At DuPont Pioneer, DNA sequencing is paramount for R&D to reveal the genetic basis for traits of interest in commercial crops such as maize, soybean, sorghum, sunflower, alfalfa, canola, wheat, rice, and others. They cannot afford to wait the years it has historically taken for high-quality reference genomes to be produced. Nor can they rely on a single reference to represent the genetic diversity in its germplasm.
The Agilent 5200, 5300, and 5400 Fragment Analyzer instruments are fast, high-resolution benchtop capillary electrophoresis (CE) platforms that utilize proprietary markers to accurately size fragments ranging from 10 to 50 kb. This platform allows important DNA quality checkpoints to be completed in one hour for de novo large-genome sequencing projects and other PacBio applications leveraging multi-kilobase read lengths. The instrument can be used in place of time-consuming QC steps involving pulsed field gel electrophoresis (PFGE), saving time by avoiding multiple overnight gel runs when preparing large-insert SMRTbell libraries. Alternative DNA-sizing instruments cannot accurately resolve large DNA fragments in this range.
Explore how high-quality genomes contribute to critical scientific endeavors.
Single Molecule, Real-Time (SMRT) Sequencing on the Sequel II System enables easy and affordable generation of high-quality de novo assemblies. With megabase size contig N50s, accuracies >99.99%, and phased haplotypes, you can do more biology – capturing undetected SNVs, fully intact genes, and regulatory elements embedded in complex regions.
Explore how highly accurate long-read sequencing enabled sequencing the large and highly complex California redwood genome.
Interested to learn about pangenomes? Explore this guide to learn how they provide a more complete picture of the core genes of a given species and how that can provide better biological understanding.
Learn how Single Molecule, Real-Time (SMRT) Sequencing and the Sequel IIe System and will accelerate your research by delivering highly accurate long reads to provide the most comprehensive view of genomes, transcriptomes and epigenomes.
By 2050, there will be 9 billion people on the planet. What will they eat? This is the question that led Rod Wing, Director of the Arizona Genomics Institute, into the field of plant genomics. What has been accomplished so far in the mission to come up with some super green crops? And how does Rod see anti-GMO sentiment and the recent trend toward gluten free diets factoring in? After answering these questions, he dives into a discussion on which sequencing instruments he has used for plant work. Unsurprisingly, Rod prefers the PacBio long reads even though the cost is…
Brett Hannigan, Computational Biology Project Leader at DNAnexus, demonstrates a fast, accurate, and cost-efficient solution for diploid-aware de novo genome assembly utilizing FALCON on the DNAnexus platform.
Grant Cramer from the University of Nevada, Reno, and Dario Cantu from the Univeristy of Callifornia, Davis, discuss past challenges with sequencing Clone 8 of Cabernet Sauvignon (Vitis vinifera). An assembly of the genome was attempted with approximately 110x Illumina reads and 5x PacBio reads. The PacBio SMRT Sequencing read made major improvements in the assembly compared with the results of Illumina reads only. However, the assembly results were still unsatisfactory, so an additional 100-fold SMRT Sequencing coverage had been generated. An update on the current sequencing results and status of the assembly are presented.
Fritz Sedlazeck, a postdoc at Johns Hopkins University, describes his structural variant detection tool Sniffles in this poster from AGBT 2016. Included: examples of structural variants that could not be detected with other algorithms.
See what PacBio users had to say about SMRT Sequencing at the Plant and Animal Genome (PAG) Conference in San Diego. This brief video captures highlights from posters, presentations, and the exhibit hall. See how SMRT Sequencing benefits plant and animal scientists in their genomic investigations. [Engligh, some Mandarin]
At PAG 2017, Rod Wing presented five new, high-quality rice genome assemblies developed with SMRT Sequencing, including one that has eight complete chromosomes including centromeres. He also offered an early look at data generated with the Sequel System for a new assembly underway. This work is done with the goal of developing rice varieties that will be better suited to feeding a rapidly growing global population.