The complete chloroplast genome and phylogenomic analysis of Camellia sinensis var. sinensis cultivar ‘Liupao’, a landrace from Guangxi, China

References

• Chinese Tea Tree Variety Annals Compilation Committee. 2001. The variety annals of tea trees in China. Shanghai: Shanghai Science and Technology Publishing House. p. 187.
   Google Scholar
• Chen J, Liao CS, Liu CM, Teng MY, Qin XJ. 2020. Introduction to Guangxi clonal tea varieties suitable for Liupao tea production. South China Agric. 14(19):53–56. doi: 10.19415/j.cnki.1673-890x.2020.19.014
   Google Scholar
• Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, et al. 2021. Twelve years of SAMtools and BCFtools. GigaScience. 10(2):giab008. doi: 10.1093/gigascience/giab008.
   PubMed Web of Science ®Google Scholar
• Dong M, Liu SQ, Xu ZG, Hu ZY, Ku WZ, Wu L. 2018. The complete chloroplast genome of an economic plant, Camellia sinensis cultivar Anhua, China. Mitochondrial DNA B Resour. 3(2):558–559. doi: 10.1080/23802359.2018.1462124.
   PubMed Web of Science ®Google Scholar
• Fan L, Li L, Hu YF, Huang YB, Hong YC, Zhang B. 2022. Complete chloroplast genomes of five classical Wuyi tea varieties (Camellia sinensis, Synonym: thea bohea L.), the most famous Oolong tea in China. Mitochondrial DNA B Resour. 7(4):655–657. doi: 10.1080/23802359.2022.2062263.
   PubMed Web of Science ®Google Scholar
• Hao WJ, Ma JQ, Ma CL, Jin JQ, Chen L. 2019. The complete chloroplast genome sequence of Camellia tachangensis F.C. Zhang (Theaceae). Mitochondrial DNA B Resour. 4(2):3344–3345. doi: 10.1080/23802359.2019.1673247.
   PubMed Web of Science ®Google Scholar
• Hao WJ, Wang SL, Yao MZ, Ma JQ, Xu YX, Chen L. 2019. The complete chloroplast genome of an albino tea, Camellia sinensis cultivar ‘Baiye 1’. Mitochondrial DNA B Resour. 4(2):3143–3144. doi: 10.1080/23802359.2019.1667889.
   PubMed Web of Science ®Google Scholar
• Huang H, Shi C, Liu Y, Mao S, Gao L. 2014. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol Biol. 14(1):151. doi: 10.1186/1471-2148-14-151.
   PubMedGoogle Scholar
• Huang HC, Jiang WX, Liang CX, Yao X, Nie HQ, Bai TD. 2021. EST-SSR-based analysis on genetic diversity of ancient Liupao tea trees and their progeny in Guangxi. Mol Plant Breed. 19(7):2410–2418.
   Google Scholar
• Jin JJ, Yu WB, Yang JB, Yu S, dePamphilis CW, Yi TS, Li DZ. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241. doi: 10.1186/s13059-020-02154-5.
   PubMed Web of Science ®Google Scholar
• Lee DJ, Kim CK, Lee TH, Lee SJ, Moon DG, Kwon YH, Cho JY. 2020. The complete chloroplast genome sequence of economical standard tea plant, Camellia sinensis L. cultivar Sangmok, in Korea. Mitochondrial DNA B Resour. 5(3):2835–2836. doi: 10.1080/23802359.2020.1790311.
   PubMedGoogle Scholar
• Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: 1303.3997v1302 [q-bio.GN].
   Google Scholar
• Li HT, Luo Y, Gan L, Ma PF, Gao LM, Yang JB, Cai J, Gitzendanner MA, Fritsch PW, Zhang T, et al. 2021. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol. 19(1):232. doi: 10.1186/s12915-021-01166-2.
   PubMed Web of Science ®Google Scholar
• Li L, Hu Y, He M, Zhang B, Wu W, Cai PM, Huo D, Hong YC. 2021. Comparative chloroplast genomes of the tea plants and the implications for the different origins of the two Assam teas. BMC Genomics. 22(1):138. doi: 10.1186/s12864-021-07427-2.
   PubMed Web of Science ®Google Scholar
• Li L, Hu YF, Wu LH, Chen RB, Luo SC. 2021. The complete chloroplast genome sequence of Camellia sinensis cv. Dahongpao: a most famous variety of Wuyi tea (Synonym: thea bohea L.). Mitochondrial DNA B Resour. 6(1):3–5. doi: 10.1080/23802359.2020.1844093.
