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<p>As an economically significant group, Apioideae continues to face controversies in species delimitation, which hinders the effective exploitation and utilization of its genetic resources. We sequenced chloroplast (cp) genomes of seven plants of the Apioideae. They are 146,553 bp to 156,156 bp in length and the total number of annotated genes is 129 to 134, including 85 to 88 protein coding genes, 36 to 38 tRNA genes, and 8 rRNA genes. <i>Ycf 3</i>, <i>rps 12</i> and <i>clpP</i> genes contain two introns. The contraction of the inverted repeat (IR) boundary region is particularly pronounced in the cp genomes of <i>Angelica paeoniifolia</i> R.H. Shan &amp; C. C.Yuan and <i>Hymenidium apiolens</i> C. B. Clarke Pimenov &amp; Kljuykov, resulting in a significant difference in the length of the IR region compared to the remaining five species. Four mutation hotspot regions, i.e. <i>psbI-trnS-</i>GCU<i>-trnG-</i>GCC, <i>psbC</i>, <i>ndhA-ndhH</i> and <i>rrn23-trnA-</i>UGC, are identified in the large single copy (LSC) and small&#xa0;single&#xa0;copy&#xa0;(SSC) regions, showing potential for serving as molecular markers for the Apioideae. Results suggest 108 species can divided into six groups. Genera <i>Hymenidium, Angelica</i> and <i>Pleurospermum</i> are not monophyletic, demonstrating that current morphological classifications conflict with genomic evidence. We propose reclassifying <i>H. apiolens</i>, <i>Ple. rivulorum</i>, <i>H. dentatum</i> and <i>H. hookeri</i> into genus <i>Hymenidium</i>, and transferring seven genus <i>Hymenidium</i> species from Pleurospermeae to genus <i>Pleurospermum</i>. The phylogenomic placement of <i>A. paeoniifolia</i> compels us to reconsider its taxonomic classification. The phylogenomic relationships within Group1 remain uncertain and require further investigation incorporating more data.</p>

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Characterization and phylogenomic inference of chloroplasts in seven apioideae species

  • 期刊论文

  • 发表日期：

    2025年12月16日

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  • Xinyi Liao,
  • Riwa Mahai,
  • Xiaoyun Wang,
  • Jun Yuan

摘要

As an economically significant group, Apioideae continues to face controversies in species delimitation, which hinders the effective exploitation and utilization of its genetic resources. We sequenced chloroplast (cp) genomes of seven plants of the Apioideae. They are 146,553 bp to 156,156 bp in length and the total number of annotated genes is 129 to 134, including 85 to 88 protein coding genes, 36 to 38 tRNA genes, and 8 rRNA genes. Ycf 3, rps 12 and clpP genes contain two introns. The contraction of the inverted repeat (IR) boundary region is particularly pronounced in the cp genomes of Angelica paeoniifolia R.H. Shan & C. C.Yuan and Hymenidium apiolens C. B. Clarke Pimenov & Kljuykov, resulting in a significant difference in the length of the IR region compared to the remaining five species. Four mutation hotspot regions, i.e. psbI-trnS-GCU-trnG-GCC, psbC, ndhA-ndhH and rrn23-trnA-UGC, are identified in the large single copy (LSC) and small single copy (SSC) regions, showing potential for serving as molecular markers for the Apioideae. Results suggest 108 species can divided into six groups. Genera Hymenidium, Angelica and Pleurospermum are not monophyletic, demonstrating that current morphological classifications conflict with genomic evidence. We propose reclassifying H. apiolens, Ple. rivulorum, H. dentatum and H. hookeri into genus Hymenidium, and transferring seven genus Hymenidium species from Pleurospermeae to genus Pleurospermum. The phylogenomic placement of A. paeoniifolia compels us to reconsider its taxonomic classification. The phylogenomic relationships within Group1 remain uncertain and require further investigation incorporating more data.