Launched in 1996, NARMS is a U. S. public health surveillance system that tracks antimicrobial susceptibility of select foodborne enteric bacteria. We hear a lot about the growing crisis of antibiotic resistance in human health, but it turns out this is just the most visible place it appears as it moves through our complex modern environment. For example, when intensive farming is used to feed large urban populations, antibiotic resistance can first emerge on farms and gain access to human communities through the food system. One of the key groups on the front lines of monitoring antibiotic resistance from farm…
Matt Hufford, associate professor at Iowa State University, helped produce a 26-line maize pangenome assembly collection Maize researchers have been rejoicing over a New Year’s gift delivered by a group of 33 scientists: A 26-line “pangenome” reference collection. The multi-institutional consortium of researchers used the Sequel System and BioNano Genomics optical mapping to create the assemblies and high-confidence annotations. They released the results on January 9, and in several presentations at the Plant and Animal Genome XXVIII Conference, less than two years after the ambitious project was funded by a $2.8 million National Science Foundation grant. The collection includes comprehensive,…
100 high-quality assemblies released by the Vertebrate Genome Project include the genome of the critically endangered vaquita porpoise With her distinctive dark eyeshadow, grey lipstick-like markings and delicate disposition, she was a natural film star. And her life certainly provided enough drama for any Hollywood blockbuster, complete with high-speed boat chases in pursuit of black market “cocaine of the sea” cartels. Unfortunately, her ending was not a happy one. But efforts by an international consortium of conservation geneticists are making sure her legacy isn’t lost. The DNA of one of the last remaining vaquita porpoises in the world has been…
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…
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…
With its unique medicinal and psychoactive compounds, the popularity of cannabis is spreading… well, like a weed. Now legal in 10 states for recreational use, and in 33 for medical use (with the FDA approval of the first oral cannabis drug for epilepsy on June 25, 2018), the once-forbidden plant is primed to become one of the most talked-about — and valuable — agriculture crops. But what needs to be done to take this promising crop into the clinic? Sound science, accurate testing protocols, and strident tracking systems — all of which can be achieved through genomics, according to Kevin…
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…
It took nearly 20 years until the technology was right, and five years of hard graft by more than 100 scientists from 16 institutions, but the result was worth it, according to University of Illinois plant biology professor Ray Ming. One of several authors of a paper published and featured on the cover of Nature Genetics reporting the assembly of a 3.13 Gb reference genome of the incredibly complex autopolyploid sugarcane Saccharum spontaneum L, Ming said he dreamed about having a reference genome for sugarcane while working on sugarcane genome mapping in the late 1990s. But sequencing technology was not…
Cotton crops the world over have benefited from the pest-killing protein from Bacillus thuringiensis (Bt), first used in sprays and then, in 1996, transgenic crops, resulting in reduced insecticide use, enhanced biological control, and increased farmer profits. But the precious plants are under threat once again by a tiny but mighty pest: pink bollworm (Pectinophora gossypiella). In India, where more than 7 million farmers have planted 10.8 million hectares of transgenic Bt cotton, the lepidopteran pest has developed resistance to two different forms of the toxin that made the transgenic crops so effective, creating catastrophic economic losses. Scientists have been…
It’s one of the most ambitious sequencing projects ever attempted — the assembly of all 1.5 million known species of animals, plants, protozoa and fungi on Earth — and SMRT Sequencing will play a major part. The global Earth BioGenome Project and its UK arm, the Darwin Tree of Life Project, were launched in London today in a gathering of the key scientific partners and funders from around the globe. A greater understanding of Earth’s biodiversity and the responsible stewarding of its resources are among the most crucial scientific and social challenges of the new millennium, and overcoming these challenges…
Genome-wide association studies (GWAS) may be powerful tools for the identification of genes underlying complex traits, but what if you have an incredibly complex, uncharacterized genome, with no sequenced progenitor or related species? A team of scientists from the Chinese Academy of Agricultural Sciences in Changsha, China came up with a solution: a transcriptome-referenced association study (TRAS), powered by our Iso-Seq method. The approach, outlined in this DNA Research paper, utilized a transcriptome generated by SMRT Sequencing as a reference to score population variation at both transcript sequence and expression levels. The team, led by Touming Liu and first author Xiaojun…