNA sequencing as we know it originated in the late…
Seeking to sequence and characterize entire transcriptomes in one go? Our new Iso-Seq protocol and reverse-transcriptase PCR kit makes it easier, speedier and cheaper. Run on the new Sequel II System, the completely revamped Iso-Seq Express workflow achieves whole transcriptome characterization from a single SMRT Cell 8M delivering up to 400 Gb, and at a third of the cost, or less. Yield has also increased on the Sequel System, with 3.0 sequencing chemistry typically delivering up to 30 Gb per SMRT Cell 1M for our RNA sequencing application. The new protocol requires three times less RNA input (300 ng) and…
Single Molecule, Real-Time (SMRT) Sequencing continues to get smarter and more powerful, with the recent launch of the Sequel II system increasing capabilities and efficiencies of the long-read DNA and RNA PacBio sequencing technology even further. In a special issue devoted entirely to the technology in the MDPI open access journal Genes, guest editors Adam Ameur of Uppsala University and Matthew S. Hestand of the Cincinnati Children’s Hospital Medical Center present eight articles highlighting research conducted using SMRT Sequencing. As this special issue demonstrates, the benefits of SMRT Sequencing to many different areas of research are becoming evident, not only…
Plasmodium falciparum Malaria is a complicated killer, and efforts to develop effective vaccines have been hindered by gaps in our understanding of both the parasite that causes the infection, Plasmodium falciparum, and its transmitter, the mosquito. Like many virulent parasites, P. falciparum has evaded close genetic scrutiny due to its complex and changing composition. Its 23 Mb haploid genome is extremely AT rich (~80%) and contains stretches of highly repetitive sequences, especially in telomeric and subtelomeric regions. To make matters more complicated, it expands its genetic diversity during mitosis via homologous recombination, leading to the acquisition of new variants of…
We’re thrilled to announce the launch of the Sequel II System, reducing project costs and timelines with approximately eight times the data output compared to the previous Sequel System. It enables customers to comprehensively detect human variants ranging in size from single nucleotide changes to large, complex structural variants. The system is also ideal for standard applications such as de novo assembly of large genomes and whole transcriptome analysis using the Iso-Seq method. The Sequel II System is based on the proven technology and workflow underlying the previous version of the system, but contains updated hardware to process the new…
Maya and her partner, Sgt. Nic Banuelos, of the UWPD K9 unit First there was Shadow, the poodle owned by gene-entrepreneur Craig Venter. Then there was Tasha, a female Boxer. Will the next de-coded dog be Maya, a German Shepherd Dog that helps police the campus at the University of Wisconsin-Madison? Maya has been basking in social media celebrity alongside her human companion Sgt. Nic Banuelos, PhD students Lauren Baker and Emily Binversie, technician Jorden Gruel, veterinary surgeon-scientists Susannah Sample and Peter Muir, and Peter’s woven likeness, after winning the 2019 Plant and Animal SMRT Grant, co-sponsored by Histogenetics. We…
What has four legs, lots of fat and fur, and will possibly help uncover novel mechanisms to combat diabetes? Photo courtesy of WSU Bear Center Grizzly bears! If humans were to undergo regular, extended cycles of weight gain and inactivity, they’d likely end up with obesity, muscle atrophy, or type 2 diabetes. But grizzly bears experience no ill effects from their annual fat gain and sedentary hibernation. Somehow they are able to switch their insulin resistance between seasons, and researchers at Washington State University are hoping to figure out how, with possible therapeutic value for humans. We’re proud to support…
UPDATED Dec. 3, 2018 Congratulations to the Italian team on the publication of their European barn swallow genome! The paper is now available at GigaScience. ORIGINAL POST Oct. 3, 2018 With its bold blue plumage, russet throat and chipper chirps, the barn swallow is beloved by many avian enthusiasts. It’s also a favorite of scientists, becoming a flagship species for conservation biology. Numerous evolutionary and ecological studies have focused on its biology, life history, sexual selection, response to climate change, and the divergence between its eight subspecies in Europe, Asia and North America. But the full potential of such studies has…
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…
When humans are infected with the Marburg virus, the result is often lethal, with hemorrhagic fever and other symptoms similar to Ebola. When bats are infected, the result is…. nothing. The tiny mammals remain asymptomatic. In order to crack this antiviral mystery, a multi-institutional team of scientists sequenced, assembled and analyzed the genome of the bat species Rousettus aegyptiacus, a natural reservoir of Marburg virus and the only known reservoir for any filovirus. Their findings contradicted previous hypotheses about bat antiviral immunity, which assumed that bats had enhanced antiviral defenses, controlling viral replication early in infection, and developing effective adaptive immune…
Computational biologist Doreen Ware harvests maize tissue for RNA isolation. Photo by Miriam Chua c/o USDA 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, but an important study…
The PacBio team was honored to attend an excellent Keystone Symposium in Hannover, Germany recently. The event, “One Million Genomes: From Discovery to Health,” offered a rare look at large-scale human genome projects, with many top-notch speakers. The meeting featured speakers from many national genomics efforts, including China, Estonia, Israel, the UK, and the US. Each of these individual national efforts is essential to overcome the representation bias seen in human genome databases today. Underrepresented groups are currently less likely to get actionable results from clinical genetic tests, a situation that threatens to confer the benefits of precision medicine…
When German diver Joachim Kreiselmaier reached the deepest parts of the Danube-Aach cave system, he couldn’t believe his eyes: a “strange fish,” with a pale body coloration and smaller eyes and larger nares and barbels than the loaches typically spotted nearby. He had discovered the first cavefish in Europe, and the northernmost in the world. “This is spectacular, as it was believed that the Pleistocene glaciations prevented fish from colonizing subterranean habitats north of 41° latitude,” said ecologist Jasminca Behrmann-Godel of the Limnological Institute of the University of Konstanz, who examined the fish Kreiselmaier brought back to the surface. “Initial…