biostudies-literatureJiang SKey Research & Development Project of Hunan Provincial Department of Science and TechnologyNational Natural Science Foundation of ChinaNational Key Research and Development Program of China837-848https://www.ebi.ac.uk/biostudies/studies/S-EPMC9110604biostudies-literatureUnknown28(4)More than 600 species in over 40 genera have been identified in family Theaceae worldwide. The accurate identification of Theaceae plants can ensure the market economic order, and it plays a vital role in achieving the sustainable utilization of germplasm resources. DNA barcoding, one of the most potential species identification technologies at present, has advanced in the rapid, accurate and repetitive discrimination of species. In this study, matK + ndhF + ycf1 was observed as the optimal combined candidate gene sequence of DNA barcodes by analyzing genetic information of four single chloroplast DNA sequences, including matK, rbcL, ndhF and ycf1, as well as six combined gene sequences. Subsequently, the experiments were performed on phylogenetic analysis based on genetic distance to study the phylogenetic relationship of Theaceae plants and evaluate the species identification accuracy of matK + ndhF + ycf1. Lastly, the species-specific DNA barcodes were designed by searching the variable sites (one type of single nucleotide polymorphism sites) for the accurate identification of Camellia amplexicaulis, Franklinia alatamaha, Gordonia brandegeei and Stewartia micrantha. The previous methods of screening and testing candidate gene sequences were optimized, and innovation was made in the above methods. The process of making visual DNA barcodes was standardized. Besides, DNA barcoding technology increased the accuracy of species identification and DNA barcoding was analyzed in accordance with the theories of population genetics (e.g., neutral theory of molecular evolution). The results of the study will lay a basis for the identification and protection of Theaceae species and germplasm resources.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1007/s12298-022-01175-7.Physiology and molecular biology of plants : an international journal of functional plant biologyThe specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants.PMC91106042017YFF02103012019NK208131872866Qin PLi YPeng GXie HGuo XChen FJiang SfalseThe specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants.More than 600 species in over 40 genera have been identified in family Theaceae worldwide. The accurate identification of Theaceae plants can ensure the market economic order, and it plays a vital role in achieving the sustainable utilization of germplasm resources. DNA barcoding, one of the most potential species identification technologies at present, has advanced in the rapid, accurate and repetitive discrimination of species. In this study, matK + ndhF + ycf1 was observed as the optimal combined candidate gene sequence of DNA barcodes by analyzing genetic information of four single chloroplast DNA sequences, including matK, rbcL, ndhF and ycf1, as well as six combined gene sequences. Subsequently, the experiments were performed on phylogenetic analysis based on genetic distance to study the phylogenetic relationship of Theaceae plants and evaluate the species identification accuracy of matK + ndhF + ycf1. Lastly, the species-specific DNA barcodes were designed by searching the variable sites (one type of single nucleotide polymorphism sites) for the accurate identification of Camellia amplexicaulis, Franklinia alatamaha, Gordonia brandegeei and Stewartia micrantha. The previous methods of screening and testing candidate gene sequences were optimized, and innovation was made in the above methods. The process of making visual DNA barcodes was standardized. Besides, DNA barcoding technology increased the accuracy of species identification and DNA barcoding was analyzed in accordance with the theories of population genetics (e.g., neutral theory of molecular evolution). The results of the study will lay a basis for the identification and protection of Theaceae species and germplasm resources.<h4>Supplementary information</h4>The online version contains supplementary material available at 10.1007/s12298-022-01175-7.2022-01-01T00:00:00Z2022 Apr2026-05-09T13:44:49.637Z2025-04-07T03:19:26.282ZS-EPMC91106043559248710.1007/s12298-022-01175-7