   PubMed Web of Science ®Google Scholar
• Liu XD, Yang C, Tang ZB, Liu YF. 2013. Research on the genetic marks of tea plants that suitable to make Liubao tea and their roles in the breeding of Liubao tea. Chin Agric Sci Bull. 29(4):136–140.
   Google Scholar
• Ma SC, Yang M, Long ZR. 2016. Liubaocha Daguan. Guilin: Lijiang Publishing House. p. 245–250.
   Google Scholar
• Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 37(5):1530–1534. doi: 10.1093/molbev/msaa015.
   PubMed Web of Science ®Google Scholar
• Nakamura T, Yamada KD, Tomii K, Katoh K. 2018. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 34(14):2490–2492. doi: 10.1093/bioinformatics/bty121.
   PubMed Web of Science ®Google Scholar
• Qiao DH, Yang C, Guo Y. 2023. The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar ‘FuDingDaBaiCha’. Mitochondrial DNA B Resour. 8(1):100–104. doi: 10.1080/23802359.2022.2161327.
   PubMed Web of Science ®Google Scholar
• Qiu RJ, Ma SC, Huang LY, Lonag ZR, Yu CP, Cao ZH, Zheng XQ. 2017. Preliminary study on Liupao tea germplasm resources. J Tea. 43(1):28–31.
   Google Scholar
• Rawal HC, Kumar PM, Bera B, Singh NK, Mondal TK. 2020. Decoding and analysis of organelle genomes of Indian tea (Camellia assamica) for phylogenetic confirmation. Genomics. 112(1):659–668. doi: 10.1016/j.ygeno.2019.04.018.
   PubMed Web of Science ®Google Scholar
• Shi C, Liu Y, Huang H, Xi EH, Zhang HB, Gao LZ, Su B. 2013. Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PloS One. 8(3):e59620. doi: 10.1371/journal.pone.0059620.
   PubMed Web of Science ®Google Scholar
• Shi LC, Chen HM, Jiang M, Wang LQ, Wu X, Huang LF, Liu C. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47(W1):W65–W73. doi: 10.1093/nar/gkz345.
   PubMed Web of Science ®Google Scholar
• Wang F, Zhang BH, Wen D, Liu R, Yao XZ, Chen Z, Mu R, Pei HM, Liu M, Song BX, et al. 2022. Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers. Front Plant Sci. 13:1004387. doi: 10.3389/fpls.2022.1004387.
   PubMed Web of Science ®Google Scholar
• Wang LB, Huang LY, Teng CQ, Wu LY, Cheng H, Yu CP, Wang LY. 2022. Genetic and phylogenetic analysis for germplasm resources of Camellia sinensis from Wuzhou city. J Tea Sci. 42(5):601–609.
   Google Scholar
• Wang PJ, Yu JX, Jin S, Chen S, Yue C, Wang WL, Gao SL, Cao HL, Zheng YC, Gu MY, et al. 2021. Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome. Hortic Res. 8(1):107.
   PubMed Web of Science ®Google Scholar
• Wang XC, Feng H, Chang YX, Ma CL, Wang LY, Hao XY, Li A, Cheng H, Wang L, Cui P, et al. 2020. Population sequencing enhances understanding of tea plant evolution. Nat Commun. 11(1):4447. doi: 10.1038/s41467-020-18228-8.
   PubMed Web of Science ®Google Scholar
• Wei CL, Yang H, Wang SB, Zhao J, Liu C, Gao LP, Xia EH, Lu Y, Tai YL, She GB, et al. 2018. Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci U S A. 115(18):E4151–E4158. doi: 10.1073/pnas.1719622115.
   PubMed Web of Science ®Google Scholar
• Wickham H. 2016. Data Analysis. In: Wickham H, editor. Ggplot2: elegant graphics for data analysis. Cham: springer International Publishing. p. 189–201.
   Google Scholar
• Xia EH, Tong W, Hou Y, An YL, Chen LB, Wu Q, Liu YL, Yu J, Li FD, Li RP, et al. 2020. The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into its genome evolution and adaptation. Mol Plant. 13(7):1013–1026. doi: 10.1016/j.molp.2020.04.010.
