Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data

Ri-Hong Jiang; Si-Qi Liang; Fei Wu; Li-Ming Tang; Bo Qin; Ying-Ying Chen; Yao-Heng Huang; Kai-Xiang Li; Xian-Chun Zhang

doi:10.3389/fpls.2023.1183653

Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data

Front Plant Sci. 2023 Jun 6:14:1183653. doi: 10.3389/fpls.2023.1183653. eCollection 2023.

Authors

Ri-Hong Jiang¹, Si-Qi Liang^{2

3

4}, Fei Wu^{3

5

6}, Li-Ming Tang⁷, Bo Qin¹, Ying-Ying Chen¹, Yao-Heng Huang¹, Kai-Xiang Li¹, Xian-Chun Zhang^{2

3}

Affiliations

¹ Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China.
² State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.
³ China National Botanical Garden, Beijing, China.
⁴ College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
⁵ Beijing Botanical Garden, Beijing, China.
⁶ Beijing Floriculture Engineering Technology Research Centre, Beijing, China.
⁷ Guangxi Forestry Industry Group Stock Corporation, Nanning, China.

Abstract

Germplasm resources are the source of herbal medicine production. The cultivation of superior germplasm resources helps to resolve the conflict between long-term population persistence and growing market demand by consistently producing materials with high quality. The fern species Cibotium barometz is the original plant of cibotii rhizoma ("Gouji"), a traditional Chinese medicine used in the therapy of pain, weakness, and numbness in the lower extremities. Long-history medicinal use has caused serious wild population decline in China. Without sufficient understanding of the species and lineage diversity of Cibotium, it is difficult to propose a targeted conservation scheme at present, let alone select high-quality germplasm resources. In order to fill such a knowledge gap, this study sampled C. barometz and relative species throughout their distribution in China, performed genome skimming to obtain plastome data, and conducted phylogenomic analyses. We constructed a well-supported plastome phylogeny of Chinese Cibotium, which showed that three species with significant genetic differences are distributed in China, namely C. barometz, C. cumingii, and C. sino-burmaense sp. nov., a cryptic species endemic to NW Yunnan and adjacent regions of NE Myanmar. Moreover, our results revealed two differentiated lineages of C. barometz distributed on the east and west sides of a classic phylogeographic boundary that was probably shaped by monsoons and landforms. We also evaluated the resolution of nine traditional barcode loci and designed five new DNA barcodes based on the plastome sequence that can distinguish all these species and lineages of Chinese Cibotium accurately. These novel findings on a genetic basis will guide conservation planners and medicinal plant breeders to build systematic conservation plans and exploit the germplasm resources of Cibotium in China.

Keywords: Cibotium barometz; Cibotium sino-burmaense; DNA barcoding; chloroplast genome; conservation; endangered species; germplasm resource; species diversity.

Grants and funding

This research was supported by “Evaluation of the Germplasm Resources of the Protected Plant Cibotium barometz” project (GuiLinYan[RC]2302) of Guangxi Forestry Research Institute, the National Plant Specimen Resource Center Project (NPSRC) (E0117G1001), the “Field Survey and Conservation Studies of some State Key Protected Fern Species” project in National Forestry and Grassland Administration, the “2022 Central Financial Forestry Reform and Development Funds: Collection, Conservation and Use of Germplasm Resources of Cibotium barometz” of Department of Forestry of Guangxi Zhuang Autonomous Region, as well as “Survey and Collection of Germplasm Resources of Woody and Herbaceous Plants in Guangxi, China” (GXFS-2021-34).