Biotechnology Bulletin ›› 2024, Vol. 40 ›› Issue (2): 20-30.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0451
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YANG Yu-qing1(), TAN Juan1, WANG Fang1, PENG Shun-li1, CHEN Jie1, TAN Ming-yan1, LYU Mei-yan1, ZHOU Fu-yu2(), LIU Sheng-chuan1()
Received:
2023-05-11
Online:
2024-02-26
Published:
2024-03-13
Contact:
ZHOU Fu-yu, LIU Sheng-chuan
E-mail:1067503542@qq.com;zfygztea@126.com;gtscliu@163.com
YANG Yu-qing, TAN Juan, WANG Fang, PENG Shun-li, CHEN Jie, TAN Ming-yan, LYU Mei-yan, ZHOU Fu-yu, LIU Sheng-chuan. Research and Application Progress in Chloroplast Genome of Tea Plant(Camellia sinensis)[J]. Biotechnology Bulletin, 2024, 40(2): 20-30.
Fig. 1 Comparison of the LSC, IR and SSC border regions among the chloroplast genomes of five tea cultivars Boxes above and below the lines are forward strands and reverse strands, respectively
资源 Resource | 来源 Origin | 登录号 Accession | 叶绿体基因组特征 Chloroplast genome characteristics | 参考文献Reference | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Genome/bp | CDS/bp | GC/% | LSC/bp | SSC/bp | IR/bp | Gene | tRNA | rRNA | ||||
Chamnok | 韩国 Korea | LC525850 | 156 356 | ND | ND | ND | ND | ND | ND | ND | ND | |
黔茶1号 Qiancha1 | 中国 China | MZ043860 | 157 024 | ND | 37.30 | 86 585 | 18 277 | 26 081 | 137 | 37 | 8 | [ |
大红袍 Dahongpao | 中国 China | MT773374 | 157 077 | ND | 37.29 | 86 633 | 18 282 | 26 081 | 137 | 28 | 4 | [ |
武夷水仙 Wuyi Narcissus | 中国 China | MT612435 | 156 762 | ND | ND | 86 301 | 18 079 | 26 090 | 137 | 37 | 8 | [ |
信阳10号 Xinyang 10 | 中国 China | MZ153237 | 157 041 | ND | 37.29 | 86 594 | 18 291 | 26 078 | 113 | 30 | 4 | [ |
白叶1号 Baiye 1 | 中国 China | MN086819 | 156 691 | ND | 37.30 | 86 585 | 18 276 | 26 083 | 130 | 35 | 8 | [ |
安化茶 Anhua | 中国 China | MH042531 | 157 025 | 80 620 | 37.30 | 86 585 | 18 276 | 26 082 | 135 | 37 | 8 | [ |
云抗10号 Yunkang 10 | 中国 China | MH019307 | 157 100 | 79 092 | 37.29 | ND | ND | ND | 141 | 47 | 8 | [ |
白鸡冠 Baijiguan | 中国 China | MT773373 | 157 099 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
肉桂 Rougui | 中国 China | MT773375 | 157 093 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
水金龟 Shuijingui | 中国 China | MT773376 | 157 126 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
铁罗汉 Tieluohan | 中国 China | MT773377 | 157 041 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
半天妖 Bantianyao | 中国 China | MW046255 | 157 024 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
鸭屎香 Yashixiang | 中国 China | OL690370 | 157 057 | ND | ND | ND | ND | ND | ND | ND | ND | |
印度茶 Indian tea | 印度 India | MH460639 | 157 353 | ND | 37.34 | 87 213 | 18 078 | 26 031 | 126 | 29 | 8 | [ |
龙井43 Longjin 43 | 中国 China | KF562708 | 157 085 | 80 650 | 37.30 | 86 642 | 18 283 | 26 080 | 134 | 39 | 8 | [ |
铁观音 Tieguanyin | 中国 China | MW148820 | 157 126 | ND | 37.30 | 86 904 | 18 532 | 26 095 | 132 | 37 | 8 | [ |
黄金芽 Huangjinya | 中国 China | ND | 158 916 | ND | 37.22 | 86 654 | 16 463 | 27 900 | 113 | 24 | 5 | [ |
华白1号 Huabai 1 | 中国 China | ND | 157 028 | 79 093 | 37.30 | 86 590 | 18 277 | 26 081 | 113 | 24 | 5 | [ |
