<em>Haematococcus pluvialis genome annotation and protein sequences.</em>

The green microalga<em> Haematococcus pluvialis</em> can synthesize high amounts of astaxanthin, which is a valuable antioxidant that has been utilized in human health, cosmetics, and aquaculture. To illustrate detailed molecular clues to astaxanthin yield, we performed PacBio HIFI along with Hi-C sequencing to construct an improved chromosome-level haplotypic genome assembly with 32 chromosomes and a genome size of 316.0 Mb. Its scaffold N50 (942.6 kb) and contig N50 (304.8 kb) have been upgraded remarkably from our previous genome draft, and a total of 30,575 protein-coding genes were predicted. We also established a high-evidence phylogenetic tree from seven representative algae species, with the main aim to calculate their divergence times and identify expanded/contracted gene families. We also characterized genome-wide localizations on chromosomes of some important genes such as five <em>BKTs </em>(encoding beta-carotene ketolases) that are putatively involved in astaxanthin production. In summary, we reported the first chromosome-scale map of <em>H. pluvialis</em>, which provides a valuable genetic resource for in-depth biomedical investigations on this momentous green alga and commercial astaxanthin bioproduction.绿色微藻雨生红球藻（Haematococcus pluvialis）可合成大量虾青素——一种极具应用价值的抗氧化剂，已被广泛应用于人类健康、化妆品及水产养殖领域。为阐明虾青素产量调控的分子机制，本研究采用PacBio HIFI与Hi-C测序技术，构建了包含32条染色体、基因组大小为316.0 Mb的升级版染色体水平单倍型基因组组装结果。该组装的支架N50（scaffold N50，942.6 kb）与重叠群N50（contig N50，304.8 kb）相较本团队此前的基因组草图均得到显著优化，同时共预测得到30575个蛋白质编码基因。本研究还基于7种代表性藻类构建了高可信度系统发育树，核心目标为计算其物种分化时间并鉴定扩张/收缩的基因家族。此外，本研究对部分潜在参与虾青素合成的重要基因在染色体上的全基因组定位进行了解析，例如5个编码β-胡萝卜素酮化酶（beta-carotene ketolase）的BKT基因（BKTs）。综上，本研究首次发布了雨生红球藻（H. pluvialis）的染色体尺度基因组图谱，可为针对这一重要绿藻的深入生物医学研究以及商业化虾青素生物生产提供宝贵的遗传资源。