Scholarlink

Background <p><i>Youngia japonica</i> is a synanthropic species of the Asteraceae family valued for its dual applications in both medicine and cuisine. It exhibits strong stress tolerance as well as resistance to pests and diseases. However, the genetic basis and evolutionary history underlying these traits remain poorly understood. In this study, we performed chromosome-level whole-genome sequencing to investigate the evolutionary history of this human-associated plant.</p> Results <p>Our analyses revealed that <i>Y. japonica</i> possesses a relatively compact genome of 1.14 Gb. Repetitive sequences account for 80.95% of the genome, with recent bursts of long terminal repeat (LTR) retrotransposons contributing 60.22%. PSMC analysis indicated that the effective population size of <i>Y. japonica</i> expanded significantly approximately one million years ago (MYA), before declining markedly between ~ 1 MYA and 0.1 MYA. Notably, the Guangxi population experienced a secondary expansion after 0.1 MYA, whereas the Guangzhou population continued to decline. Comparative genomic analyses identified significant expansions in several functional gene families, including F-box proteins, MYB transcription factors, and HSP70 molecular chaperones. Disease resistance-related gene families, such as TIR-NBS-LRR, RPP8-like proteins, and TIR-domain-containing genes, also showed notable expansion in <i>Y. japonica</i> and other examined Asteraceae species. Furthermore, 211 genes involved in cell differentiation, DNA replication, and cell cycle regulation were detected under positive selection.</p> Conclusion <p><i>Youngia japonica</i> shares the conserved Asteraceae whole-genome triplication (WGT) event but shows no evidence of recent whole-genome duplication (WGD). Repetitive element proliferation appears to be the primary contributor to its genome size expansion. Recent LTR retrotransposon bursts, together with the expansion of F-box, MYB, disease resistance, and HSP70 gene families, likely represent key evolutionary mechanisms facilitating adaptation in synanthropic Asteraceae species such as <i>Y. japonica</i>. Signals of positive selection further suggest that the fine-tuned regulation of cell division and growth constitutes an important cellular basis for adaptive evolution in this species.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Chromosome-level genome assembly of Youngia japonica reveals evolutionary dynamics underlying adaptation in a synanthropic Asteraceae species

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月18日

查看全文
  • Yulan Peng,
  • Xuemei Pu,
  • Tingying Cao,
  • Wenbin Ju,
  • Fuhua Bian,
  • Yanjie Wang

摘要

Background

Youngia japonica is a synanthropic species of the Asteraceae family valued for its dual applications in both medicine and cuisine. It exhibits strong stress tolerance as well as resistance to pests and diseases. However, the genetic basis and evolutionary history underlying these traits remain poorly understood. In this study, we performed chromosome-level whole-genome sequencing to investigate the evolutionary history of this human-associated plant.

Results

Our analyses revealed that Y. japonica possesses a relatively compact genome of 1.14 Gb. Repetitive sequences account for 80.95% of the genome, with recent bursts of long terminal repeat (LTR) retrotransposons contributing 60.22%. PSMC analysis indicated that the effective population size of Y. japonica expanded significantly approximately one million years ago (MYA), before declining markedly between ~ 1 MYA and 0.1 MYA. Notably, the Guangxi population experienced a secondary expansion after 0.1 MYA, whereas the Guangzhou population continued to decline. Comparative genomic analyses identified significant expansions in several functional gene families, including F-box proteins, MYB transcription factors, and HSP70 molecular chaperones. Disease resistance-related gene families, such as TIR-NBS-LRR, RPP8-like proteins, and TIR-domain-containing genes, also showed notable expansion in Y. japonica and other examined Asteraceae species. Furthermore, 211 genes involved in cell differentiation, DNA replication, and cell cycle regulation were detected under positive selection.

Conclusion

Youngia japonica shares the conserved Asteraceae whole-genome triplication (WGT) event but shows no evidence of recent whole-genome duplication (WGD). Repetitive element proliferation appears to be the primary contributor to its genome size expansion. Recent LTR retrotransposon bursts, together with the expansion of F-box, MYB, disease resistance, and HSP70 gene families, likely represent key evolutionary mechanisms facilitating adaptation in synanthropic Asteraceae species such as Y. japonica. Signals of positive selection further suggest that the fine-tuned regulation of cell division and growth constitutes an important cellular basis for adaptive evolution in this species.