茶树叶绿体基因组的研究与应用进展

doi:10.13560/j.cnki.biotech.bull.1985.2023-0451

摘要/Abstract

摘要：

多数植物叶绿体基因组为双链环状DNA，具有保守的四分体结构、非重组、单倍体、单亲遗传、进化速率适中、序列和结构高度保守等特征，可为植物进化等提供有用信息。茶树种质资源丰富，其复杂的起源、进化、分类等方面缺乏有效鉴评，而有碍于对其高效保护与创新利用。目前，叶绿体基因组测序技术快速发展并向三代过渡，33份茶树资源的叶绿体基因组已在NCBI公布，茶树叶绿体基因组基因类型、基因序列特征已被部分揭示，且已应用于茶树资源的分类鉴定、起源进化、白化机制等方面研究，但仍有不少茶树资源的叶绿体基因组未被破译。本文简述了植物叶绿体基因组的起源、遗传方式、基本特征；重点述评了茶树叶绿体基因组测序技术、基因组特征、基因类型、基因序列等最新研究成果；概述了茶树叶绿体基因组应用现状；最后探讨了茶树叶绿体基因组未来的应用与发展方向。

关键词: 茶树, 叶绿体基因组, 基因, 分类鉴定, 进化

Abstract:

Most plant chloroplast genomes are double-stranded circular DNA with a conserved tetrad structure, non-recombination, haploid, uniparental inheritance, moderate evolutionary rate, and highly conserved sequence and structure, and may provide useful information for the evolution of plants. Due to abundant tea germplasm resources, their complex origin, evolution and classification remain largely elusive, resulting in hindering their efficient protection and innovative utilization. In recent, the rapid development of chloroplast genome sequencing technologies has been greatly promoted and being changed into the third-generation sequencing. About 33 sequenced chloroplast genomes from tea plants have been published on NCBI, and the gene types and gene sequence characteristics of chloroplast genomes in tea plants have been partially revealed, and used in the study of classification, identification, origin, evolution, and albino mechanism for tea plants. However, many chloroplast genomes of tea resources remain undeciphered. While reviewing the origin, inheritance, and basic characteristics of plant chloroplast genomes, the paper focused on the review of the sequencing technology, genomic features, gene types, and gene sequences of the published chloroplast genomes from tea plants. The paper briefly presented the application status of tea plant chloroplast genome and finally, and discussed the future application and development direction of tea plant chloroplast genomes.

Key words: tea plant, chloroplast genome, gene, classification and identification, evolution

杨雨青, 谭娟, 汪芳, 彭顺利, 陈婕, 谭明燕, 吕美艳, 周富裕, 刘声传. 茶树叶绿体基因组的研究与应用进展[J]. 生物技术通报, 2024, 40(2): 20-30.

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.

图/表 4

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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
资源 Resource	来源 Origin	登录号 Accession	Genome/bp	CDS/bp	GC/%	LSC/bp	SSC/bp	IR/bp	Gene	tRNA	rRNA	参考文献Reference
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	[4]
大红袍 Dahongpao	中国 China	MT773374	157 077	ND	37.29	86 633	18 282	26 081	137	28	4	[6]
武夷水仙 Wuyi Narcissus	中国 China	MT612435	156 762	ND	ND	86 301	18 079	26 090	137	37	8	[6]
信阳10号 Xinyang 10	中国 China	MZ153237	157 041	ND	37.29	86 594	18 291	26 078	113	30	4	[8]
白叶1号 Baiye 1	中国 China	MN086819	156 691	ND	37.30	86 585	18 276	26 083	130	35	8	[23]
安化茶 Anhua	中国 China	MH042531	157 025	80 620	37.30	86 585	18 276	26 082	135	37	8	[24]
云抗10号 Yunkang 10	中国 China	MH019307	157 100	79 092	37.29	ND	ND	ND	141	47	8	[26]
白鸡冠 Baijiguan	中国 China	MT773373	157 099	ND	37.30	ND	ND	ND	137	37	8	[28]
肉桂 Rougui	中国 China	MT773375	157 093	ND	37.30	ND	ND	ND	137	37	8	[28]
水金龟 Shuijingui	中国 China	MT773376	157 126	ND	37.30	ND	ND	ND	137	37	8	[28]
铁罗汉 Tieluohan	中国 China	MT773377	157 041	ND	37.30	ND	ND	ND	137	37	8	[28]
半天妖 Bantianyao	中国 China	MW046255	157 024	ND	37.30	ND	ND	ND	137	37	8	[28]
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	[32]
龙井43 Longjin 43	中国 China	KF562708	157 085	80 650	37.30	86 642	18 283	26 080	134	39	8	[33]
铁观音 Tieguanyin	中国 China	MW148820	157 126	ND	37.30	86 904	18 532	26 095	132	37	8	[34]
黄金芽 Huangjinya	中国 China	ND	158 916	ND	37.22	86 654	16 463	27 900	113	24	5	[35]
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	[35]
西莲1号 Xilian 1	中国 China	ND	157 038	ND	37.30	86 612	18 282	26 072	114	30	4	[31]
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	[36]
德宏茶 Dehungensis	中国 China	KJ806279	157 110	ND	37.30	86 656	18 276	26 089	ND	ND	ND	[37]
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	[37]
茶 C. sinensis var. sinensis	中国 China	KJ806281	157 117	80 542	37.29	86 663	18 276	26 089	ND	ND	ND	[37]
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	[37]
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	[38]
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	[38]
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	[38]
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	[38]
毛叶茶 C. ptilophylla	中国 China	ND	157 097	ND	37.30	86 631	18 286	26 090	132	34	8	[39]
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	[40]
Sangmok	韩国 Korea	LC488797	153 044	ND	37.20	64 665	19 155	24 627	97	29	5	[41]
Kuntze	韩国 Korea	KC143082	157 103	ND	ND	ND	ND	ND	ND	ND	ND	[42]

