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Background <p>Convallarioideae, a subfamily of Asparagaceae, encompasses a wide range of morphologically diverse lineages previously classified under different traditional families and holds significant economic value. Despite its importance, chloroplast genome data for Convallarioideae remain limited, hindering a comprehensive understanding of their genome structural evolution and phylogenetic relationships. This study aims to provide a detailed characterization of chloroplast genome features and to conduct robust phylogenetic analyses of this subfamily using an expanded dataset of chloroplast genomes.</p> Results <p>The plastomes of the subfamily exhibit a typical circular quadripartite structure with conserved genomic organization and gene content. However, variations were observed in genome size, SSRs, and codon usage across the subfamily. Nine highly variable regions and positive selection genes were identified. Phylogenetic analyses based on complete plastid genomes resolved the non-monophyly of Polygonateae. Compared to <i>Eriospermum mackenii</i>, the chloroplast genomes of tribe Rusceae, tribe Dracaeneae, and the <i>Polygonatum</i>-<i>Disporopsis</i> lineage showed significant size reduction.</p> Conclusions <p>Chloroplast genomes across Convallarioideae exhibit remarkable structural conservation. The phylogenetic analyses revealed weakly resolved backbone relationships among core members of this subfamily. Indels in the LSC region and gene loss were identified as key drivers of structural divergence in plastome size. These results clarify the interplay between genomic architecture and phylogenetic discordance, advancing our understanding of genomic evolution within Convallarioideae.</p>

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Conserved genome structure and phylogenetic insights for the heterogeneous subfamily of Convallarioideae (Asparagaceae) revealed from plastome data

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年5月27日

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  • Shao-De Wu,
  • Ran Meng,
  • Ze-Long Nie,
  • Ming-Yang Song,
  • Xing-Ru Chen,
  • Jun Wen,
  • Ying Meng

摘要

Background

Convallarioideae, a subfamily of Asparagaceae, encompasses a wide range of morphologically diverse lineages previously classified under different traditional families and holds significant economic value. Despite its importance, chloroplast genome data for Convallarioideae remain limited, hindering a comprehensive understanding of their genome structural evolution and phylogenetic relationships. This study aims to provide a detailed characterization of chloroplast genome features and to conduct robust phylogenetic analyses of this subfamily using an expanded dataset of chloroplast genomes.

Results

The plastomes of the subfamily exhibit a typical circular quadripartite structure with conserved genomic organization and gene content. However, variations were observed in genome size, SSRs, and codon usage across the subfamily. Nine highly variable regions and positive selection genes were identified. Phylogenetic analyses based on complete plastid genomes resolved the non-monophyly of Polygonateae. Compared to Eriospermum mackenii, the chloroplast genomes of tribe Rusceae, tribe Dracaeneae, and the Polygonatum-Disporopsis lineage showed significant size reduction.

Conclusions

Chloroplast genomes across Convallarioideae exhibit remarkable structural conservation. The phylogenetic analyses revealed weakly resolved backbone relationships among core members of this subfamily. Indels in the LSC region and gene loss were identified as key drivers of structural divergence in plastome size. These results clarify the interplay between genomic architecture and phylogenetic discordance, advancing our understanding of genomic evolution within Convallarioideae.