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.