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
资源 Resource	来源 Origin	登录号 Accession	Genome/bp	CDS/bp	GC/%	LSC/bp	SSC/bp	IR/bp	Gene	tRNA	rRNA	参考文献Reference
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	[4]
大红袍 Dahongpao	中国 China	MT773374	157 077	ND	37.29	86 633	18 282	26 081	137	28	4	[6]
武夷水仙 Wuyi Narcissus	中国 China	MT612435	156 762	ND	ND	86 301	18 079	26 090	137	37	8	[6]
信阳10号 Xinyang 10	中国 China	MZ153237	157 041	ND	37.29	86 594	18 291	26 078	113	30	4	[8]
白叶1号 Baiye 1	中国 China	MN086819	156 691	ND	37.30	86 585	18 276	26 083	130	35	8	[23]
安化茶 Anhua	中国 China	MH042531	157 025	80 620	37.30	86 585	18 276	26 082	135	37	8	[24]
云抗10号 Yunkang 10	中国 China	MH019307	157 100	79 092	37.29	ND	ND	ND	141	47	8	[26]
白鸡冠 Baijiguan	中国 China	MT773373	157 099	ND	37.30	ND	ND	ND	137	37	8	[28]
肉桂 Rougui	中国 China	MT773375	157 093	ND	37.30	ND	ND	ND	137	37	8	[28]
水金龟 Shuijingui	中国 China	MT773376	157 126	ND	37.30	ND	ND	ND	137	37	8	[28]
铁罗汉 Tieluohan	中国 China	MT773377	157 041	ND	37.30	ND	ND	ND	137	37	8	[28]
半天妖 Bantianyao	中国 China	MW046255	157 024	ND	37.30	ND	ND	ND	137	37	8	[28]
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	[32]
龙井43 Longjin 43	中国 China	KF562708	157 085	80 650	37.30	86 642	18 283	26 080	134	39	8	[33]
铁观音 Tieguanyin	中国 China	MW148820	157 126	ND	37.30	86 904	18 532	26 095	132	37	8	[34]
黄金芽 Huangjinya	中国 China	ND	158 916	ND	37.22	86 654	16 463	27 900	113	24	5	[35]
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	[35]
西莲1号 Xilian 1	中国 China	ND	157 038	ND	37.30	86 612	18 282	26 072	114	30	4	[31]
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	[36]
德宏茶 Dehungensis	中国 China	KJ806279	157 110	ND	37.30	86 656	18 276	26 089	ND	ND	ND	[37]
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	[37]
茶 C. sinensis var. sinensis	中国 China	KJ806281	157 117	80 542	37.29	86 663	18 276	26 089	ND	ND	ND	[37]
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	[37]
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	[38]
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	[38]
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	[38]
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	[38]
毛叶茶 C. ptilophylla	中国 China	ND	157 097	ND	37.30	86 631	18 286	26 090	132	34	8	[39]
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	[40]
Sangmok	韩国 Korea	LC488797	153 044	ND	37.20	64 665	19 155	24 627	97	29	5	[41]
Kuntze	韩国 Korea	KC143082	157 103	ND	ND	ND	ND	ND	ND	ND	ND	[42]

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

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