A high-quality reference genome assembly provides insight into fucoxanthin biosynthesis in Isochrysis galbana

Isochrysis galbana is considered as an ideal medicinal model for producing physiologically active substances, and used for fucoxanthin and DHA production in large-scale industrial application. Here, we report a high-quality genome sequence of I. galbana LG007, which has a 92.73 Mb genome size, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenomic inferences showed that E. huxleyi, I. galbana and C. tobinii shared a common Haptophyta ancestor. Evolutionary analysis revealed an estimated divergence time of I. galbana from its close relative E. huxleyi of ~133 million years ago, and I. galbana underwent one round of whole-genome duplication. Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, especially triacylglycerol and unsaturated fatty acids. Domain identification of one novel fucoxanthin biosynthesis gene that encodes diadinoxanthin-fucoxanthin hydroxylase (DFH) was analyzed. Transcriptome and WGCNA analysis revealed that differentially expressed genes or transcription factors significantly correlated with fucoxanthin synthesis, including IgMYB98, ZDS, PDS and LHCX2. These findings will help to understand lipid and fucoxanthin biosynthesis and its regulation, providing an valuable reference for promoting the development of medicine and health products for fucoxanthin with I. galbana.