Scaffolded and annotated nuclear and organelle genomes of the North American brown alga Saccharina latissima

Authors: DEWEESE, KELLY - University Of Southern California; MOLANO, GARY - University Of Southern California; CALHOURN, SARA - Lawrence Berkeley National Laboratory; LIPZEN, ANNA - Lawrence Berkeley National Laboratory; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; WILLIAMS, MELISSA - Hudsonalpha Institute For Biotechnology; PLOTT, CHRISTOPHER - Hudsonalpha Institute For Biotechnology; TALAG, JAYSON - Arizona Genomics Institute; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; Jannink, Jean Luc; GRIGORIEV, IGOR - Lawrence Berkeley National Laboratory; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; YARISH, CHARLES - University Of Connecticut; NUZHDIN, SERGEY - University Of Southern California; LINDELL, SCOTT - Woods Hole Oceanographic Institute (WHOI)

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2025
Publication Date: 5/14/2025
Citation: Deweese, K., Molano, G., Calhourn, S., Lipzen, A., Jenkins, J., Williams, M., Plott, C., Talag, J., Grimwood, J., Jannink, J., Grigoriev, I.V., Schmutz, J., Yarish, C., Nuzhdin, S., Lindell, S. 2025. Scaffolded and annotated nuclear and organelle genomes of the North American brown alga Saccharina latissima. Frontiers in Genetics. 16:1494480. https://doi.org/10.3389/fgene.2025.1494480.
DOI: https://doi.org/10.3389/fgene.2025.1494480

Interpretive Summary: Sugar kelp (Saccharina latissima) is a type of large brown seaweed that’s important both for ocean ecosystems and as a food crop, especially in the North Atlantic and Pacific. Farmers have been growing more of it in recent years because it can be densely seeded, like its close relative grown in Asia (Saccharina japonica). However, breeding better sugar kelp plants has been limited because scientists haven’t had enough detailed genetic information. This study fills that gap by producing a high-quality reference genome — essentially a complete map of the kelp’s DNA — from a female plant collected in Connecticut. The new genome is made up of 218 large DNA segments, contains over 25,000 predicted genes, and matches well with other kelp genomes in structure and completeness. The researchers have already used an earlier version of this genome in initial breeding trials. Having this genetic resource will make it much easier for scientists to study sugar kelp biology, breed improved varieties, and support conservation efforts.

Technical Abstract: Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica. While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.