茶树基因组与测序技术的研究进展

摘要/Abstract

摘要： 茶树具有高度杂合、基因组庞大及高度重复等特点,这导致茶树基因组的前期研究进展缓慢。基因组测序技术的迅速发展有力推动茶树基因组的解析与完善。综述了基因组测序技术的发展,将近年来茶树基因组的组装与研究进展按照草图水平、染色体水平和单体型水平进行分类,探讨茶树基因组未来的应用与发展方向,为茶树功能基因组学研究和精确分子育种提供参考。

关键词: 茶树, 测序技术, 基因组, 染色体水平, 单体型

Abstract: The tea plant has the characteristics of high heterozygosity, large genome and high duplication, which has led to the slow progress of the preliminary research on the tea plant genomes. The rapid development of genome sequencing technologies has strongly promoted the deciphering and improvement of the tea plant genomes. This article reviewed the development of genome sequencing technologies, and classified the assembly and research progress of tea plant genomes in recent years according to the draft level, chromosome level and haplotype level. By discussing the future application and development direction of tea plant genomes, it provided a reference for the functional genomics research and precision molecular breeding in tea plants.

Key words: Camellia sinensis, sequencing technology, genome, chromosome level, haplotype

中图分类号:

S571.1
Q52

王鹏杰, 杨江帆, 张兴坦, 叶乃兴. 茶树基因组与测序技术的研究进展[J]. 茶叶科学, 2021, 41(6): 743-752.

WANG Pengjie, YANG Jiangfan, ZHANG Xingtan, YE Naixing. Research Advance of Tea Plant Genome and Sequencing Technologies[J]. Journal of Tea Science, 2021, 41(6): 743-752.

