Abstract
Camellia sinensis (L.) O. Kuntze var. assamica cv. Duntsa (herein C. duntsa) has been used since ancient times in Hunan, China. To understand the genetic background information of C. duntsa and clarify the relationship between C. duntsa and other tea cultivars and varieties (taxa), the complete chloroplast genome of C. duntsa was sequenced using the Illumina NovaSeq platform, which was then compared with other published chloroplast genomes from tea plants. The C. duntsa chloroplast genome is 157,025 bp in length with a guanine–cytosine content of 37.30%. It consists of a short single-copy region (18,277 bp), a large single-copy region (86,586 bp), and two inverted repeat regions (26,081 bp). A total of 135 genes were identified, comprising 87 protein-coding genes, eight ribosomal RNA genes, 37 transfer RNA genes, and three pseudogene genes (two ycf15 and one ycf1). In addition, 968 long repetitive sequences were detected by comparative analysis with other tea plant chloroplast genes, of which 409 were forward, 557 were palindromic, and two were reverse. A total of 241–249 simple sequence-repeat loci were analyzed for comparison; most of these were single nucleic acid loci composed of A/T. In addition, six mutation hotspots (rpoC1, ycf1, petB, ndhD, rpl16, and rpoC2) were identified. Phylogenetic analysis showed that C. duntsa has a relatively close evolutionary relationship with C. sinensis var. sinensis cultivars anhua and fudingdabaicha and with Camellia ptilophylla Hung T. Chang. These results can provide valuable information for a better understanding of chloroplast evolution in Camellia species.
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Data availability
The newly sequenced and annotated chloroplast genome has been submitted to NCBI (https://www.ncbi.nlm.nih.gov; Accession No. OL450397).
Abbreviations
- C. duntsa :
-
Camellia sinensis var. Assamica cv. Duntsa
- C. assamica :
-
Camellia sinensis var. Assamica
- C. kuntza :
-
Camellia sinensis cv. Kuntza
- C. dehungensis :
-
Camellia sinensis var. Dehungensis
- C. pubilimba :
-
Camellia sinensis var. Pubilimba
- C. sinensis :
-
Camellia sinensis var. sinensis
- C. yunkang 10:
-
Camellia sinensis var. assamica cv. Yunkang10
- C. anhua:
-
Camellia sinensis var. sinensis cv. Anhua
- C. baiye 1:
-
Camellia sinensis var. sinensis cv. Baiye 1
- C. wuyi Narcissus:
-
Camellia sinensis var. sinensis cv. Wuyi Narcissus
- C. baijiguan:
-
Camellia sinensis var. sinensis cv. Baijiguan
- C. shuijingui:
-
Camellia sinensis var. sinensis cv. Shuijingui
- C. fudingdabaicha:
-
Camellia sinensis var. sinensis cv. Fudingdabaicha
- C. taliensis :
-
Camellia taliensis
- C. grandibracteata :
-
Camellia grandibracteata
- C. ptilophylla :
-
Camellia ptilophylla
- C. songzhong:
-
Camellia sinensis var. sinensis cv. Songzhong
- C. huangjinye:
-
Camellia sinensis var. sinensis cv. Huangjinye
- C. huangjinyacha:
-
Camellia sinensis var. sinensis cv. Huangjinyacha
- C. zijuanhua:
-
Camellia sinensis var. sinensis cv. Zijuanhua
- C. xilian 1:
-
Camellia sinensis var. sinensis cv. Xilian 1
References
Chen X, Zhou J, Cui Y et al (2018) Identification of Ligularia herbs using the complete chloroplast genome as a super-barcode. Front Pharmacol 9:695
Chen X, Cui Y, Nie L et al (2019a) Identification and phylogenetic analysis of the complete chloroplast genomes of three Ephedra herbs containing ephedrine. Biomed Res Int 2019:e5921725. https://doi.org/10.1155/2019/5921725
Chen Y, Hu N, Wu H (2019b) Analyzing and characterizing the chloroplast genome of Salix wilsonii. Biomed Res Int 2019:e5190425. https://doi.org/10.1155/2019/5190425
Chi X, Wang J, Gao Q et al (2018) The complete chloroplast genomes of two Lancea species with comparative analysis. Molecule 23:602. https://doi.org/10.3390/molecules23030602
Daniell H, Lin C-S, Yu M, Chang W-J (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17:134. https://doi.org/10.1186/s13059-016-1004-2
Fu Z, Song J, Jameson PE (2017) A rapid and cost effective protocol for plant genomic DNA isolation using regenerated silica columns in combination with CTAB extraction. J Integr Agric 16:1682–1688. https://doi.org/10.1016/S2095-3119(16)61534-4
Gu C, Ma L, Wu Z et al (2019) Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales. BMC Plant Biol 19:281. https://doi.org/10.1186/s12870-019-1870-3
Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol 28:583–600. https://doi.org/10.1093/molbev/msq229
Huang H, Shi C, Liu Y et al (2014) Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol Biol 14:151. https://doi.org/10.1186/1471-2148-14-151
Jiao L, Lu Y, He T et al (2019) A strategy for developing high-resolution DNA barcodes for species discrimination of wood specimens using the complete chloroplast genome of three Pterocarpus species. Planta 250:95–104. https://doi.org/10.1007/s00425-019-03150-1
