The Genomics Laboratory of the David H. Murdock Research Institute (DHMRI) has expanded its capabilities to include the Pacific BioSciences’ Sequel System, which is the most recent generation of the company’s SMRT technology.
PacBio is recognized for its long read lengths, consensus accuracy, low degree of bias and epigenetic characterization capabilities. DHMRI Genomics Laboratory Leader Jorge Marques Signes, PhD, views the long read length as the most critical benefit to DHMRI’s collaborators.
“The long read length generated by PacBio technology allows us to contribute more substantially to the many plant genome projects we support,” he said. “We already have multiple libraries prepared for different plant species.”
DHMRI Bioinformatics Project Leader Garron Wright points to isoform sequencing (Iso-Seq) as an equally important benefit of PacBio’s system. “This is a powerful technique for identifying gene variations,” he said. “Shorter read technology results in the generation of smaller bits of the puzzle. It is not as efficient and results in too many errors in computation. With Iso-Seq, we have generated unique full length cDNA sequences and easily study alternatively spliced exons and transcriptional sites.”
DHMRI collaborates with academic and industry scientists across the US and internationally. Massimo Iorizzo, PhD, is one of those collaborators. He is an assistant professor of Fruit and Vegetable Genetics and Nutritional Genomics with the NC State Plants for Human Health Institute (PHHI), which is next door to the DHMRI on the NC Research Campus. He is an expert in plant genomics and is involved in multiple plant genome projects, including studies of carrot, blueberry, cucumber, spinach, pineapple and banana.
He worked with DHMRI using carrot and blueberry samples to successfully validate their PacBio system. “Having access to the PacBio platform right here on the North Carolina Research campus is extremely beneficial to our community,” Iorizzo continued, “because it expands the capabilities of DHMRI’s genomics laboratory and helps scientists who are working on plant, human or any type of genomic project to obtain higher quality genome assemblies and gene prediction that facilitate the identification of genes controlling important traits, such as diseases in human or nutrient accumulation in plants.
Jessica Schlueter, PhD, an associate professor of bioinformatics with the UNC Charlotte College of Computing and Informatics, studies genome duplication in plants such as soybean and oat. “Sequencing using the PacBio system has enabled us to look at more complex genomes in a way that we could not before,” she said, “but has required us to often send our DNA to labs across the country. With the PacBio system now running at the DHMRI, there is a sense of security in knowing that our samples are close and will be handled well.”
The addition of the PacBio Sequel technology compliments DHMRI’s full suite of genomic capabilities that includes Illumina, NanoString and 10X Genomics Chromium platforms.
“All of these platforms give us the opportunity to work more closely with our campus partners and scientists in organizations across the nation to implement new protocols and applications for these platforms in the plant, health and nutrition fields,” emphasized Simon Gregory, PhD, DHMRI Genomics Laboratory Director.
Additionally, DHMRI offers expertise integrating analytical technologies including metabolomics, proteomics, NMR, clinical chemistry and bioinformatics. The institute also supports research and development with a microscopy suite and an onsite Center for Laboratory Animal Sciences.