参考文献

[1] 叶乃兴. 茶学研究法[M]. 北京: 中国农业出版社, 2011.
Ye N X.Research methods of tea science [M]. Beijing: China Agriculture Press, 2011.
[2] Drew L.The growth of tea[J]. Nature, 2019, 566: s2-s4.
[3] Chen J D, Zheng C, Ma J Q, et al.The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant[J]. Horticulture Research, 2020, 7: 63. doi: 10.1038/s41438-020-0288-2.
[4] Xia E H, Tong W, Wu Q, et al.Tea plant genomics: achievements, challenges and perspectives[J]. Horticulture Research, 2020, 7: 7. doi: 10.1038/s41438-019-0225-4.
[5] Xia E H, Zhang H B, Sheng J, et al.The tea tree genome provides insights into tea flavor and independent evolution of caffeine biosynthesis[J]. Molecular Plant, 2017, 10(6): 866-877.
[6] Wei C L, Yang H, Wang S, et al.Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality[J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(18): E4151-E4158.
[7] Zhang Q J, Li W, Li K, et al.The chromosome-level reference genome of tea tree unveils recent bursts of non-autonomous LTR retrotransposons to drive genome size evolution[J]. Molecular Plant, 2020, 13(7): 935-938.
[8] Wang X, Feng H, Chang Y, et al.Population sequencing enhances understanding of tea plant evolution[J]. Nature Communications, 2020, 11(1): 4447. doi: 10.1038/s41467-020-18228-8.
[9] Zhang W Y, Zhang Y J, Qiu H J, et al.Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties[J]. Nature Communication, 2020, 11(1): 3719. doi: 10.1038/s41467-020-17498-6.
[10] Xia E H, Tong W, Hou Y, et al.The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into genome evolution and adaptation of tea plants[J]. Molecular Plant, 2020, 13(7): 1013-1026.
[11] Jia X, Zhang W, Fernie A R, et al.Camellia sinensis (Tea)[J]. Trends in Genetics, 2021, 37(1): 201-202.
[12] Sanger F, Nicklen S, Coulson A R.DNA sequencing with chain-terminating inhibitors[J]. Proceedings of the National Academy of Sciences of the United States of America, 1977, 74(12): 5463-5467.
[13] Arabidopsis G I.Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J]. Nature, 2000, 408(6814): 796-815.
[14] Venter J C, Adams M D, Myers E W, et al.The sequence of the human genome[J]. Science, 2001, 291(5507): 1304-1351.
[15] Lander E S, Linton L M, Birren B, et al.Initial sequencing and analysis of the human genome[J]. Nature, 2001, 409(6822): 860-921.
[16] Yu J, Hu S, Wang J, et al.A draft sequence of the rice genome (Oryza sativa L. ssp. indica)[J]. Science, 2002, 296(5565): 79-92.
[17] Tuskan G A, Difazio S, Jansson S, et al.The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)[J]. Science, 2006, 313(5793): 1596-1604.
[18] Jaillon O, Aury J, Noel B, et al.The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla[J]. Nature, 2007, 449(7161): 463-467.
[19] Ming R, Hou S, Feng Y, et al.The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)[J]. Nature, 2008, 452(7190): 991-996.
[20] Paterson A H, Bowers J E, Bruggmann R, et al.The Sorghum bicolor genome and the diversification of grasses[J]. Nature, 2009, 457(7229): 551-556.
[21] Schnable P S, Ware D, Fulton R S, et al.The B73 maize genome: complexity, diversity, and dynamics[J]. Science, 2009, 326(5956): 1112-1115.
[22] Margulies M, Egholm M, Altman W E, et al.Genome sequencing in microfabricated high-density picolitre reactors[J]. Nature, 2005, 437(7057): 376-380.
[23] Levy S E, Myers R M.Advancements in next-generation sequencing[J]. Annual Review of Genomics and Human Genetics, 2016, 17: 95-115.
[24] Huang S, Li R, Zhang Z, et al.The genome of the cucumber, Cucumis sativus L.[J]. Nature Genetics, 2009, 41(12): 1275-1281.
[25] Argout X, Salse J, Aury J, et al.The genome of Theobroma cacao[J]. Nature Genetics, 2011, 43(2): 101-108.
[26] Wang X, Wang H, Wang J, et al.The genome of the mesopolyploid crop species Brassica rapa[J]. Nature Genetics, 2011, 43(10): 1035-1039.
