Tackling larger and larger genomes has been an attractive pursuit for many scientists as sequencing technologies improve at rapid rates. But what about the other end of the spectrum — the tiny organisms that comprise much of the diversity of life? An obvious obstacle to decoding the DNA of small organisms such as insects, nematodes and other arthropods is collecting enough of it to actually sequence (usually multiple micrograms worth). Until recently, the solution was to pool DNA from many of these tiny creatures to create a representative sample, and extrapolate the biology of the individual constituents from there. But…
Photo of a pale spear-nosed bat (Phyllostomus discolor) courtesy of the Rossiter Lab (@rossiterlab) Bat lovers and animal researchers have been waiting for insights into the evolution and remarkable genetic adaptations of our winged mammalian friends, ever since the global Bat1K initiative announced its quest to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies. Now, the first six reference-quality genomes have been released on the Hiller Lab Genome Browser, and described in a pre-print by Sonja Vernes (@Sonja_Vernes), Michael Hiller (@hillermich) and Gene Myers (@TheGeneMyers) of the Max Planck Institute, Emma Teeling (@EmmaTeeling1) of…
Cover artwork by Daisy S. Lim It was the first multicellular eukaryotic genome sequenced to apparent completion, but it turns out the Caenorhabditis elegans reference that’s been used as a resource for the past 20 years does not exactly correspond with any N2 strain that exists today. Assembled using sequence data from N2 and CB1392 populations of uncertain lineage grown in at least two different laboratories during the 1980s and 1990s, accuracy of the C. elegans reference genome is limited both by genetic variants and by the limitations of the technology of the time (clone-based Sanger technology). It is believed…
It was the coolest critter Erin Bernberg (@ErinBernberg) had ever worked with – quite literally. The senior scientist at the University of Delaware Sequencing and Genotyping Center, a PacBio certified service provider, received a shipment of tiny, live ice worms from Washington State University and immediately faced several challenges. How would she get them out of their ice cubes? How would she isolate DNA from the delicate, dark pigmented creatures? And would she be able to extract enough DNA to sequence? Thanks to the new PacBio low DNA input protocol, the answer to the last question was yes. In fact,…
To enable better understanding of biology, sequencing data must be accurate and complete. This is especially true when seeking out variants and determining their implications. Luckily, technical and software improvements for SMRT Sequencing are making it easier to efficiently generate genome assemblies with unparalleled accuracy. As presented in a webinar by PacBio Staff Scientist Sarah Kingan (@drsarahdoom) and GoogleAI Genomics Project Lead Andrew Carroll (@acarroll_ATG), HiFi reads enabled by circular consensus sequencing (CCS) on the new Sequel II System challenge the notion that sequencing technologies require a tradeoff between length and accuracy. Highly accurate long reads (HiFi reads) offer the…
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…
Two years ago, Carola Greve and colleagues at the Zoological Research Museum Alexander Koenig in Bonn, Germany, were seeking to #SeqtheSlug as part of the 2017 Plant and Animal SMRT Grant competition, and the popular project was a close runner-up. Greve didn’t give up on her quest to sequence the ‘solar-powered’ sea slug. We caught up with her recently at the SMRT Leiden Scientific Symposium, where her update on the sea slug project earned her a Best Poster award. Why the sea slug? Although Mollusca represents the second largest animal phylum with around 85,000 extant species, only 23 mollusc genomes…
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…
What can a cute, cuddly, stingless bee from the Brazilian rainforest teach us about eusociality and mitochondrial evolution? Natalia S Araujo wants to find out, and she’s not the only one. As the only bee species in which true polygyny (multiple fertile queens in the same colony) occurs, there is great interest in Melipona bicolor, and its mitochondrial genome (mt genome) was one of the first sequenced in bees. But the sequence was incomplete and lacked information about its mitochondrial gene expression pattern. So Araujo, a postdoctoral researcher of animal genomics in the GIGA Institute of the University of Liège,…
USDA campaign poster to stop the spread of the invasive pest UPDATE October 2019 – This paper has now been published in Gigascience. Stop, Scrape, Squash… and Sequence! The latest invasive insect to hit headlines, the spotted lanternfly, has a voracious, indiscriminate appetite, with a particular taste for apples, grapes and maple — bad news for the wine, orchard and syrup industries of New England, where the Asian pest has been spotted. But there’s good news too, thanks to the expanded capacity of the new Sequel II System. USDA scientists were able to generate a high-quality, 2.3 Gb de novo…
Ángel Vergara Cruces By Ángel Vergara Cruces, Universidad de Málaga Plant geneticists have achieved a sweet feat: the first assembly of the octoploid strawberry genome. As reported in Nature Genetics earlier this year, a team led by Steven J. Knapp of the University of California-Davis and Patrick P. Edger of Michigan State University, identified more than 100,000 genes in their high-quality assembly and annotation of the commercial strawberry, Fragaria x ananassa. The main challenge when assembling a polyploid genome is that similar regions in different subgenomes (so-called homeologous regions) can lead to uncertainty about where to assign a given read…
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…
The modern world might benefit from a return to our ancient roots by expanding the cultivation of one of the first domesticated crops, broomcorn millet. Foodies will appreciate that the crop, a staple in many semi-arid regions of Asia and Europe, is gluten-free and extremely nutritious, with higher levels of protein, several minerals, and antioxidants than most other cereals. Farmers will appreciate that the drought-resistant plant has the highest water-use efficiency among all cereal crops, (i.e. the highest amount of grains produced with the same amount of water), a short life cycle (60–90 days), and a high harvest index. And…
For the thousands of scientists who attended The Plant and Animal Genome Conference in San Diego this January, the sentiment seemed to be “ask not if PacBio is for you, but how PacBio can work best for you.” The answer that emerged during PacBio’s PAG workshop and subsequent SMRT Informatics Developers Conference was a complex one. Recent developments, such as new chemistry, new SMRT Cells, the SMRTbell Express Template Prep Kit, and SMRT Link 6.0 software have already led to faster and easier library prep, longer reads with more data and reliability, better transcript characterization (Iso-Seq) and phasing (FALCON-Unzip) capabilities…