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Arizona Scientists Deploy BAC Expertise and SMRT Sequencing for Crop Genomes

Tuesday, May 17, 2016

At the University of Arizona, a leading genomics research facility benefits from decades of BAC-based sequencing expertise, original studies of crop genomes, and a unique emphasis on high molecular weight DNA. Rod Wing, founding director of the Arizona Genomics Institute (AGI) and a professor in the School of Plant Sciences, Ecology & Evolutionary Biology at the university, was a pioneer in building BAC-based reference genomes in the ’90s. Today, that carefully honed expertise in isolating large DNA fragments gives him and his lab a real advantage for making the most of long-read sequencing.

Wing’s efforts primarily focus on plant genomes, but his service facility performs genomic studies on a wide variety of organisms for investigators at the university and around the world. He says the PacBio platform is useful for customers interested in sequencing any kind of crop, as well as animals and other organisms. “If your genome is littered with repetitive elements that are highly similar, PacBio allows you to get through those elements and back into some more unique sequence for a better assembly,” he notes. “Our facility can work on pretty much any organism — we just have to have some good DNA.”

To meet his own research goal of building high-quality reference genomes for every species of rice, 23 in total, Wing chose SMRT Sequencing. “PacBio is revolutionizing our approach for whole genome shotgun, BAC, and targeted sequencing,” he says. The rice genome assemblies his team is building will be essential to improving rice crops for higher yield, expanded growing areas, and stress resistance.

In recent work to sequence the African rice genome, a few highly repetitive and rearranged BACs were particularly challenging to get through with other platforms. “It was taking us months to try to get through this one region,” Wing recalls. Using SMRT Sequencing, he produced the full sequence of this region “in a nice single piece within a couple of days.” For particularly difficult regions like that one, PacBio sequencing is a very powerful targeted approach, he adds. With a few other rice genomes, his team is pooling BACs, 32 at a time, in individual SMRT Cells. “Around 85 to 90 percent of those BACs are completely circularized,” he says. “It’s pretty easy to go through a genome using this approach.”

Beyond the highly accurate, long-read sequence data he obtains from SMRT Sequencing, Wing also likes the PacBio platform for full-length isoform sequencing and its ability to characterize the methylome. He notes that now they can take rice tissues at several developmental stages and under many different environmental conditions, isolate RNA, and do Iso-Seq analysis on those samples to enable whole plant transcriptome analysis. This could help the community map gene networks and pinpoint the biological mechanisms behind traits such as bigger leaves, water uptake, and more.

To learn more about Wing’s rice genome projects and his service facility, check out this case study.

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