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The complete chloroplast genome and characteristics analysis of Callistemon rigidus R.Br.

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Abstract

Callistemon rigidus R.Br. one of the traditional Chinese medicinal plants, is acrid-flavored and mild-natured, with the prominent effects reducing swelling, resolving phlegm, and dispelling rheumatism. Clinically, it has been commonly used to treat cold, cough and asthma, pain and swelling from impact injuries, eczema, rheumatic arthralgia. The chloroplast genome study on Callistemon rigidus R.Br. is a few seen. This study demonstrates the data collected from the assembly and annotation of the chloroplast (cp) genome of Callistemon rigidus R.Br., followed by furthers comparative analysis with the cp genomes of closely related species. C. rigidus R.Br. showed a cp genome in the size of 158, 961 bp long with 36.78% GC content, among which a pair of inverted repeats (IRs) of 26, 671 bp separated a large single-copy (LSC) region of 87, 162 bp and a small single-copy (SSC) region of 18, 457 bp. Altogether 131 genes were hosted, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. 284 simple sequence repeats (SSRs) were also marked out. A comparative analysis of the genome structure and the sequence data of closely related species unveiled the conserved gene order in the IR and LSC/SSC regions, a quite constructive finding for future phylogenetic research. Overall, this study providing C. rigidus R.Br. genomic resources could positively contribute to the evolutionary study and the phylogenetic reconstruction of Myrtaceae.

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Acknowledgements

We would like to thank all researchers that read and helped us to perform this project.

Funding

The study was supported by the start-up foundation of introducing talents for scientific research, Nanjing Institute of Industry Technology (No. 201050619YK701), and the start-up foundation of Nanjing Forestry University (No. 163108059).

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Author notes

  1. Fenxiang Liu and Ali Movahedi contributed equally to this work.

Authors and Affiliations

  1. School of Business and Trade, Nanjing Institute of Industry Technology, Nanjing, 210023, China

    Fenxiang Liu, Jigang Xie & Yu Zhang

  2. Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China

    Ali Movahedi

  3. Department of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, 210023, China

    Wenguo Yang

  4. Genepioneer Biotechnologies Inc., Nanjing, 210023, China

    Lei Xu

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  1. Fenxiang Liu
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Contributions

This experiment was designed and the manuscript was written by FXL. Also, LX, JX, and YZ reviewed and confirmed. This study was supervised and funded by WY and AM.

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Correspondence to Ali Movahedi or Wenguo Yang.

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Supplementary file1 Figure S1. Statistical chart of long repeats. (JPG 147 kb)

11033_2020_5567_MOESM2_ESM.jpg

Supplementary file2 Figure S2. Mauve alignment of plastid genomes of 8 species of Myrtaceae. The C. rigidus R.Br.genome is shown at the top as the reference genome. Within each of the alignments, local collinear blocks are represented by blocks of the same color connected by lines. Note: The rectangular block in the figure represents the similarity between genomes, and the lines between the rectangular blocks represent the collinear relationship. The short squares represent the gene locations of the genomes. Among them, white represents CDs, green represents tRNA, and red represents rRNA (JPG 549 kb)

11033_2020_5567_MOESM3_ESM.xlsx

Supplementary file3 Table S1. Summary of the plastid genome features of the 30 Myrtaceae, 1 Punica granatum, and 1 Lagerstroemia venusta studied. (XLSX 13 kb)

11033_2020_5567_MOESM4_ESM.xlsx

Supplementary file4 Table S2. Codon-anticodon recognition patterns and codon usage of the Callistemon rigidus R.Br. plastid (XLSX 12 kb)

Supplementary file5 Table S3. Intron number of ycf3 in the Callistemon rigidus R.Br. plastid (XLSX 9 kb)

11033_2020_5567_MOESM6_ESM.xlsx

Supplementary file6 Table S4. Simple sequence repeats (SSRs) in the Callistemon rigidus R.Br. plastid genome (XLSX 19 kb)

Supplementary file7 Table S5. Long repeat sequences in the Callistemon rigidus R.Br. plastid genome (XLSX 11 kb)

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Liu, F., Movahedi, A., Yang, W. et al. The complete chloroplast genome and characteristics analysis of Callistemon rigidus R.Br.. Mol Biol Rep 47, 5013–5024 (2020). https://doi.org/10.1007/s11033-020-05567-4

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