The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

Alves-Lima, C.; Montecinos, G.; Escalona, M.; Calhoun, S.; Marimuthu, M.; Nguyen, O.; Berault, E.; Lipzen, A.; Grigoriev, I. V.; Raimondi, P.; Nuzhdin, S. V.; Alberto, F.

doi:10.1101/2025.07.16.665147

bioRxiv · 10.1101/2025.07.16.665147

The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

Alves-Lima, C.·Montecinos, G.·Escalona, M.·Calhoun, S.·Marimuthu, M.·Nguyen, O.·Berault, E.·Lipzen, A.·Grigoriev, I. V.·Raimondi, P.·Nuzhdin, S. V.·Alberto, F.

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Abstract

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelps accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of Nereocystis luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80x of coverage and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Mb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and M. pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPases enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

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Alves-Lima, C., Montecinos, G., Escalona, M., Calhoun, S., Marimuthu, M., Nguyen, O., Berault, E., Lipzen, A., Grigoriev, I. V., Raimondi, P., Nuzhdin, S. V., Alberto, F.. 2025-07-21. The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana. https://doi.org/10.1101/2025.07.16.665147

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