[27] Varshney R K, Chen W, Li Y, et al.Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers[J]. Nature Biotechnology, 2011, 30(1): 83-89.
[28] Xu Q, Chen L L, Ruan X, et al.The draft genome of sweet orange (Citrus sinensis)[J]. Nature Genetics, 2013, 45(1): 59-92.
[29] Guo S, Zhang J, Sun H, et al.The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions[J]. Nature Genetics, 2013, 45(1): 51-58.
[30] 杨官品, 郭栗. 基因组的测序技术及其发展趋势[J]. 中国海洋大学学报(自然科学版), 2017, 47(s1): 48-57.
Yang G P, Guo L.Technologies available for genome sequencing and their advancements[J]. Periodical of Ocean University of China, 2017, 47(s1): 48-57.
[31] Levy S E, Boone B E.Next-generation sequencing strategies[J]. Cold Spring Harbor Perspectives in Medicine, 2019, 9(7): a25791. doi: 10.1101/cshperspect.a025791.
[32] Wenger A M, Peluso P, Rowell W J, et al.Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome[J]. Nature Biotechnology, 2019, 37(11): 1155-1162.
[33] Zhang J S, Zhang X T, Tang H B, et al.Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.[J]. Nature Genetics, 2018, 50(11): 1565-1573.
[34] Zhang X, Wang G, Zhang S, et al.Genomes of the banyan tree and pollinator wasp provide insights into fig-wasp coevolution[J]. Cell, 2020, 183(4): 875-889.
[35] Chen H T, Zeng Y, Yang Y Z, et al.Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa[J]. Nature Communications, 2020, 11(1): 2494. doi: 10.1038/s41467-020-16338-x.
[36] Burton J N, Adey A, Patwardhan R P, et al.Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions[J]. Nature Biotechnology, 2013, 31(12): 1119-1125.
[37] Dong Y, Xie M, Jiang Y, et al.Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)[J]. Nature Biotechnology, 2013, 31(2): 135-141.
[38] 陈萍. BioNano图谱数据建模及光学图谱在水稻基因组的应用研究[D]. 北京: 中国科学院大学, 2019.
Chen P.BioNano data modeling and application research of optical atlas in rice genome [D]. Beijing: Chinese Academy of Sciences University, 2019.
[39] Kronenberg Z N, Rhie A, Koren S, et al.Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C[J]. Nature Communications, 2021, 12(1): 1935. doi: 10.1038/s41467-020-20536-y.
[40] Zhang X T, Wu R X, Wang Y B, et al.Unzipping haplotypes in diploid and polyploid genomes[J]. Computational and Structural Biotechnology Journal, 2019, 18: 66-72.
[41] Zhang X T, Zhang S C, Zhao Q, et al.Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data[J]. Nature Plants, 2019, 5(8): 833-845.
[42] Xia E, Li F, Tong W, et al.The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data[J]. Scientific Data, 2019, 6(1): 122. doi: 10.1038/s41597-019-0127-1.
[43] Xia E H, Li F D, Tong W, et al.Tea Plant Information Archive (TPIA): A comprehensive genomics and bioinformatics platform for tea plant[J]. Plant Biotechnology Journal, 2019, 17(10): 1938-1953.
[44] Wang P, Yu J, Jin S, et al.Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome[J]. Horticulture Research, 2021, 8: 107. doi: 10.1038/s41438-021-00542-x.
[45] Zhang X.Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant, Camellia sinensis[J]. Nature Genetics, 2021. doi: 10.1038/s41588-021-00895-y.
[46] Wang P, Jin S, Chen X, et al.Chromatin accessibility and translational landscapes of tea plants under chilling stress[J]. Horticulture Research, 2021, 8: 96. doi: 10.1038/s41438-021-00542-x.
[47] Zhou Q, Tang D, Huang W, et al.Haplotype-resolved genome analyses of a heterozygous diploid potato[J]. Nature Genetics, 2020, 52(10): 1018-1023.
[48] Zhang W, Luo C, Scossa F, et al.A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants[J]. Plant Journal, 2020, 105(1): 197-208.
[49] Huang X H, Yang S H, Gong J Y, et al.Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis[J]. Nature Communications, 2015, 6: 6258. doi: 10.1038/ncomms7258.
