Salvia miltiorrhiza Bunge, also known as red sage or Danshen, is an important traditional Chinese medicine (TCM) that has been used for thousands of years to treat cardiovascular and other diseases. It is also considered an important model TCM plant. Here, a high‐quality reference genome of S. miltiorrhiza was generated by combining PacBio long‐read sequencing and chromatin interaction mapping (Hi‐C) technologies, resulting in the chromosome‐scale assembly of a 594.75‐Mb genome sequence with a contig N50 of 2.70 Mb. This assembly shows the highest level of continuity for a Danshen genome generated thus far. The S. miltiorrhiza genome contained 32,483 protein‐coding genes, with a repetitive DNA content of approximately 64.84%. The high percentage of young LTRs suggests that multiple TE transposition bursts occurred recently in S. miltiorrhiza. Genes unique to secondary metabolism pathways were expanded in the S. miltiorrhiza genome. A new CYP450 gene cluster was identified in the phloem of red roots where active components were synthesized. This reference genome sequence will facilitate future studies aimed at the elucidation of the secondary metabolism synthesis pathway and the genetic improvement of S. miltiorrhiza.

中文翻译：

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丹参的高质量参考基因组序列可深入了解其红色根茎中丹参酮的合成

丹参（Salvia miltiorrhiza Bunge），又称丹参或丹参，是一种重要的传统中药（TCM），已被使用了数千年，用于治疗心血管疾病和其他疾病。它也被认为是重要的中药示范工厂。在这里，通过结合PacBio长读测序和染色质相互作用图谱（Hi-C）技术生成了优质的链球菌参考基因组，从而使594.75-Mb基因组序列与重叠群N50形成了染色体规模的组装。 2.70 Mb。该程序集显示了迄今为止生成的丹参基因组的最高连续性水平。该丹参基因组包含32483个蛋白质编码基因，重复DNA含量约为64.84％。年轻的LTR的高比例表明，多个TE换位爆发在最近发生丹参。次生代谢途径独特的基因在S. miltiorrhiza基因组中得到扩展。在合成了活性成分的红根韧皮部中发现了新的CYP450基因簇。该参考基因组序列将有助于今后的研究，目的是阐明次级代谢合成途径和乳链球菌的遗传改良。