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<p><i>Actinidia</i> species are fruit trees with various functions, such as providing edible fruit, serving as ornamental plants, and having medicinal benefits. However, the taxonomy of <i>Actinidia</i> species is controversial due to widespread hybridization, the history of divergence and polyploid speciation among <i>Actinidia</i> species also remains unclear. In this study, we conducted comparative analyses of the chloroplast genomes and ploidy among multiple <i>Actinidia</i> species. The genes <i>clpP</i>, <i>infA</i>, <i>ndhD</i>, <i>ndhK</i>, and <i>rpl20</i> were absent from these chloroplast genomes. The <i>ycf2</i> and <i>rpl20</i> genes in the <i>Actinidia</i> species were under positive selection. Several regions (<i>rps16</i>–<i>trnQ</i>-UUG, <i>trnS</i>-GCU–<i>trnR</i>-UCU, <i>ndhC</i>–<i>trnV</i>-UAC, <i>rbcL</i>–<i>accD</i>, <i>rps12</i>–<i>psbB</i>, <i>trnN</i>-GUU–<i>ndhF</i>, <i>ycf1</i>–<i>trnN</i>-GUU, and <i>trnH</i>-GUG–<i>psbA</i>) and genes (<i>ycf1</i>, <i>ycf2</i>, <i>accD</i>, <i>rpl20</i>) exhibited high variability, which could potentially serve as molecular markers in species delineation and other phylogenetic studies. Through divergence time estimation, the <i>Actinidia</i> genus originated 23 million years ago (Ma), and experienced a tetraploidization event in ~ 20&#xa0;Ma. Subsequently, <i>Actinidia</i> has undergone extensive diploidization. Our findings will provide valuable information in species identification, breeding programs, and conservation efforts for <i>Actinidia</i> species.</p>

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Comparative chloroplast genomics provides insights into the phylogenetic relationships and evolutionary history for Actinidia species

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  • 发表日期：

    2025年4月17日

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  • Qianhui Lin,
  • Siqi Hu,
  • Zhenhua Wu,
  • Yahui Huang,
  • Shuo Wang,
  • Wenbo Shi,
  • Bingyue Zhu

摘要

Actinidia species are fruit trees with various functions, such as providing edible fruit, serving as ornamental plants, and having medicinal benefits. However, the taxonomy of Actinidia species is controversial due to widespread hybridization, the history of divergence and polyploid speciation among Actinidia species also remains unclear. In this study, we conducted comparative analyses of the chloroplast genomes and ploidy among multiple Actinidia species. The genes clpP, infA, ndhD, ndhK, and rpl20 were absent from these chloroplast genomes. The ycf2 and rpl20 genes in the Actinidia species were under positive selection. Several regions (rps16–trnQ-UUG, trnS-GCU–trnR-UCU, ndhC–trnV-UAC, rbcL–accD, rps12–psbB, trnN-GUU–ndhF, ycf1–trnN-GUU, and trnH-GUG–psbA) and genes (ycf1, ycf2, accD, rpl20) exhibited high variability, which could potentially serve as molecular markers in species delineation and other phylogenetic studies. Through divergence time estimation, the Actinidia genus originated 23 million years ago (Ma), and experienced a tetraploidization event in ~ 20 Ma. Subsequently, Actinidia has undergone extensive diploidization. Our findings will provide valuable information in species identification, breeding programs, and conservation efforts for Actinidia species.