[50] Shao L, Xing F, Xu C, et al.Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis[J]. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(12): 5653-5658.
[51] Zheng Y C, Wang P J, Chen X J, et al.Transcriptome and metabolite profiling reveal novel insights into volatile heterosis in the tea plant (Camellia sinensis)[J]. Molecules, 2019, 24(18): 3380. doi: 10.3390/molecules24183380.
[52] 叶乃兴. 乌龙茶种质资源的利用与品种创新[J]. 福建茶叶, 2006(3): 2-4.
Ye N X.Utilization of oolong tea germplasm resources and cultivar innovation[J]. Tea In Fujian, 2006(3): 2-4.
[53] Zeng L, Zhou X, Su X, et al.Chinese oolong tea: an aromatic beverage produced under multiple stresses[J]. Trends in Food Science and Technology, 2020, 106: 242-253.
[54] 王让剑, 杨军, 孔祥瑞, 等. 利用SSR标记分析金观音(半)同胞茶树品种遗传差异[J]. 茶叶科学, 2017, 37(2): 139-148.
Wang R J, Yang J, Kong X R, et al.Genetic analysis of full- and half-sib families of tea cultivar jinguanyin based on SSR molecular markers[J]. Journal of Tea Science, 2017, 37(2): 139-148.
[55] 姚雪倩, 郑玉成, 王鹏杰, 等. 金观音与其亲本差异基因表达的遗传分析[J]. 福建农林大学学报(自然科学版), 2019, 48(2): 155-160.
Yao X Q, Zheng Y C, Wang P J, et al.Genetic analysis of differential gene expression between Jinguanyin and its parents[J]. Journal of Fujian Agriculture and Forestry University (Natural Science Edition), 2019, 48(2): 155-160.
[56] 郭吉春, 杨如兴, 张文锦, 等. 茶树杂交种金观音与黄观音的选育及应用[J]. 贵州科学, 2008, 26(2): 20-24.
Guo J C, Yang R X, Zhang W J, et al.Breeding and application of two tea hybrid Jinguanyin and Huangguanyin[J]. Guizhou Science, 2008, 26(2): 20-24.
[57] 郭吉春, 叶乃兴, 何孝延. 茶树杂交一代展叶期的遗传变异[J]. 茶叶科学, 2004, 24(4): 255-259.
Guo J C, Ye N X, He X Y.Genetic variation in the leaf-expansion period of the first hybrid generation tea plants[J]. Journal of Tea Science, 2004, 24(4): 255-259.
[58] 陈荣冰, 黄福平, 陈常颂, 等. 高香型优质乌龙茶新品系瑞香选育简报[J]. 茶叶科学, 2004, 24(1): 29-32.
Chen R B, Huang F P, Chen C S, et al.Breeding report on strong aroma and good quality newly bred oolong variety Rui xiang[J]. Journal of Tea Science, 2004, 24(1): 29-32.
[59] 钟秋生, 林郑和, 陈常颂, 等. “春闺”绿茶香气成分鉴定分析[J]. 茶叶通讯, 2021, 48(1): 33-39.
Zhong Q S, Lin Z H, Chen C S, et al.Identification and analysis of aroma components in Chungui green tea[J]. Journal of Tea Communication, 2021, 48(1): 33-39.
[60] Chen X, Wang P, Zheng Y, et al.Comparison of metabolome and transcriptome of flavonoid biosynthesis pathway in a purple-leaf tea germplasm Jinmingzao and a green-leaf tea germplasm Huangdan reveals their relationship with genetic mechanisms of color formation[J]. International Journal of Molecular Sciences, 2020, 21(11): 4167. doi: 10.3390/ijms21114167.
[61] 张文驹, 戎俊, 韦朝领, 等. 栽培茶树的驯化起源与传播[J]. 生物多样性, 2018, 26(4): 357-372.
Zhang W J, Rong J, Wei C L, et al.Domestication origin and spread of cultivated tea plants[J]. Biodiversity Science, 2018, 26(4): 357-372.
[62] 唐蝶, 周倩. 植物基因组组装技术研究进展[J]. 生物技术通报, 2021, 37(6): 1-12.
Tang D, Zhou Q.Research advances in plant genome assembly[J]. Biotechnology Bulletin, 2021, 37(6): 1-12.
[63] Ma J, Yao M, Ma C, et al.Construction of a SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis)[J]. PLoS One, 2016, 9(3): e93131. doi: 10.1371/journal.pone.0093131.
[64] 李小杰, 马建强, 姚明哲, 等. 茶氨酸合成酶基因的SNP挖掘和遗传定位[J]. 茶叶科学, 2017, 37(3): 251-257.
Li X J, Ma J Q, Yao M Z, et al.SNP detection and mapping of theanine synthetase gene in tea plant[J]. Journal of Tea Science, 2017, 37(3): 251-257.
[65] Xu L, Wang L, Wei K, et al.High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing[J]. BMC Genomics, 2018, 19(1): 955. doi: 10.1186/s12864-018-5291-8.
[66] Fang K, Xia Z, Li H, et al.Genome-wide association analysis identified molecular markers associated with important tea flavor-related metabolites[J]. Horticulture Research, 2021, 8(1): 42. doi: 10.1038/s41438-021-00477-3.