西莲1号 Xilian 1 | 中国 China | ND | 157 038 | ND | 37.30 | 86 612 | 18 282 | 26 072 | 114 | 30 | 4 | [ |
福鼎大白茶 Fuding Dabaicha | 中国 China | MZ817088 | 157 025 | ND | 37.30 | 86 585 | 18 277 | 26 081 | 137 | 37 | 8 | [ |
德宏茶 Dehungensis | 中国 China | KJ806279 | 157 110 | ND | 37.30 | 86 656 | 18 276 | 26 089 | ND | ND | ND | [ |
白毛茶 C. sinensis var. pubilimba | 中国 China | KJ806280 | 157 086 | 80 622 | 37.30 | 86 679 | 18 267 | 26 096 | ND | ND | ND | [ |
茶 C. sinensis var. sinensis | 中国 China | KJ806281 | 157 117 | 80 542 | 37.29 | 86 663 | 18 276 | 26 089 | ND | ND | ND | [ |
阿萨姆茶 C. sinensis var. assamica | 中国 China | ND | 157 121 | ND | 37.29 | 86 651 | 18 286 | 26 092 | ND | ND | ND | [ |
阿萨姆茶株系25E C. sinensis var. assamica isolate 25E | 中国 China | MH394410 | 157 028 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
阿萨姆茶株系25D C. sinensis var. assamica isolate 25D | 中国 China | MH394409 | 157 028 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
阿萨姆茶株系25B C. sinensis var. assamica isolate 25B | 中国 China | MH394408 | 157 028 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
阿萨姆茶株系25A C. sinensis var. assamica isolate 25A | 中国 China | MH394407 | 157 029 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
毛叶茶 C. ptilophylla | 中国 China | ND | 157 097 | ND | 37.30 | 86 631 | 18 286 | 26 090 | 132 | 34 | 8 | [ |
阿萨姆茶 C. sinensis var. assamica | 中国 China | JQ975030 | 157 162 | ND | ND | 86 609 | 18 285 | 26 134 | 133 | ND | ND | [ |
Sangmok | 韩国 Korea | LC488797 | 153 044 | ND | 37.20 | 64 665 | 19 155 | 24 627 | 97 | 29 | 5 | [ |
Kuntze | 韩国 Korea | KC143082 | 157 103 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
Table 1 Published chloroplast genomes of tea plants
资源 Resource | 来源 Origin | 登录号 Accession | 叶绿体基因组特征 Chloroplast genome characteristics | 参考文献Reference | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Genome/bp | CDS/bp | GC/% | LSC/bp | SSC/bp | IR/bp | Gene | tRNA | rRNA | ||||
Chamnok | 韩国 Korea | LC525850 | 156 356 | ND | ND | ND | ND | ND | ND | ND | ND | |
黔茶1号 Qiancha1 | 中国 China | MZ043860 | 157 024 | ND | 37.30 | 86 585 | 18 277 | 26 081 | 137 | 37 | 8 | [ |
大红袍 Dahongpao | 中国 China | MT773374 | 157 077 | ND | 37.29 | 86 633 | 18 282 | 26 081 | 137 | 28 | 4 | [ |
武夷水仙 Wuyi Narcissus | 中国 China | MT612435 | 156 762 | ND | ND | 86 301 | 18 079 | 26 090 | 137 | 37 | 8 | [ |
信阳10号 Xinyang 10 | 中国 China | MZ153237 | 157 041 | ND | 37.29 | 86 594 | 18 291 | 26 078 | 113 | 30 | 4 | [ |
白叶1号 Baiye 1 | 中国 China | MN086819 | 156 691 | ND | 37.30 | 86 585 | 18 276 | 26 083 | 130 | 35 | 8 | [ |
安化茶 Anhua | 中国 China | MH042531 | 157 025 | 80 620 | 37.30 | 86 585 | 18 276 | 26 082 | 135 | 37 | 8 | [ |
云抗10号 Yunkang 10 | 中国 China | MH019307 | 157 100 | 79 092 | 37.29 | ND | ND | ND | 141 | 47 | 8 | [ |
白鸡冠 Baijiguan | 中国 China | MT773373 | 157 099 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
肉桂 Rougui | 中国 China | MT773375 | 157 093 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
水金龟 Shuijingui | 中国 China | MT773376 | 157 126 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
铁罗汉 Tieluohan | 中国 China | MT773377 | 157 041 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
