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…
[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…
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…
A new preprint from scientists at Uppsala University’s SciLifeLab reports the de novo genome sequencing and assembly of two Swedish individuals using PacBio SMRT Sequencing. By comparing the Swedish genomes to the human reference (GRCh38), the team found a substantial amount of novel sequence which is not present in the reference – along with over 17,000 structural variants. Further comparison of the Swedish genomes to other population-specific reference genome assemblies – including a Korean and a Chinese genome – identified novel sequences that appear to be population-specific as well as several megabases that seem to be more universal in the…
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…
A new publication from scientists at The Rockefeller University and PacBio presents reference-grade, phased diploid genome assemblies for two important avian models for vocal learning, Anna’s hummingbird and zebra finch. Results are expected to help establish genome quality standards for the G10K and B10K sequencing projects, in addition to providing a better foundation for neuroscience studies. Published in GigaScience, “De Novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads” comes from lead author Jonas Korlach, senior author Erich Jarvis, and collaborators. The team undertook this project to improve the quality…
UPDATED September 14, 2018 The expanded G10K project, The Vertebrate Genome Project, released its first batch of 15 high-quality assemblies. ORIGINAL POST October 25, 2016 We’re excited to announce that we’ll be working closely with two programs that are committing significant resources toward generating reference-quality genomes of thousands of vertebrate species. Both the Genome 10K (G10K) and Bird 10,000 Genomes (B10K) initiatives have invested in SMRT Sequencing to build high-quality de novo genome assemblies for the next phase of their programs. By sequencing large numbers of vertebrates, the groups hope to develop resources that will be useful for species conservation…
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…
A new publication reports the discovery and analysis of a nightmare bacterium that’s genetically resistant to all commercially available classes of antibiotics. The paper, “Stepwise evolution of pandrug-resistance in Klebsiella pneumonia,” came out this month in Scientific Reports from Nature. Lead authors Hosam Zowawi and Brian Forde, along with senior author David Paterson and several collaborators, studied an isolate recovered from the urine of an 87-year-old patient who was hospitalized in the United Arab Emirates last year. They used SMRT Sequencing to characterize the strain and its genetic mechanisms for drug resistance. That strain, MS6671, “was found to be non-susceptible to…