   PubMed Web of Science ®Google Scholar
• Xia EH, Zhang HB, Sheng J, Li K, Zhang QJ, Kim C, Zhang Y, Liu Y, Zhu T, Li W, et al. 2017. The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis. Mol Plant. 10(6):866–877. doi: 10.1016/j.molp.2017.04.002.
   PubMed Web of Science ®Google Scholar
• Yan MH, Liu K, Wang M, Lyu Y, Zhang Q. 2021. Complete chloroplast genome of Camellia sinensis cv. Xinyang 10 and its phylogenetic evolution. J Tea Sci. 41(6):777–788.
   Google Scholar
• Yang C, Qiao DH, Guo Y, Chen J, Chen ZW. 2022. The complete chloroplast genome sequence of Camellia sinensis cultivar ‘Qiancha1’ from Guizhou Province, China. Mitochondrial DNA B Resour. 7(2):404–405. doi: 10.1080/23802359.2021.2005490.
   PubMed Web of Science ®Google Scholar
• Ye JP, He TQ, Jiang MG. 2009. Adaptability test of Liupao Brick tea of Lingyun Baihao tea variety. Guangdong Tea Ind. (6):33–35.
   Google Scholar
• Ye JP, He TQ, Jiang MG. 2010. Techniques for manufacture of Liupao Brick tea by leaves of Linyun Baihao tea variety. China Tea. 32(8):22–23.
   Google Scholar
• Ye XQ, Zhao ZH, Zhu QW, Wang YY, Lin ZX, Ye CY, Fan LJ, Xu HR. 2014. Entire chloroplast genome sequence of tea (Camellia sinensis cv. Longjing 43): a molecular phylogenetic analysis. J Zhejiang Univ. 40(4):404–412.
   Google Scholar
• Yu XQ, Gao LM, Soltis DE, Soltis PS, Yang JB, Fang L, Yang SX, Li DZ. 2017. Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family. New Phytol. 215(3):1235–1248. doi: 10.1111/nph.14683.
   PubMed Web of Science ®Google Scholar
• Zeng CX, Hollingsworth PM, Yang J, He ZS, Zhang ZR, Li DZ, Yang JB. 2018. Genome skimming herbarium specimens for DNA barcoding and phylogenomics. Plant Methods. 14(:43. doi: 10.1186/s13007-018-0300-0.
   PubMed Web of Science ®Google Scholar
• Zhang F, Li W, Gao C, Zhang D, Gao L. 2019. Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica. Sci Data. 6(1):209. doi: 10.1038/s41597-019-0201-8.
   PubMed Web of Science ®Google Scholar
• Zhang F, Wen LX, Peng JR, Huang SH, Tan YW, Huang XX. 2018. Research progress of Guangxi Liupao tea. J Tea Commun. 45(3):13–16.
   Google Scholar
• Zhang QJ, Li W, Li K, Nan H, Shi C, Zhang Y, Dai ZY, Lin YL, Yang XL, Tong Y, et al. 2020. The chromosome-level reference genome of tea tree unveils recent bursts of non-autonomous LTR retrotransposons in driving genome size evolution. Mol Plant. 13(7):935–938. doi: 10.1016/j.molp.2020.04.009.
   PubMed Web of Science ®Google Scholar
• Zhang WY, Zhang YJ, Qiu HJ, Guo YF, Wan HL, Zhang XL, Scossa F, Alseekh S, Zhang QH, Wang P, et al. 2020. Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nat Commun. 11(1):3719. doi: 10.1038/s41467-020-17498-6.
   PubMed Web of Science ®Google Scholar
• Zhang XT, Chen S, Shi LQ, Gong DP, Zhang SC, Zhao Q, Zhan DL, Vasseur L, Wang YB, Yu JX, et al. 2021. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nat Genet. 53(8):1250–1259. doi: 10.1038/s41588-021-00895-y.
   PubMed Web of Science ®Google Scholar
• Zhou WQ, Nong YF, Su SM, Guo WS, Zhang XY. 2013. On the relationship between the quality of Liupao tea and Liupao population tea plants. Chin for Food Ind. (6):34–35.
   Google Scholar
• Zhou YH, Qiao XY, Ma CL, Qiao TT, Jin JQ, Yao MZ, Chen L. 2011. Genetic diversity and structure of tea landraces from Guangxi based on EST-SSR analysis. Sci Silvae Sin. 47(3):59–67.
   Google Scholar