At CROPS 2017, SMRT Sequencing Powers Reference Plant Genome Assemblies
Tuesday, June 6, 2017
This week the HudsonAlpha Institute for Biotechnology and the University of Georgia are co-hosting CROPS 2017, a meeting focused on genomic technologies and their use in crop improvement and breeding programs. The three-day event attracts over 200 attendees involved in research and breeding for a range of important crop species. PacBio was proud to be a sponsor of the conference.
HudsonAlpha’s Jeremy Schmutz kicked off the meeting with an introductory talk about trends in plant genomics, expanded transcriptome resources, and the improved representation of all plant genomes with many new genome assemblies. Schmutz, who also works with the Joint Genome Institute, highlighted efforts to generate higher-quality, more complete reference genomes for economically important plants used for food, fiber, or biomass. He told attendees that SMRT Sequencing has made a significant difference in those efforts. His team has generated high-quality plant assemblies with the PacBio RS II Sequencing System and more recently with the Sequel System for several cotton genomes as well as Brachypodium, peanut, sorghum, and more.
According to Schmutz, the big difference with SMRT Sequencing is that the assemblies it produces are of high enough quality to be useful for functional studies such as genotype-phenotype associations, which are essential for breeding and selection programs. “We can now generate high-quality reference genomes for most plants,” he said. “PacBio has made that possible.” Schmutz noted that SMRT Sequencing has been successful even for very challenging plant genomes with highly repetitive elements, GC-rich regions, areas of high and low complexity, and of course varying degrees of ploidy.
Schmutz, his colleague Jane Grimwood and their team at the Genome Sequencing Center have made the transition to the higher-capacity Sequel System, which enables comparable results with lower project costs. Schmutz said they are generating, on average, 4 Gb to 8 Gb per SMRT Cell. For a project sequencing the 2.6 Gb Brazilian cotton genome, he said, the preliminary assembly is at least as good as a previous cotton assembly generated on the PacBio RS II — but data collection took just five weeks, compared with almost five months for the older assembly. Even in this preliminary stage, the Sequel System cotton assembly has an impressive contig N50 of 2.2 Mb.
Schmutz noted that the point of the CROPS meeting wasn’t to present new assemblies for their own sake; it’s all about how these resources are being used by the plant community. By including scientists studying many different crop species, he hopes to accelerate the uptake of new genome-based approaches to as many research groups as possible. The meeting covered topics such as breeding and selection strategies, functional work to identify the mechanisms underlying important traits, and automated phenotyping. “We really focus on the translation of genomics directly into crop improvement platforms,” Schmutz said.