Li Y, Sylvester SP, Li M et al (2019) The complete plastid genome of Magnolia zenii and genetic comparison to Magnoliaceae species. Molecules 24:261. https://doi.org/10.3390/molecules24020261
Li H-T, Luo Y, Gan L et al (2021a) Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol 19:232. https://doi.org/10.1186/s12915-021-01166-2
Li L, Hu Y, He M et al (2021b) Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia. BMC Genom 22:138. https://doi.org/10.1186/s12864-021-07427-2
Li J, Tang H, Luo H et al (2023) Complete mitochondrial genome assembly and comparison of Camellia sinensis var. Assamica cv. Duntsa. Front Plant Sci 14:1117002
Liu S, An Y, Li F et al (2018) Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers for genetic studies in tea plant (Camellia sinensis). Mol Breed 38:59. https://doi.org/10.1007/s11032-018-0824-z
Maier RM, Neckermann K, Igloi GL, Kössel H (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251:614–628. https://doi.org/10.1006/jmbi.1995.0460
Palmer JD, Stein DB (1986) Conservation of chloroplast genome structure among vascular plants. Curr Genet 10:823–833. https://doi.org/10.1007/BF00418529
Peng J, Zhao Y, Dong M et al (2021) Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes. BMC Ecol Evol 21:71. https://doi.org/10.1186/s12862-021-01800-1
Qin Z, Cai Z, Xia G, Wang M (2013) Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants. BMC Genom 14:56. https://doi.org/10.1186/1471-2164-14-56
Rawal HC, Borchetia S, Bera B et al (2021) Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea. Sci Rep 11:110. https://doi.org/10.1038/s41598-020-80431-w
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC et al (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34:3299–3302. https://doi.org/10.1093/molbev/msx248
Sun J, Wang Y, Liu Y et al (2020) Evolutionary and phylogenetic aspects of the chloroplast genome of Chaenomeles species. Sci Rep 10:11466. https://doi.org/10.1038/s41598-020-67943-1
Tian X, Ye J, Song Y (2019) Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae. PeerJ 7:e7662. https://doi.org/10.7717/peerj.7662
Tillich M, Lehwark P, Pellizzer T et al (2017) GeSeq—versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:W6–W11. https://doi.org/10.1093/nar/gkx391
Vijayan K, Zhang W-J, Tsou C-H (2009) Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences. Am J Bot 96:1348–1360. https://doi.org/10.3732/ajb.0800205
Wang X, Zhou T, Bai G, Zhao Y (2018) Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships. Sci Rep 8:12379. https://doi.org/10.1038/s41598-018-30398-6
Wicke S, Schneeweiss GM, dePamphilis CW et al (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76:273–297. https://doi.org/10.1007/s11103-011-9762-4
Yang A-H, Zhang J-J, Yao X-H, Huang H-W (2011) Chloroplast microsatellite markers in Liriodendron tulipifera (Magnoliaceae) and cross-species amplification in L. chinense. Am J Bot 98:e123–e126. https://doi.org/10.3732/ajb.1000532
Yang J-B, Yang S-X, Li H-T et al (2013) Comparative chloroplast genomes of Camellia species. PLoS ONE 8:e73053. https://doi.org/10.1371/journal.pone.0073053
Yang J, Vázquez L, Chen X et al (2017) Development of chloroplast and nuclear DNA markers for Chinese Oaks (Quercus Subgenus Quercus) and assessment of their utility as DNA barcodes. Front Plant Sci 8:256182
Zhang W, Zhao Y, Yang G et al (2019) Determination of the evolutionary pressure on Camellia oleifera on Hainan Island using the complete chloroplast genome sequence. PeerJ 7:e7210. https://doi.org/10.7717/peerj.7210
Zhu H, Liu J, Li H et al (2023) Complete chloroplast genome structural characterization and comparative analysis of Viburnum japonicum (adoxaceae). Forests 14:1819. https://doi.org/10.3390/f14091819
Acknowledgements
The authors thank Guo-Li Xiao, Da-Yong Liu, Wen-Hua Zhu, and Rong-Fu Yang for their help with sample collection.
Funding
This work was supported by the Natural Science Foundation of Hunan Province (Grant No. S2024JJQYLH0589).
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JL, L-ZX, and HL: conceived and designed the study. X-YQ, HT, and JT: performed data collection and database creation. X-YQ, YQ, and T-TL: performed data analysis. JL and X-YQ: performed sample collection. JL: wrote the first draft of the manuscript. L-ZX and HL: revised the paper. The final version of the manuscript has been read and approved by all authors. All listed authors have made substantial, direct, and intellectual contributions to the work and approved it for publication.
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Li, J., Qiu, XY., Qin, Y. et al. The chloroplast genome of Camellia sinensis var. assamica cv. Duntsa (Theaceae) and comparative genome analysis: mutational hotspots and phylogenetic relationships. Genet Resour Crop Evol (2024). https://doi.org/10.1007/s10722-024-02002-6
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DOI: https://doi.org/10.1007/s10722-024-02002-6