Bioinformatics for Seaweed Genomics
The Bioinformatics CRO made the 2024 Inc 5000 list! Find our announcement here on LinkedIn.
To start our series exploring some of the exciting work The Bioinformatics CRO has contributed to over the years, we’d like to highlight a collaboration with Forjazul. Forjazul is dedicated to identifying and characterizing genetic diversity in seaweed in order to unlock its unique agricultural potential.
Scott Fahrenkrug at Forjazul is committed to the vision of seaweed as an efficient, sustainable, climate-change resilient agricultural crop in the ocean. Ingredients from seaweed are already being sold as food and cosmetic ingredients and as crop biostimulants. At scale, seaweed is a compelling replacement for petroleum in plastics, textiles, and maybe even jet fuel. Understanding the genetic potential and diversity of seaweed is a research aim in itself with important implications for protecting seaweed species and production in the face of changing ocean conditions. Like every other modern crop, a genetic improvement program requires a molecular genetics infrastructure, which for seaweeds Fahrenkrug found in short supply.
Fahrenkrug moved to start solving this problem in collaboration with Micheal Roleda at the Marine Science Institute in the University of the Philippines. Although a seaweed newbie, with more than 30 years of experience in animal genetics he knew what needed to be done, but as a new start-up he wanted to keep costs to a minimum. That’s where The Bioinformatics CRO came in, with our computational biologists providing qualified scientific and technical expertise to develop the type of biologist driven genome analysis that Fahrenkrug and Forjazul were looking for.
The Forjazul platform enables a Kappaphycus alvarezii genome JBrowse, with an extensive, quantitative Genome/Transcriptome Annotation Explorer, and ShinyKaGE, an integrated suite of Shiny tools for the analysis and interpretation of seaweed gene expression in production and response to stress.
The demands of the project extended from the development and integration of several novel transcriptome assemblies of Kappaphycus alvarezii to annotation by a litany of homology and orthology based comparative analyses. More than 20 other seaweed species were analyzed using the same system, facilitating orthology analysis by Orthofinder, eggNOG and MCL. Furthermore, to greatly enhance the analysis of results, we implemented a series of Cytoscape cluster and pathway viewers and a novel tokenization-based annotation scoring system that leverages the Annotation Explorer to identify and rank functional candidates using even complex Boolean arguments.
“We are all so proud of KaGE, a comprehensive vision realized,” says Fahrenkrug.
Fahrenkrug emphasizes the benefits of partnering with The Bioinformatics CRO on this project: as a start-up, Forjazul would have had to expand and take on multiple long-term employees to develop these tools alone. The CRO provided deep technical expertise to create efficient tools which can now be used for future analysis.
The data infrastructure developed during this project is central to expanding seaweed genetic development programs in Brazil, Malaysia, Indonesia and the Philippines. The Forjazul system also sits at the heart of an Illumina-supported seaweed genome and transcriptome sequencing project focused on Eucheumatoid seaweed species. You can learn more about that project from Illumina here.
Thanks to our work with Scott Fahrenkrug, Forjazul has identified novel genetic targets for enhancing Kappaphycus alvarezii production in Brazil and likely the world. “With the blueprints in our hands”, Fahrenkrug says, “we can play an important part in building the sustainability and productivity of the seaweed industry, multiplying biomass production, creating jobs, capturing and enhancing the value of carbon, and developing novel products that use seaweed as a sustainable chassis.”