半天妖 Bantianyao | 中国 China | MW046255 | 157 024 | ND | 37.30 | ND | ND | ND | 137 | 37 | 8 | [ |
鸭屎香 Yashixiang | 中国 China | OL690370 | 157 057 | ND | ND | ND | ND | ND | ND | ND | ND | |
印度茶 Indian tea | 印度 India | MH460639 | 157 353 | ND | 37.34 | 87 213 | 18 078 | 26 031 | 126 | 29 | 8 | [ |
龙井43 Longjin 43 | 中国 China | KF562708 | 157 085 | 80 650 | 37.30 | 86 642 | 18 283 | 26 080 | 134 | 39 | 8 | [ |
铁观音 Tieguanyin | 中国 China | MW148820 | 157 126 | ND | 37.30 | 86 904 | 18 532 | 26 095 | 132 | 37 | 8 | [ |
黄金芽 Huangjinya | 中国 China | ND | 158 916 | ND | 37.22 | 86 654 | 16 463 | 27 900 | 113 | 24 | 5 | [ |
华白1号 Huabai 1 | 中国 China | ND | 157 028 | 79 093 | 37.30 | 86 590 | 18 277 | 26 081 | 113 | 24 | 5 | [ |
西莲1号 Xilian 1 | 中国 China | ND | 157 038 | ND | 37.30 | 86 612 | 18 282 | 26 072 | 114 | 30 | 4 | [ |
福鼎大白茶 Fuding Dabaicha | 中国 China | MZ817088 | 157 025 | ND | 37.30 | 86 585 | 18 277 | 26 081 | 137 | 37 | 8 | [ |
德宏茶 Dehungensis | 中国 China | KJ806279 | 157 110 | ND | 37.30 | 86 656 | 18 276 | 26 089 | ND | ND | ND | [ |
白毛茶 C. sinensis var. pubilimba | 中国 China | KJ806280 | 157 086 | 80 622 | 37.30 | 86 679 | 18 267 | 26 096 | ND | ND | ND | [ |
茶 C. sinensis var. sinensis | 中国 China | KJ806281 | 157 117 | 80 542 | 37.29 | 86 663 | 18 276 | 26 089 | ND | ND | ND | [ |
阿萨姆茶 C. sinensis var. assamica | 中国 China | ND | 157 121 | ND | 37.29 | 86 651 | 18 286 | 26 092 | ND | ND | ND | [ |
阿萨姆茶株系25E C. sinensis var. assamica isolate 25E | 中国 China | MH394410 | 157 028 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
阿萨姆茶株系25D C. sinensis var. assamica isolate 25D | 中国 China | MH394409 | 157 028 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
阿萨姆茶株系25B C. sinensis var. assamica isolate 25B | 中国 China | MH394408 | 157 028 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
阿萨姆茶株系25A C. sinensis var. assamica isolate 25A | 中国 China | MH394407 | 157 029 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
毛叶茶 C. ptilophylla | 中国 China | ND | 157 097 | ND | 37.30 | 86 631 | 18 286 | 26 090 | 132 | 34 | 8 | [ |
阿萨姆茶 C. sinensis var. assamica | 中国 China | JQ975030 | 157 162 | ND | ND | 86 609 | 18 285 | 26 134 | 133 | ND | ND | [ |
Sangmok | 韩国 Korea | LC488797 | 153 044 | ND | 37.20 | 64 665 | 19 155 | 24 627 | 97 | 29 | 5 | [ |
Kuntze | 韩国 Korea | KC143082 | 157 103 | ND | ND | ND | ND | ND | ND | ND | ND | [ |
分类 Category | 分组 Group | 基因名 Name of gene |
---|---|---|
光合作用 Photosynthesis | 光合系统I Photosynthetic I | psaA, psaB, psaC, psaI, psaJ |
光合系统II Photosynthetic II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
ATP合成酶ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | |
NADH脱氢酶 NADH dehydrogenase | ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH ndhI, ndhJ, ndhK | |
二磷酸核酮糖羧化酶大亚基Ribulose diphosphate carboxylase large subunit | rbcL | |
细胞色素复合物 Cytochrome complex | petA, petB, petD, petG, petL, petN | |
依赖ATP的蛋白酶单元p ATP-dependent protease subunit p | clpP | |
自我复制 Self-replication | 转运RNA tRNA | trnA-UGC, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnL-CAA, trnL-UAA, trnL-UAG, trnfM-CAU, trnM-CAU, trnN-GUU, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC, trnW-CCA, trnY-GUA |
