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.球等鞭金藻（Isochrysis galbana）是生产生理活性物质的理想药用研究模型，已被大规模工业化应用于岩藻黄素（fucoxanthin）与二十二碳六烯酸（DHA）的生产。本研究报道了该菌株LG007的高质量基因组序列，其基因组大小为92.73 Mb，contig N50为6.99 Mb，共编码14900个蛋白质编码基因。系统基因组学分析显示，艾氏球石藻（E. huxleyi）、球等鞭金藻与托氏金藻（C. tobinii）共享一个定鞭藻门（Haptophyta）共同祖先。进化分析表明，球等鞭金藻与其近缘物种艾氏球石藻的分化时间约为1.33亿年前，且球等鞭金藻经历了一轮全基因组复制事件。基因家族分析显示，脂代谢相关基因发生了显著扩张，尤其是三酰甘油（triacylglycerol）与不饱和脂肪酸相关基因。本研究对一个编码双甲藻黄素-岩藻黄素羟化酶（DFH）的新型岩藻黄素生物合成基因进行了结构域鉴定。转录组学与加权基因共表达网络分析（WGCNA）显示，与岩藻黄素合成显著相关的差异表达基因及转录因子包括IgMYB98、ZDS、PDS与LHCX2。本研究结果有助于解析脂代谢与岩藻黄素的生物合成及其调控机制，为利用球等鞭金藻开发岩藻黄素相关医药与健康产品提供了重要参考依据。