J Syst Evol ›› 2022, Vol. 60 ›› Issue (5): 1218-1228.DOI: 10.1111/jse.12829

Special Issue: Virtual Issue to Celebrate the Legacy and Life of Professor Wen-Tsai Wang

• Research Articles • Previous Articles    

Herbarium phylogenomics: Resolving the generic status of the enigmatic Pseudobartsia (Orobanchaceae)

Nan Jiang1,2,3, Li-Na Dong4, Jun-Bo Yang5, Yun-Hong Tan1,2,3, Hong Wang6, Christopher P. Randle7, De-Zhu Li5*, and Wen-Bin Yu1,2,3*   

  1. 1 Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China
    2 Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, Yunnan, China
    3 Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
    4 Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, Guangxi, China
    5 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
    6 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
    7 Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77341, USA

    *Authors for correspondence. De‐Zhu Li. E‐mail: dzl@mail.kib.ac.cn; Wen‐Bin Yu. E‐mail: yuwenbin@xtbg.ac.cn
  • Received:2020-08-25 Accepted:2022-01-04 Online:2022-03-03 Published:2022-09-01


The millions of herbarium specimens in collections around the world provide historical resources for phylogenomics and evolutionary studies. Many rare and endangered species exist only as historical specimens. Here, we report a case study of the monotypic Pseudobartsia yunnanensis D. Y. Hong (=Pseudobartsia glandulosa[Bentham] W. B. Yu & D. Z. Li: Orobanchaceae) known from a single Chinese collection taken in 1940. We obtained genomic data of Pseudobartsia glandulosa using high-throughput short-read sequencing, and then assembled a complete chloroplast genome and nuclear ribosome DNA region in this study. We found that the newly assembled three plastid DNA regions (atpB-rbcL, rpl16, and trnS-G) and nuclear ribosomal internal transcribed spacer (nrITS) of Pseudobartsia glandulosa were more than 99.98% similar to published sequences obtained by target sequencing. Phylogenies of Orobanchaceae using 30 plastomes (including 10 new plastomes), using both supermatrix and multispecies coalescent approaches following a novel plastid phylogenomic workflow, recovered seven recognized tribes and two unranked groups, both of which were proposed as new tribes, that is, Brandisieae and Pterygielleae. Within Pterygielleae, all analyses strongly supported Xizangia D. Y. Hong as the first diverging genus, with Pseudobartsia D. Y. Hong as sister to Pterygiella Oliver + Phtheirospermum Bunge (excluding Phtheirospermum japonicum [Thunberg] Kanitz); this supports reinstatement of Pseudobartsia and Xizangia. Although elements of Buchnereae-Cymbarieae-Orobancheae and Brandisieae-Pterygielleae-Rhinantheae showed incongruence among gene trees, the topology of the supermatrix tree was congruent with the majority of gene trees and functional-group trees. Therefore, most plastid genes are evolving as a linkage group, allowing the supermatrix tree approach to yield internally consistent phylogenies for Orobanchaceae.

Key words: gene tree, Orobanchaceae, Phtheirospermum tenuisectum complex, plastid phylogenomics, Pterygiella complex, species tree