Skip to main content

ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Genetics, Epigenetics and Chromosome Biology
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1469375

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

Provisionally accepted
Bao-Zheng Chen Bao-Zheng Chen 1Zi-Jiang Yang Zi-Jiang Yang 2Ling Yang Ling Yang 1Yifan Zhu Yifan Zhu 1Xu-Zhen Li Xu-Zhen Li 1Lei Wang Lei Wang 1Ye-Peng Zhou Ye-Peng Zhou 1Guang-Hui Zhang Guang-Hui Zhang 1Da-Wei Li Da-Wei Li 1Yang Dong Yang Dong 1*Sheng-Chang Duan Sheng-Chang Duan 1
  • 1 Yunnan Agricultural University, Kunming, China
  • 2 Wageningen University and Research, Wageningen, Netherlands

The final, formatted version of the article will be published soon.

    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.

    Keywords: Codonopsis pilosula, Assembly, Comparative genomics, gene family, genome evolution

    Received: 23 Jul 2024; Accepted: 14 Oct 2024.

    Copyright: © 2024 Chen, Yang, Yang, Zhu, Li, Wang, Zhou, Zhang, Li, Dong and Duan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Yang Dong, Yunnan Agricultural University, Kunming, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.