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The complete chloroplast genome sequence of Clerodendranthus spicatus, a medicinal plant for preventing and treating kidney diseases from Lamiaceae family

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Abstract

Background

Clerodendranthus spicatus (Thunb.) C. Y. Wu ex H. W. Li is one of the most important medicines for the treatment of nephrology in the southeast regions of China. To understand the taxonomic classification of Clerodendranthus species and identify species discrimination markers, we sequenced and characterized its chloroplast genome in the current study.

Methods and results

Total genomic DNA were isolated from dried leaves of C. spicatus and sequenced using an Illumina sequencing platform. The data were assembled and annotated by the NOVOPlasty software and CpGAVAS2 web service. The complete chloroplast genome of C. spicatus was 152,155 bp, including a large single-copy region of 83,098 bp, a small single-copy region of 17,665 bp, and a pair of inverted repeat regions of 25,696 bp. The Isoleucine codons are the most abundant, accounting for 4.17% of all codons. The codons of AUG, UUA, and AGA demonstrated a high degree of usage bias. Twenty-eight simple sequence repeats, thirty-six tandem repeats, and forty interspersed repeats were identified. The distribution of the specific rps19, ycf1, rpl2, trnH, psbA genes were analyzed. Analysis of the genetic distance of the intergenic spacer regions shows that ndhG-ndhI, accD-psaI, rps15-ycf1, rpl20-clpP, ccsA-ndhD regions have high K2p values. Phylogenetic analysis showed that C. spicatu is closely related to two Lamiaceae species, Tectona grandis, and Glechoma longituba.

Conclusions

In this study, we sequenced and characterized the chloroplast genome of C. spicatus. Phylogenomic analysis has identified species closely related to C. spicatus, which represent potential candidates for the development of drugs improving renal functions.

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Data availability

The cp genome sequence data of C. spicatus that support the findings of this study are openly available in NCBI at GenBank database with accession number MZ063774. (https://www.ncbi.nlm.nih.gov). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA723363, SRR14350365 and SAMN18814878, respectively.

Abbreviations

LSC:

Large single copy

SSC:

Small single copy

IR:

Inverted repeat

SSR:

Simple sequence repeat

ISSR:

Inter-simple sequence repeat

cpSSR:

Chloroplast simple sequence repeat

UPGMA:

Unweighted pair-group method with arithmetic means

DNA:

DeoxyriboNucleic acid

tRNA:

Transfer RNA

rRNA:

Ribosomal RNA

RSCU:

Relative synonymous codon usage

CAI:

Codon adaptation index

TRF:

Tandem repeat finder

MISA:

MicroSatellite identification tool

EMBOSS:

European molecular biology open software suite

K2p:

Kimura 2-parameters

CDS:

Coding sequence

ML:

Maximum likelihood

MEGA:

Molecular evolutionary genetics analysis

OD:

Optical density

PCR:

Polymerase chain reaction

GC:

Guanine and cytosine

IGS:

Inter genic spacer regions

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Acknowledgements

We want to thank Mr. Yang Ni, Jingling Li, Miss Jingwen Yue, and Mr. Junchen Zhou, who have provided support in analyzing the data.

Funding

This work was supported by funds from the National Science &Technology Fundamental Resources Investigation Program of China [2018FY100705], Chinese Academy of Medical Sciences, Innovation Funds for Medical Sciences (CIFMS) [2021–I2M-1-022], National Science Foundation [81872966], Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau [2020-ZJ-Y20], the Key Scientific Research Projects of Hunan Education Department [No. 20A467], Hunan technological innovation guidance project [2018SK52001]. The funders were not involved in the study design, data collection, and analysis, decision to publish, or manuscript preparation.

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Author notes

  1. Qing Du, Mei Jiang, Sihui Sun contributed equally to this work and are co-first authors.

Authors and Affiliations

  1. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People’s Republic of China

    Qing Du, Mei Jiang, Haimei Chen & Chang Liu

  2. College of Pharmacy, Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau, Qinghai Minzu University, Xining, Qinghai, 810007, People’s Republic of China

    Qing Du

  3. School of Pharmaceutical Sciences, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, People’s Republic of China

    Mei Jiang

  4. College of Pharmacy, Xiangnan University, Chenzhou, Hunan, 423000, People’s Republic of China

    Sihui Sun, Yong Li & Bin Wang

  5. College of Pharmacy, Heze University, Heze, Shandong, 274015, People’s Republic of China

    Liqiang Wang

  6. Institute of Medical Information & Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, People’s Republic of China

    Shengyu Liu

  7. Genepioneer Biotechnologies Inc., Nanjing, Jiangsu, 210023, People’s Republic of China

    Chuanbei Jiang & Haidong Gao

  8. Fresh Sky-Right (Beijing) International Science and Technology Co. Ltd, Beijing, 100187, People’s Republic of China

    Qing Du

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Contributions

CL conceived the study; MJ and LQW collected C. spicatus samples, extracted DNA for next-generation sequencing; DQ, SSH, SYL assembled, validated the assembled genome, performed data analysis, and drafted the manuscript; LQW, HMC, CBJ, HDG, BW and YL reviewed the manuscript critically. All authors have read and agreed on the contents of the manuscript.

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Correspondence to Bin Wang or Chang Liu.

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Du, Q., Jiang, M., Sun, S. et al. The complete chloroplast genome sequence of Clerodendranthus spicatus, a medicinal plant for preventing and treating kidney diseases from Lamiaceae family. Mol Biol Rep 49, 3073–3083 (2022). https://doi.org/10.1007/s11033-022-07135-4

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