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The complete chloroplast genome of the medical plant Huperzia crispata from the Huperziaceae family: structure, comparative analysis, and phylogenetic relationships

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Abstract

Background

Huperzia crispata, belonging to the Huperziaceae family, is one of the most essential resources of huperzine A for candidate drugs to treat Alzheimer’s diseases. However, there is very limited information about H. crispat, and its taxonomic status and interspecific relationships between Huperzia species are still unclear. To investigate the taxonomic classification of Huperzia species and identify species discrimination markers, the complete chloroplast (cp) genome of H. crispata was sequenced and characterized for the first time.

Methods and Results

Total genomic DNA was isolated and sequenced using the next-generation Illumina NovaSeq 6000 platform. The data were filtered, assembled and annotated by a series software and web service. The results were as follows: the cp genome of H. crispata was 154,320 bp long with a large single-copy (LSC) region of 104,023 bp, a small single-copy (SSC) region of 19,671 bp, and a pair of inverted repeat (IRa and IRb) regions of 15,313 bp. A total of 131 genes, including 87 protein-coding genes, 36 transfer RNA genes (tRNAs), and eight ribosome RNA genes (rRNAs), were annotated in the cp genome. The contraction and expansion of the inverted repeat (IR) regions were relatively conserved in the Huperzia genus. Codon usage bias analysis showed that the encoding rate at the 3-end of codon A/T (74.34%) was significantly higher than that of C/G (25.66%). A total of 8 hotspot loci with high Pi values (> 0.06) were identified in the four Huperzia species based on nucleic acid diversity analysis. Ka/Ks selective pressure analysis demonstrated that the cemA gene is the most common gene undergoing positive selection among Huperzia. In addition, a total of 261 simple sequence repeats and 179 interspersed repeats were identified in the cp genome. Phylogenetic tree analysis based on the complete protein sequences of 23 related species of H. crispata indicated that H. serrata f. longipetiolata is a sister of H. crispata, suggesting that H. serrata f. longipetiolata and H. crispata are more closely related than H. serrata and H. lucidula.

Conclusions

The results strongly supported that H. crispata was more closely related to H. serrata f. longipetiolata than to H. serrata and H. lucidula within the Huperzia genus. The outcome provided important information for the phylogenetic analysis of the subsequent specific molecular species identification in Huperzia. The present results will provide valuable information for further research into the classification, phylogeny and species identification of Huperzia plants.

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Data Availability

The cp genome sequence data of H. crispata that support the findings of this study are openly available in NCBI at the GenBank database with accession number ON745420 (https://www.ncbi.nlm.nih.gov).

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Funding

This work was financially supported by the Key Research and Development Program of Zhejiang Province (Grant No. 2021C02043), the Yuyao Science and Technology Planning Project (Grant No. JHNS20210304) and the Zhejiang Sci-Tech University scientific research fund (Grant No. 19042142-Y).

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Authors and Affiliations

  1. Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China

    Dengpan Yin, Bo Pang, Qiao Liu, Yufeng Zhai, Nan Ma, Tongtong Chen, Qiaojun Jia & Dekai Wang

  2. Yuyao Seedling Management Station, Ningbo, 315400, Zhejiang, China

    Haibo Li

  3. Ningbo Delai Medicinal Material Planting Co., Ltd, Ningbo, 315444, Zhejiang, China

    Hongjun Shen

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  1. Dengpan Yin
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Contributions

DY, BP, QJ and DW: developed the concept and designed the lab experiments. DY, BP, HL, QL, YZ, NM, TC and HS: performed the experiments. DY and DW: wrote the paper. QJ and DW: edited the paper. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Dekai Wang.

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Yin, D., Pang, B., Li, H. et al. The complete chloroplast genome of the medical plant Huperzia crispata from the Huperziaceae family: structure, comparative analysis, and phylogenetic relationships. Mol Biol Rep 49, 11729–11741 (2022). https://doi.org/10.1007/s11033-022-07979-w

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