Abstract
INTRODUCTION: Tetraselmis helgolandica is a marine microalga belonging to the Chlorophyta phylum. It is widely distributed in the coastal waters of Asia and is commonly used as aquatic feed. T. helgolandica is characterized by its large size, preference for starch accumulation, low temperature tolerance, presence of flagella, and strong motility. However, research on T. helgolandica is limited, and its genome data remains unavailable. OBJECTIVE: We generated a high-quality, chromosome-scale genome of T. helgolandica. Through comparative genomics, we uncovered the genome characteristics and evolutionary history of T. helgolandica. Additionally, by integrating transcriptome data, we elucidated how the light-dark rhythm enhances the high starch production. METHODS: We utilized long-read sequencing data and high-throughput chromosome conformation capture data from the Oxford Nanopore platform to construct a high-quality genome of T. helgolandica. Genome annotation was performed using multiple databases, and comparative genomic analysis was conducted with nine species, including Arabidopsis thaliana, to reveal the evolutionary history. Finally, we combined transcriptome data to elucidate the molecular mechanisms underlying the high starch yield. RESULTS: Circadian rhythm significantly promote starch accumulation and increase amylose content. The chromosome-scale genome revealed it shares a common ancestor with other green algae approximately 1,017 million years ago. This relatively ancient divergence underscores its evolutionary distinction within the green lineage. It may possess a more complex protein modification mechanism and a more fully developed Golgi apparatus. Circadian rhythm broadly up-regulates key enzymes involved in starch synthesis, including GBSS and Starch Synthase, while down-regulating SS IIIa. This regulation enhances starch accumulation and increases the amylose content. CONCLUSION: This study provided a high-quality genome of T. helgolandica and revealed the potential mechanism by which the circadian rhythm promotes starch accumulation and increases the amylose ratio. The genome of T. helgolandica will serve as an important resource for evolutionary research and transgenic platform development.