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Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships

  • Plant Genetics • Original Paper
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A Correction to this article was published on 10 July 2023

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Abstract

The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar ‘Zhuyeqi’, followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of ‘Zhuyeqi’ was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of ‘Zhuyeqi’ were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of ‘Zhuyeqi’ were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to ‘Zhuyeqi’, indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.

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Data availability

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession OL450428.1. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA779759, SRR16922592, and SAMN23075201, respectively.

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Funding

This work was funded by various sources, including the Outstanding Youth Project Supported by Scientific Research Fund of Hunan Provincial Education Department, grant number: 21B0782. Additionally, it received support from the Scientific Research Fund of Hunan Provincial Education Department, grant number: 22A0608.

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Authors and Affiliations

  1. College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China

    Zhiyin Chen, Qing Liu, Ying **ao, Guihua Zhou, **g Bai & Yihui Gong

  2. Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, People’s Republic of China

    Hua Huang

  3. Tea Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China

    Penghui Yu

Authors
  1. Zhiyin Chen
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  2. Qing Liu
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  4. Guihua Zhou
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  5. Penghui Yu
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  7. Hua Huang
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Contributions

Zhiyin Chen: investigation, data curation, methodology, software, validation, writing — original draft, funding acquisition. Qing Liu and Ying **ao and Guihua Zhou: investigation, data curation, software, methodology, validation. Penghui Yu and **g Bai: investigation, data curation, software, methodology, validation. Hua Huang and Yihui Gong: conceptualization, investigation, data curation, methodology, writing — review and editing, visualization, validation, project administration, supervision, resources, funding acquisition.

Corresponding authors

Correspondence to Hua Huang or Yihui Gong.

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The experiments in this study comply with the current laws of China.

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The corresponding authors declare, on behalf of all co-authors, that the work described is original, previously unpublished research, and not under consideration for publication elsewhere.

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Communicated by: Izabela Pawłowicz

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The original online version of this article was revised: The original version of this article contains an error. The author affiliations has been re-ordered to follow the originally submitted sequence in the accepted manuscript.

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Chen, Z., Liu, Q., **ao, Y. et al. Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships. J Appl Genetics 64, 419–429 (2023). https://doi.org/10.1007/s13353-023-00767-7

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