This story was originally posted on Jan. 13
Floragenex, a 4-year-old spinout of the University of Oregon focused on serving the plant research community, last week opened a subsidiary to expand its offering to animal researchers.
The unit, called Biota Sciences, will use its restriction-site-associated DNA technology platform to provide SNP-discovery and assay-development services. The Eugene-based subsidiary also offers custom genome-research capabilities, including the ability to run genome-wide association studies, on organisms of choice.
"Floragenex was founded to focus on plants," said CEO Nathan Lillegard. "We saw an opportunity to offer SNP discovery in plants for commercial plant breeders. As we got into this we saw a lot of interest in other animal organisms.
"To stay focused on the world of plant science we are keeping Floragenix, and to recognize there are other markets worth pursuing we are launching Biota Sciences," Lillegard added. "It's the same technology, same business model, just a different customer focus."
Lillegard spoke to BioArray News during the Plant and Animal Genome Conference, held in San Diego last week.
Floragenex and Biota Sciences' restriction-site-associated DNA technology, called RAD, relies on restriction-enzyme digestion to create a DNA fragment that is sheared using a nebulizer or sonicator. From that fragment, the company makes libraries and sequences them for its customers, enabling it to provide a variety of services.
While Floragenex and Biota do not sell arrays, their SNP-discovery and assay-development projects could benefit ag-bio researchers who use focused genotyping arrays, such as those sold by Illumina, according to Lillegard.
"Say your core lab has an Illumina Golden Gate genotyping system and you want to use it. Well, if you are working with a non-model organism, you can't," Lillegard said. "We provide people with data that they can import into an Illumina or Sequenom or ABI system; whatever platform people use, we can provide them with the sequence data to use that system."
Jason Boone, the firm's research director, told BioArray News that Biota's ability to create libraries for any organism, even those lacking a reference genome, is one of its main advantages in the agbio market.
"Imagine you want to work with lions or some kind of strange sea critter. It doesn't matter, it doesn't have to have a genome," Boone said. "Using the RAD libraries, if anybody wants to do SNP genotyping or fill the genetic map in for some sort of odd shrimp or bivalve, you don't have to have any current genome sequence."
"That's where I see the market opportunity for Biota," said Lillegard. "There are people doing abalone and borneo elephants and shrimp, all kinds of different organisms that don't have a reference genome, and probably won't have a reference genome for a long time, but people still want to use genotyping and sequencing technology and that is who we are trying to service," he said.
Among to the various services Biota will provide is the ability to conduct genome-wide association studies. However, unlike traditional GWAS performed on high-density genotyping arrays sold by Affymetrix or Illumina, Biota uses RAD and second-generation sequencers in its studies.
"Floragenex actually started as an array-based company," said Lillegard. "The idea was to use arrays to look at specific areas of the genome. The founders of the company had the vision to see that next-gen sequencing was ultimately going to supplant microarrays as the dominant diagnostic technology. We have now manipulated our system to work with NGS."
Rick Nipper, vice president of research for Biota, told BioArray News that Floragenex and Biota use barcoding to run multiple samples per sequencing run, which also enables them to offer association studies.
"You could do a GWAS by just doing shotgun sequencing and basically resequence every nucleotide in the genome, but that is very computationally expensive, expensive in terms of reagents, expensive in terms of time," Nipper said. "With RAD, you can selectively genotype 100,000 loci over the genome."
"The beauty of [Floragenex and Biota's approach] is because you are only sequencing a fraction of the genome, we can load more samples on per lane, so we can do several dozen samples per run of an Illumina system," said Lillegard. "We have a very high efficiency; we take low cost per data point and turn that into a low project cost for academic, government, and commercial researchers."
Floragenex's current customer base is about 65 percent academic and 35 percent commercial, according to the firm. The company's website lists a number of customers and partners, including the University of Oregon, Oregon State University, the US Department of Agriculture, the University of Georgia, and Kansas State University. It does not specifically name any specific commercial users, but describes them as "small regional seed companies, biofuels startups, and global agribusiness firms."
Lillegard said that, in terms of using newer technologies, academics are "ahead of industry, especially in agriculture." He said that there is a number of "big ag companies that are really dialed in with a lot of molecular technologies and there are a whole bunch of laggards that are just getting into SNP genotyping now." Despite this lag, he said is confident that "sequence-based diagnostics, either by genotyping or sequencing, will be increasingly adopted."