High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites

doi:10.1016/j.pld.2025.09.005

Plant Diversity ›› 2025, Vol. 47 ›› Issue (06): 920-930.DOI: 10.1016/j.pld.2025.09.005

• Articles • Previous Articles Next Articles

High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites

You Wu^a,b,h, Rong Liu^c,h, Wei-Jia Wang^a,b, De-Zhu Li^c,d, Kevin S. Burgess^e, Wen-Bin Yu^b,f,g, Hong Wang^a

a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
c Plant Germplasm and Genomics Centre, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
d Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai'an 271018, Shandong, China;
e Department of Biomedical Sciences, Mercer University School of Medicine, Columbus, GA 31901, USA;
f Yunnan International Joint Laboratory for the Conservation and Utilization of Tropical Timber Tree Species, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
g Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
h University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China

Received:2025-04-28 Revised:2025-09-04 Online:2026-01-13 Published:2026-01-13
Contact: Kevin S.Burgess,E-mail:burgess_ks@mercer.edu;Wen-Bin Yu,E-mail:yuwenbin@xtbg.ac.cn;Hong Wang,E-mail:wanghong@mail.kib.ac.cn
Supported by:
This study was supported by the National Natural Science Foundation of China (32371700, 32071670 and 31870196), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000), the Science and Technology Basic Resources Investigation Program of China (2021FY100200), Yunnan Revitalization Talent Support Program “Young Talent” and “Innovation Team” Projects (202405AS350019), the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science (XTBG-1450101), the Key R & D program of Yunnan Province, China (202103AC100003) and the Key Basic Research program of Yunnan Province, China (202101BC070003).

High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites

You Wu^a,b,h, Rong Liu^c,h, Wei-Jia Wang^a,b, De-Zhu Li^c,d, Kevin S. Burgess^e, Wen-Bin Yu^b,f,g, Hong Wang^a

a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
c Plant Germplasm and Genomics Centre, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
d Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai'an 271018, Shandong, China;
e Department of Biomedical Sciences, Mercer University School of Medicine, Columbus, GA 31901, USA;
f Yunnan International Joint Laboratory for the Conservation and Utilization of Tropical Timber Tree Species, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
g Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;
h University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China

通讯作者: Kevin S.Burgess,E-mail:burgess_ks@mercer.edu;Wen-Bin Yu,E-mail:yuwenbin@xtbg.ac.cn;Hong Wang,E-mail:wanghong@mail.kib.ac.cn
基金资助:
This study was supported by the National Natural Science Foundation of China (32371700, 32071670 and 31870196), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000), the Science and Technology Basic Resources Investigation Program of China (2021FY100200), Yunnan Revitalization Talent Support Program “Young Talent” and “Innovation Team” Projects (202405AS350019), the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science (XTBG-1450101), the Key R & D program of Yunnan Province, China (202103AC100003) and the Key Basic Research program of Yunnan Province, China (202101BC070003).

Abstract

Abstract: Complete plastid genomes have been proposed as potential “super-barcodes” for plant identification and delineation, particularly in cases where standard DNA barcodes may be insufficient. However, few studies have systematically addressed how taxonomic complexity, especially in rapidly radiating lineages with intricate evolutionary histories, might influence the efficacy of plastome-scale barcodes. Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains, and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus. Therefore, Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity. In this study, we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes. Our results revealed that the traditional standard barcode combination (nrITS + matK + rbcL + trnH-psbA) achieved the highest discrimination rates (81.25%), closely followed by the plastid large single copy (LSC) region (80.21%), then by full plastome, the supermatrix of protein-coding genes, and hypervariable regions (79.17%). Notably, the matK and ycf1 gene alone could discriminate 78.13% of species. Key determinants of species discrimination by integrating alignment length (AL) and the proportion of parsimony-informative sites (PPIS), as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity. Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes, this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’ specific biological habits and potentially reflecting unique evolutionary patterns in the plastid genome.

Key words: Pedicularis, Himalaya-Hengduan mountains, Plastid genome, Standard barcodes, Plastome-scale barcodes, Species identification

摘要： Complete plastid genomes have been proposed as potential “super-barcodes” for plant identification and delineation, particularly in cases where standard DNA barcodes may be insufficient. However, few studies have systematically addressed how taxonomic complexity, especially in rapidly radiating lineages with intricate evolutionary histories, might influence the efficacy of plastome-scale barcodes. Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains, and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus. Therefore, Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity. In this study, we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes. Our results revealed that the traditional standard barcode combination (nrITS + matK + rbcL + trnH-psbA) achieved the highest discrimination rates (81.25%), closely followed by the plastid large single copy (LSC) region (80.21%), then by full plastome, the supermatrix of protein-coding genes, and hypervariable regions (79.17%). Notably, the matK and ycf1 gene alone could discriminate 78.13% of species. Key determinants of species discrimination by integrating alignment length (AL) and the proportion of parsimony-informative sites (PPIS), as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity. Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes, this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’ specific biological habits and potentially reflecting unique evolutionary patterns in the plastid genome.

关键词: Pedicularis, Himalaya-Hengduan mountains, Plastid genome, Standard barcodes, Plastome-scale barcodes, Species identification

You Wu, Rong Liu, Wei-Jia Wang, De-Zhu Li, Kevin S. Burgess, Wen-Bin Yu, Hong Wang. High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites[J]. Plant Diversity, 2025, 47(06): 920-930.

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High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites

High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites

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