Pulsatilla chinensis genome

Pulsatilla chinensis (Bunge) Regel, a medicinal species in the genus Pulsatilla (Ranunculaceae), exhibits significant anti-inflammatory activity due to its abundant triterpenoid saponins, enhancing its medicinal value. All 43 known Pulsatilla species lack whole genome sequencing data, hindering research on their evolution and Ranunculaceae phylogeny. Here, we present the first chromosome-level genome assembly of P. chinensis. The assembly spans 6,588.76 Mb with a contig N50 of 4.28 Mb. Using PacBio sequencing and Hi-C scaffolding, 99.32% of sequences were anchored onto eight chromosomes. We annotated 41,786 protein-coding genes through ab initio prediction, homology alignment, and transcriptome evidence, with 98.77% functionally annotated via NR, GO, and KEGG databases. Evolutionary analysis revealed that Pulsatilla shared a whole-genome duplication (WGD) event with Ranunculus, diverging 27–55 million years ago. Ancestral chromosomal reconstruction indicated seven chromosomes in Ranunculales ancestors. This assembly enables molecular studies on bioactive compounds and clarifies Pulsatilla's evolution within Ranunculaceae.

白头翁（*Pulsatilla chinensis* (Bunge) Regel）是毛茛科（Ranunculaceae）白头翁属（*Pulsatilla*）的药用物种，因其富含三萜皂苷（triterpenoid saponins）而具有显著抗炎活性，进一步提升了其药用价值。目前已报道的43种白头翁属植物均缺乏全基因组测序（whole genome sequencing）数据，这阻碍了其演化及毛茛科系统发育相关研究的开展。本研究首次报道了白头翁的染色体级基因组组装（chromosome-level genome assembly）结果：该组装序列总长6588.76 Mb，contig N50为4.28 Mb。结合PacBio测序（PacBio sequencing）与Hi-C挂载（Hi-C scaffolding）技术，99.32%的序列被锚定至8条染色体上。通过从头预测（ab initio prediction）、同源比对（homology alignment）及转录组证据（transcriptome evidence），本研究共注释得到41786个蛋白质编码基因（protein-coding genes），其中98.77%的基因可通过NR、GO及KEGG数据库完成功能注释。演化分析显示，白头翁与毛茛属（*Ranunculus*）共享一次全基因组复制（WGD，whole-genome duplication）事件，二者的分化时间为2700万至5500万年前。祖先染色体重建（ancestral chromosomal reconstruction）结果表明，毛茛目（Ranunculales）的祖先染色体数目为7条。该基因组组装可为白头翁活性成分的分子研究提供支撑，同时有助于阐明白头翁在毛茛科中的演化地位。