C.nipponicum.gff3

Cirsium nipponicum, a pharmaceutically valuable plant from the Asteraceae family, has been utilized
for over 2,000 years. Unlike other thistles, it is native to East Asia and found exclusively on Ulleung
Island in the Korea Peninsula. Despite its significance, the genome information of C. nipponicum has
remained unclear. In this study, we assembled the genome of C. nipponicum using both short reads
from Illumina sequencing and long reads from Nanopore sequencing. The assembled genome is
929.4 Mb in size with an N50 length of 0.7 Mb, covering 95.1 % of BUSCO core groups listed in
edicots_odb10. Repeat sequences accounted for 70.94 % of the assembled genome. We curated
31,263 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. nipponicum
diverged from C. cardunculus approximately 15.9 million years ago. Gene family evolutionary
analysis revealed significant expansion and contraction in genes involved in abscisic acid
biosynthesis, late endosome to vacuole transport, response to nitrate, and abaxial cell fate
specification. This study provides a reference genome of C. nipponicum, enhancing our
understanding of its genetic background and facilitating in exploration of genetic resources for
beneficial phytochemicals.