Many marine green algae thrive in intertidal zones, adapting to complex light environments that fluctuate between low underwater light and intense sunlight. Exploring their genomic bases could help to comprehend the diversity of adaptation strategies in response to environmental pressures.

Here, we developed a novel and practical strategy to assemble high-confidence algal genomes and sequenced a high-quality genome of Bryopsis corticulans, an intertidal zone macroalga in the Bryopsidales order of Chlorophyta that originated 678 million years ago.

Comparative genomic analyses revealed a previously overlooked whole genome duplication event in a closely related species, Caulerpa lentillifera. A total of 100 genes were acquired through horizontal gene transfer, including a homolog of the cryptochrome photoreceptor CRY gene. We also found that all four species studied in Bryopsidales lack key photoprotective genes (LHCSR, PsbS, CYP97A3, and VDE) involved in the xanthophyll cycle and energy-dependent quenching processes. We elucidated that the expansion of light-harvesting antenna genes and the biosynthesis pathways for siphonein and siphonaxanthin in B. corticulans likely contribute to its adaptation to intertidal light conditions.

Our study unraveled the underlying special genetic basis of Bryopsis' adaptation to intertidal environments, advancing our understanding of plant adaptive evolution.