Hemerocallis citrina Borani (huang hua cai in Chinese) is an important horticultural crop whose flower buds are widely consumed as a delicious vegetable in Asia. Here we assembled a high-quality reference genome of H. citrina using single-molecule sequencing and Hi-C technologies. The genome assembly was 3.77 Gb and consisted of 3183 contigs with a contig N50 of 2.09 Mb, which were further clustered into 11 pseudochromosomes. A larger portion (3.25 Gb or 86.20%) was annotated as a repetitive content and 54,295 protein-coding genes were annotated in the genome. Genome evolution analysis showed that H. citrina experienced a recent whole-genome duplication (WGD) event at ~15.73 million years ago (Mya), which was the main factor leading to many multiple copies of orthologous genes. We used this reference genome to predict 20 genes involved in the rutin biosynthesis pathway. Moreover, our metabolomics data revealed neither colchicine nor its precursors in H. citrina, challenging the long-standing belief that this alkaloid causes poisoning by the plant. The results of our disruptive research are further substantiated by our genomic finding that H. citrina does not contain any genes involved in colchicine biosynthesis. The high-quality genome lays a solid foundation for genetic research and molecular breeding of H. citrina.

中文翻译：

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染色体水平的黄花菜基因组为芦丁生物合成和秋水仙碱的缺乏提供了新的见解

黄花苜蓿黄花菜是一种重要的园艺作物，其花蕾在亚洲作为美味蔬菜被广泛食用。在这里，我们组装了高质量的参考基因组黄蜂使用单分子测序和 Hi-C 技术。基因组组装为 3.77 Gb，由 3183 个重叠群组成，重叠群 N50 为 2.09 Mb，进一步聚集成 11 个假染色体。较大部分（3.25 Gb 或 86.20%）被注释为重复内容，并且基因组中注释了 54,295 个蛋白质编码基因。基因组进化分析表明黄蜂最近在大约1573万年前（Mya）经历了一次全基因组复制（WGD）事件，这是导致许多直系同源基因的多个拷贝的主要因素。我们使用这个参考基因组来预测参与芦丁生物合成途径的 20 个基因。此外，我们的代谢组学数据并未显示秋水仙碱或其前体黄蜂，挑战了长期以来这种生物碱会导致植物中毒的观点。我们的基因组发现进一步证实了我们颠覆性研究的结果：黄蜂不包含任何参与秋水仙碱生物合成的基因。高质量的基因组为遗传研究和分子育种奠定了坚实的基础黄蜂。