Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae)
Abstract 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 Who...
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2025-05-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06612-9 |
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| author | Zongfang Shen Yujing Feng Michael Möller Kevin S. Burgess Hantao Qin Junbo Yang Zhiqiong Mo Hongtao Li Dezhu Li Lianming Gao |
| author_facet | Zongfang Shen Yujing Feng Michael Möller Kevin S. Burgess Hantao Qin Junbo Yang Zhiqiong Mo Hongtao Li Dezhu Li Lianming Gao |
| author_sort | Zongfang Shen |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-a570b294a7fc45c8b65f320a6ce71bdd |
| institution | DOAJ |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-a570b294a7fc45c8b65f320a6ce71bdd2025-08-20T02:55:38ZengBMCBMC Plant Biology1471-22292025-05-0125111310.1186/s12870-025-06612-9Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae)Zongfang Shen0Yujing Feng1Michael Möller2Kevin S. Burgess3Hantao Qin4Junbo Yang5Zhiqiong Mo6Hongtao Li7Dezhu Li8Lianming Gao9Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesRoyal Botanic Garden EdinburghDepartment of Biomedical Sciences, Mercer University School of MedicineGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of SciencesAbstract 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.https://doi.org/10.1186/s12870-025-06612-9Camellia sect. TheaSpecies delimitationGenomic DNA barcodesChloroplast genomesSingle-copy nuclear orthologous genes |
| spellingShingle | Zongfang Shen Yujing Feng Michael Möller Kevin S. Burgess Hantao Qin Junbo Yang Zhiqiong Mo Hongtao Li Dezhu Li Lianming Gao Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae) BMC Plant Biology Camellia sect. Thea Species delimitation Genomic DNA barcodes Chloroplast genomes Single-copy nuclear orthologous genes |
| title | Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae) |
| title_full | Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae) |
| title_fullStr | Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae) |
| title_full_unstemmed | Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae) |
| title_short | Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae) |
| title_sort | genomic dna barcodes provide novel insights into species delimitation in the complex camellia sect thea theaceae |
| topic | Camellia sect. Thea Species delimitation Genomic DNA barcodes Chloroplast genomes Single-copy nuclear orthologous genes |
| url | https://doi.org/10.1186/s12870-025-06612-9 |
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