C.nipponicum.gff3

Cirsium nipponicum, a pharmaceutically valuable plant from the Asteraceae family, has been utilizedfor over 2,000 years. Unlike other thistles, it is native to East Asia and found exclusively on UlleungIsland in the Korea Peninsula. Despite its significance, the genome information of C. nipponicum hasremained unclear. In this study, we assembled the genome of C. nipponicum using both short readsfrom Illumina sequencing and long reads from Nanopore sequencing. The assembled genome is929.4 Mb in size with an N50 length of 0.7 Mb, covering 95.1 % of BUSCO core groups listed inedicots_odb10. Repeat sequences accounted for 70.94 % of the assembled genome. We curated31,263 protein-coding genes, of which 28,752 were functionally annotated using public databases.Phylogenetic analysis of 11 plant species using single-copy orthologs revealed that C. nipponicumdiverged from C. cardunculus approximately 15.9 million years ago. Gene family evolutionaryanalysis revealed significant expansion and contraction in genes involved in abscisic acidbiosynthesis, late endosome to vacuole transport, response to nitrate, and abaxial cell fatespecification. This study provides a reference genome of C. nipponicum, enhancing ourunderstanding of its genetic background and facilitating in exploration of genetic resources forbeneficial phytochemicals.

烟管蓟（Cirsium nipponicum）是菊科（Asteraceae）中极具药用价值的物种，其药用历史已长达两千余年。与其他蓟类植物不同，该物种原产于东亚，且仅见于朝鲜半岛的郁陵岛（Ulleung Island）。尽管其药用价值显著，但目前关于烟管蓟的基因组信息仍不甚明晰。本研究结合Illumina测序（Illumina）产生的短读长数据与Nanopore测序（Nanopore）产生的长读长数据，完成了烟管蓟的基因组组装。组装后的基因组大小为929.4 Mb，Contig N50长度为0.7 Mb，覆盖了eudicots_odb10数据库中95.1%的BUSCO真双子叶植物核心保守基因簇。重复序列占组装后基因组总长度的70.94%。本研究共注释得到31263个蛋白质编码基因，其中28752个基因通过公共数据库完成了功能注释。基于单拷贝同源基因（single-copy orthologs）对11个植物物种开展系统发育分析，结果显示烟管蓟与C. cardunculus的分化时间约为1590万年前。基因家族进化分析显示，参与脱落酸（abscisic acid）生物合成、晚期内体向液泡转运、硝酸盐响应以及远轴细胞命运特化的基因家族发生了显著的扩张与收缩。本研究构建了烟管蓟的参考基因组，有助于深化对其遗传背景的认知，并为挖掘有益植物次生代谢产物的遗传资源提供重要支撑。