AUTHOR=Chen Bao-Zheng , Yang Zi-Jiang , Yang Ling , Zhu Yi-Fan , Li Xu-Zhen , Wang Lei , Zhou Ye-Peng , Zhang Guang-Hui , Li Da-Wei , Dong Yang , Duan Sheng-Chang 

TITLE=Chromosome-scale genome assembly of Codonopsis pilosula and comparative genomic analyses shed light on its genome evolution

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 15 - 2024

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1469375

DOI=10.3389/fpls.2024.1469375

ISSN=1664-462X

ABSTRACT=Codonopsis pilosula, renowned for its edibility and medicinal properties, is a significant plant in traditional Chinese medicine. However, the lack of available genomic resources has hindered further research. This study presents the first chromosome-scale genome assembly of C. pilosula using PacBio CLR reads and Hi-C scaffolding technology. The assembly resulted in a high-quality genome of 679.20 Mb. The genome was anchored to 8 pseudo-chromosomes, with an anchoring rate of 96.5% and a scaffold N50 of 80.50 Mb. The completeness of assembly was determined to be 97.6% by using Benchmarking with Universal Single-Copy Orthologs (BUSCO). Notably, repetitive elements constituted ~76.8% of the genome, with long terminal repeat retrotransposons (LTR-RTs) dominating this group of elements (~39.17% of the genome). Using Ks analysis and syntenic depth analysis, the polyploidization history of three platycodonoid clade species was found to involve only the γ-WGT event. The ancestral karyotype of three platycodonoid clade species was identified as having 9 protochromosomes through karyotype evolutionary analysis. Moreover, non-WGD genes contributing to gene family expansion have been shown to have a positive impact, especially those arising from tandem duplications. These insights are crucial for understanding the genetic diversity and evolutionary biology of C. pilosula, contributing to its conservation and sustainable use.