Chimonanthus salicifolius isolate:LYLM-1 Genome sequencing and assembly. Chimonanthus salicifolius isolate:LYLM-1

Chimonanthus salicifolius, a member of the family Calycanthaceae of magnoliids, is one of the most famous traditional medicinal plants in Eastern China. Here, we report a chromosome-level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with contig N50 value up to 2.2 Mb and containing 36,651 annotated protein-coding genes. Comparative and evolutionary analyses revealed that C. salicifolius was sister to the eudicots and that two whole-genome duplication events occurred approximately 88 and 69 million years ago. Notably, long genes that the gene length >20 kb were abundant in the C. salicifolius genome. These long genes are involved in many important plant growth and development processes and are widely present among magnoliids and basal angiosperms, indicating that they might represent a characteristic of primitive angiosperm genomes. We also investigate the gene expression profiles of flowering and flavonoid synthesis genes, including chalcone synthase (CHS) and flavonol synthase (FLS), which might play important roles in the flavonoid metabolic pathway. The data obtained in this study not only provide a representative genome sequence from the magnoliids but also open the door to functional genomic research and molecular breeding of C. salicifolius.

柳叶蜡梅（Chimonanthus salicifolius）隶属于木兰类（magnoliids）蜡梅科（Calycanthaceae），是中国东部极具知名度的传统药用植物之一。本研究报道了柳叶蜡梅的染色体级基因组组装（chromosome-level genome assembly），其基因组序列总长度达820.1 Mb，重叠群N50（contig N50）高达2.2 Mb，共注释得到36651个蛋白质编码基因。比较进化分析结果显示，柳叶蜡梅与真双子叶植物（eudicots）互为姊妹类群，且其祖先曾发生两次全基因组复制事件，分别发生于约8800万年前和6900万年前。值得关注的是，柳叶蜡梅基因组中富集了大量长度超过20 kb的长基因，这类长基因参与诸多关键的植物生长发育过程，且广泛存在于木兰类和基部被子植物（basal angiosperms）中，提示这类长基因或为原始被子植物基因组的特征之一。本研究同时分析了开花相关基因与黄酮类合成相关基因的表达谱，包括查尔酮合酶（chalcone synthase, CHS）和黄酮醇合酶（flavonol synthase, FLS），上述基因可能在黄酮类代谢通路（flavonoid metabolic pathway）中发挥重要调控作用。本研究获得的基因组数据不仅为木兰类植物提供了具有代表性的基因组序列资源，也为柳叶蜡梅的功能基因组研究（functional genomic research）与分子育种（molecular breeding）奠定了重要基础。