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Background <p>Species delimitation within <i>Camellia</i> sect. <i>Thea</i> is taxonomically challenging due to its complex evolutionary history. This study aims to utilize nuclear and chloroplast data as genomic DNA barcodes to delimit species within this economically important group of plants.</p> Results <p>Whole genome sequencing (WGS) data were obtained for 98 accessions representing all but one species in <i>C</i>. sect. <i>Thea</i>. Based on 759 high-quality SCNs, 98 whole chloroplast genomes, and by using 2× coverage clean reads from WGS for Skmer analyses, we found that combining the findings from these three data sets resulted in nearly complete species delimitation and resolution of all interspecific relationships within <i>C</i>. sect. <i>Thea</i>. We also found support for the taxonomic elevation of two varieties (<i>C</i>. <i>sinensis</i> var. <i>assamica</i> and <i>C</i>. <i>tachangensis</i> var. <i>remotiserrata</i>) to species status (<i>C</i>. <i>assamica</i> and <i>C</i>. <i>remotiserrata</i>, respectively). Furthermore, we confirmed that <i>C</i>. <i>formosensis</i> represents a distinct species. Gene tree discordances, chloroplast-nuclear conflicts and complex network-like phylogenetic relationships were observed in <i>C</i>. sect. <i>Thea</i>.</p> Conclusion <p>Compared with the use of single parentally inherited chloroplast data sources, utilizing both uniparentally inherited chloroplast data and biparentally inherited nuclear data improved the species delimitation of taxa within <i>C</i>. sect. <i>Thea</i>. The intricate phylogenetic relationships observed are likely a result of widespread past hybridization and chloroplast capture events among species within this group, which may have blurred the species boundaries. Our novel approach to species delimitation within <i>C</i>. sect. <i>Thea</i> may serve as a blueprint for employing genomic DNA barcodes in other taxa with complex histories, and will significantly contribute to the conservation of cultivated tea plant species and their wild relatives.</p>

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Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年5月1日

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  • Zongfang Shen,
  • Yujing Feng,
  • Michael Möller,
  • Kevin S. Burgess,
  • Hantao Qin,
  • Junbo Yang,
  • Zhiqiong Mo,
  • Hongtao Li,
  • Dezhu Li,
  • Lianming Gao

摘要

Background

Species delimitation within Camellia sect. Thea is taxonomically challenging due to its complex evolutionary history. This study aims to utilize nuclear and chloroplast data as genomic DNA barcodes to delimit species within this economically important group of plants.

Results

Whole genome sequencing (WGS) data were obtained for 98 accessions representing all but one species in C. sect. Thea. Based on 759 high-quality SCNs, 98 whole chloroplast genomes, and by using 2× coverage clean reads from WGS for Skmer analyses, we found that combining the findings from these three data sets resulted in nearly complete species delimitation and resolution of all interspecific relationships within C. sect. Thea. We also found support for the taxonomic elevation of two varieties (C. sinensis var. assamica and C. tachangensis var. remotiserrata) to species status (C. assamica and C. remotiserrata, respectively). Furthermore, we confirmed that C. formosensis represents a distinct species. Gene tree discordances, chloroplast-nuclear conflicts and complex network-like phylogenetic relationships were observed in C. sect. Thea.

Conclusion

Compared with the use of single parentally inherited chloroplast data sources, utilizing both uniparentally inherited chloroplast data and biparentally inherited nuclear data improved the species delimitation of taxa within C. sect. Thea. The intricate phylogenetic relationships observed are likely a result of widespread past hybridization and chloroplast capture events among species within this group, which may have blurred the species boundaries. Our novel approach to species delimitation within C. sect. Thea may serve as a blueprint for employing genomic DNA barcodes in other taxa with complex histories, and will significantly contribute to the conservation of cultivated tea plant species and their wild relatives.