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Background <p><i>Lycoris chunxiaoensis </i>is a recently described species that shares high morphological similarity with <i>L. radiata</i>. Resolving the exact phylogenetic position and evolutionary origin of species within the genus <i>Lycoris</i> is often challenged by complex evolutionary processes.</p> Results <p>We sequenced and assembled the complete chloroplast genome of <i>L. chunxiaoensis</i> and conducted comparative genomic and phylogenetic analyses. The phylogenetic reconstructions revealed cytonuclear discordance: the plastid phylogeny placed <i>L. chunxiaoensis</i> as sister to <i>Lycoris rosea</i>, whereas the nuclear ribosomal ITS phylogeny clustered it with <i>Lycoris radiata</i>. Furthermore, karyotype and fluorescence in situ hybridization (FISH) analyses showed that <i>L. chunxiaoensis</i> (2n = 3x = 33) shares cytogenetic similarity with <i>L. radiata</i>.</p> Conclusions <p>Phylogenetic analyses based on the chloroplast genome and ITS datasets revealed differences in the phylogenetic placement of <i>L. chunxiaoensis</i>. In the plastome-based phylogeny, <i>L. chunxiaoensis</i> was recovered as sister to <i>L. rosea</i>, whereas in the ITS-based phylogeny it was placed within the same clade as <i>L. radiata</i>. This incongruence between chloroplast genome and ITS sequence suggests potential cytonuclear discordance and indicates a complex evolutionary history within <i>Lycoris</i>.</p>

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Chloroplast genomics and nuclear ribosomal ITS phylogeny reveal pronounced cytonuclear discordance in Lycoris chunxiaoensis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月26日

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  • Shi-Yu Huang,
  • Jia Yao,
  • Yu-Tong Han,
  • Yong-Chun Zhang,
  • Xuan-Min Guang,
  • Feng Yang,
  • Hong-Fei Li,
  • Yuan Tian,
  • Fu-Yuan Zhu,
  • Ke-Wang Xu,
  • Liu-Yan Yang,
  • Qing-Zhu Li

摘要

Background

Lycoris chunxiaoensis is a recently described species that shares high morphological similarity with L. radiata. Resolving the exact phylogenetic position and evolutionary origin of species within the genus Lycoris is often challenged by complex evolutionary processes.

Results

We sequenced and assembled the complete chloroplast genome of L. chunxiaoensis and conducted comparative genomic and phylogenetic analyses. The phylogenetic reconstructions revealed cytonuclear discordance: the plastid phylogeny placed L. chunxiaoensis as sister to Lycoris rosea, whereas the nuclear ribosomal ITS phylogeny clustered it with Lycoris radiata. Furthermore, karyotype and fluorescence in situ hybridization (FISH) analyses showed that L. chunxiaoensis (2n = 3x = 33) shares cytogenetic similarity with L. radiata.

Conclusions

Phylogenetic analyses based on the chloroplast genome and ITS datasets revealed differences in the phylogenetic placement of L. chunxiaoensis. In the plastome-based phylogeny, L. chunxiaoensis was recovered as sister to L. rosea, whereas in the ITS-based phylogeny it was placed within the same clade as L. radiata. This incongruence between chloroplast genome and ITS sequence suggests potential cytonuclear discordance and indicates a complex evolutionary history within Lycoris.