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Identification of Laportea bulbifera using the complete chloroplast genome as a potentially effective super-barcode

  • Plant Genetics • Original Paper
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Abstract

Laportea bulbifera, a Miao medicine grown in karst areas, has exerted a unique curative effect on skin itching in the elderly, with an annual sales of > 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation high-throughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence is used as a potentially effective super-barcode and the highly variable regions (ycf1, matK, and ndhD) can be used as potentially specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species.

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Data availability

The original contributions presented in the study are publicly available. This data can be found here: The chloroplast genomes assembled in this study were deposited in GenBank with the accession numbers ON320386.

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Acknowledgements

I would like to thank my supervisor, LX, for her guidance during this research. I would also like to thank my tutors, LW, YS, QY, RG, and MW, for their valuable guidance throughout my studies. I would particularly like to acknowledge my teammate, CL, GD, and TW for their wonderful collaboration and patient support.

Funding

This research was funded by the National Natural Science Foundation of China and Karst Science Research Center of Guizhou Province (U1812403-1), National Key R&D Program of China from the Ministry of Science and Technology of China (grant No. 2019YFC1711100), the CACMS Innovation Fund (CI2021A05103). National Natural Science Foundation of China (81891010, 81891013).

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Authors and Affiliations

  1. Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China

    Wenting Wang, Xingwen Wang, Yuhua Shi, Qinggang Yin, Ranran Gao, Mengyue Wang, Li Xiang & Lan Wu

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  1. Wenting Wang
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  8. Lan Wu
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Contributions

LX acquired the funding and conceived the research. WW and LX collected plant material. WW analyzed the data. WW and XW contributed equally to this manuscript. LX revised the manuscript. LW, YS, QY, RG, and MW provide guidance in the analysis and manuscript writing process. WW edited and approved the final manuscript. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Li Xiang or Lan Wu.

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Wang, W., Wang, X., Shi, Y. et al. Identification of Laportea bulbifera using the complete chloroplast genome as a potentially effective super-barcode. J Appl Genetics 64, 231–245 (2023). https://doi.org/10.1007/s13353-022-00746-4

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