核糖体RNA rRNA | rrn16, rrn23, rrn4.5, rrn5 | |
RNA聚合酶亚基RNA polymerase subunit | rpoA, rpoB, rpoC1, rpoC2 | |
核糖体大亚基Ribosomal large subunit | rpl2, rpl14, rpl16, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 | |
核糖体小亚基Ribosomal small subunit | rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19 | |
生物合成 Biosynthesis | 成熟酶Maturase | matK |
囊膜蛋白 Envelope membrane protein | cemA | |
乙酰辅酶A羧化酶亚基 Acetyl-CoA carboxylase | accD | |
c型细胞色素合成 c-type cytochrome synthesis | ccsA | |
转录起始因子 Translation Initiation factor | InfA | |
未知功能Unknown function | 假定叶绿体开放阅读框 Hypothetical chloroplast open reading frame | ycf1, ycf2, ycf3, ycf4, ycf5, ycf6, ycf15 |
Table 2 Gene types of the chloroplast genome in tea plants
分类 Category | 分组 Group | 基因名 Name of gene |
---|---|---|
光合作用 Photosynthesis | 光合系统I Photosynthetic I | psaA, psaB, psaC, psaI, psaJ |
光合系统II Photosynthetic II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
ATP合成酶ATP synthase | atpA, atpB, atpE, atpF, atpH, atpI | |
NADH脱氢酶 NADH dehydrogenase | ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH ndhI, ndhJ, ndhK | |
二磷酸核酮糖羧化酶大亚基Ribulose diphosphate carboxylase large subunit | rbcL | |
细胞色素复合物 Cytochrome complex | petA, petB, petD, petG, petL, petN | |
依赖ATP的蛋白酶单元p ATP-dependent protease subunit p | clpP | |
自我复制 Self-replication | 转运RNA tRNA | trnA-UGC, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU, trnI-GAU, trnK-UUU, trnL-CAA, trnL-UAA, trnL-UAG, trnfM-CAU, trnM-CAU, trnN-GUU, trnP-UGG, trnQ-UUG, trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC, trnV-UAC, trnW-CCA, trnY-GUA |
核糖体RNA rRNA | rrn16, rrn23, rrn4.5, rrn5 | |
RNA聚合酶亚基RNA polymerase subunit | rpoA, rpoB, rpoC1, rpoC2 | |
核糖体大亚基Ribosomal large subunit | rpl2, rpl14, rpl16, rpl20, rpl22, rpl23, rpl32, rpl33, rpl36 | |
核糖体小亚基Ribosomal small subunit | rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, rps16, rps18, rps19 | |
生物合成 Biosynthesis | 成熟酶Maturase | matK |
囊膜蛋白 Envelope membrane protein | cemA | |
乙酰辅酶A羧化酶亚基 Acetyl-CoA carboxylase | accD | |
c型细胞色素合成 c-type cytochrome synthesis | ccsA | |
转录起始因子 Translation Initiation factor | InfA | |
未知功能Unknown function | 假定叶绿体开放阅读框 Hypothetical chloroplast open reading frame | ycf1, ycf2, ycf3, ycf4, ycf5, ycf6, ycf15 |
Fig. 2 Gene map of the complete chloroplast genome of cultivated tea plants The inner circle corresponds to the GC content, and the next circle corresponds to the GC skew. The next three circles correspond to the genes. Genes with clockwise arrows represent reverse strands, while genes with counterclockwise arrows represent forward strands. Blue, red and aqua colors of the blocks represent protein-coding genes, introns and RNA, respectively. The third circle corresponds to the shared genes among three cultivated tea plant. The fourth circle corresponds to the unique genes of Camellia sinensis var. sinensis Anhua and Camellia sinensis var. sinensis Longjing43. The fifth circle corresponds to the unique genes of Camellia sinensis var. assamica cv. Yunkang10
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