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

Kelly DeWeese¹Gary Molano¹Sara Calhoun²Anna Lipzen²Jerry Jenkins³Melissa Williams³Christopher Plott³Jayson Talag⁴Jane Grimwood³Jean-Luc Jannink^5,6Igor V. Grigoriev^2,7Jeremy Schmutz³Charles Yarish^8,9Sergey Nuzhdin¹⁰Scott Lindell^8*

• ¹University of Southern California, Los Angeles, United States
• ²Joint Genome Institute, Berkeley Lab (DOE), Berkeley, California, United States
• ³HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States
• ⁴Arizona Genomics Institute, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona, United States
• ⁵Robert W. Holley Center for Agriculture and Health, Agricultural Research Service (USDA), Ithaca, New York, United States
• ⁶Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, New York, United States
• ⁷Department of Plant & Microbial Biology, College of Natural Resources, University of California, Berkeley, Berkeley, California, United States
• ⁸Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States
• ⁹Department of Ecology and Evolutionary Biology, College of Liberal Arts and Sciences, University of Connecticut, Storrs, Connecticut, United States
• ¹⁰Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States

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 have so far limited molecular breeding adoption in 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.