Population sequencing enhances understanding of tea plant evolution

Wang, Xinchao; Hu, Feng; Chang, Yuxiao; Ma, Chun-Lei; Wang, Liyuan; Hao, Xinyuan; Li, Alun; Cheng, Hao; Wang, Lu; Cui, Peng; Jin, Jiye; Wang, Xiaobo; Wei, Kang; Ai, Cheng; Zhao, Sheng; Wu, Zhichao; Li, Youyong; Liu, Benying; Wang, Guodong; Liang, Chen; Ruan, Jue; Yang, Yajun

doi:10.1038/s41467-020-18228-8

Cited by 131 publications

(114 citation statements)

References 57 publications

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“…However, SVs have not yet been investigated in tea plants by comparing high-quality genomes. Here, we identified 45,304, 44,358, and 26,754 SVs by comparing HD to the three published SCZ-Chr 15 , LJ43 17 and DASZ 19 genomes (Table 3 and Fig. 4a ).…”

Section: Resultsmentioning

confidence: 99%

“… a SV frequency plot of HD and three other tea plant genomes on 15 chromosomes. HD: Huangdan, SCZ: Suchazao 15 , LJ43: Longjing 43 17 , DASZ: An ancient tea tree 19 . b Venn plot of three sets of SV-annotated genes.…”

Section: Resultsmentioning

confidence: 99%

“… a Phylogenetic tree analysis of CBFs from four tea resources and Arabidopsis thaliana . HD: Huangdan, SCZ: Suchazao 15 , LJ43: Longjing 43 17 , DASZ: An ancient tea tree 19 . b Three AtCBFs arranged in tandem on chromosome 4 in Arabidopsis .…”

Section: Resultsmentioning

confidence: 99%

“…The genomic sequences of two major tea plant varieties, namely, Camellia sinensis vars. sinensis (CSS) 9 , 14 – 17 and assamica (CSA) 18 have been resolved, especially those of three CSS cultivars (cultivars Shuchazao 9 , 15 , Biyun 16 , and Longjin 43 17 ) whose high-precision chromosome-level genomic sequences have been obtained. In addition, the high-quality genome of an ancient tea tree has been published 19 .…”

Section: Introductionmentioning

confidence: 99%

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Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome

Wang

Jin

et al. 2021

Horticulture Research

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Tea plants (Camellia sinensis) are commercially cultivated in >60 countries, and their fresh leaves are processed into tea, which is the most widely consumed beverage in the world. Although several chromosome-level tea plant genomes have been published, they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species. Here, we present a phased chromosome-scale assembly for an elite oolong tea cultivar, “Huangdan”, that is well known for its high levels of aroma. Based on the two sets of haplotype genome data, we identified numerous genetic variations and a substantial proportion of allelic imbalance related to important traits, including aroma- and stress-related alleles. Comparative genomics revealed extensive structural variations as well as expansion of some gene families, such as terpene synthases (TPSs), that likely contribute to the high-aroma characteristics of the backbone parent, underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea. Our results uncovered the genetic basis of special features of this oolong tea cultivar, providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome

Wang

Jin

et al. 2021

Horticulture Research

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“…However, the functions of related genes have not yet been proved definitively in transgenic tea plants. In recent years, with publication of tea genome [ 51 , 52 , 53 ], the functional characterization of these genes has begun to become clear. The cytosol was the main site of l -theanine biosynthesis in tea root tissue, and cytosol-expressed CsTS1 was shown to encode l -theanine synthase.…”

Section: Discussionmentioning

confidence: 99%

Effects of Long-Term Nitrogen Fertilization on the Formation of Metabolites Related to Tea Quality in Subtropical China

Chen

Wang

et al. 2021

Metabolites

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As a main agronomic intervention in tea cultivation, nitrogen (N) application is useful to improve tea yield and quality. However, the effects of N application on the formation of tea quality-related metabolites have not been fully studied, especially in long-term field trials. In this study, a 10-year field experiment was conducted to investigate the effect of long-term N application treatments on tea quality-related metabolites, their precursors, and related gene expression. Long-term N application up-regulated the expression of key genes for chlorophyll synthesis and promoted its synthesis, thus increasing tea yield. It also significantly increased the contents of total free amino acids, especially l-theanine, in fresh tea leaves, while decreasing the catechin content, which is conducive to enhancing tea liquor freshness. However, long-term N application significantly reduced the contents of benzyl alcohol and 2-phenylethanol in fresh tea leaves, and also reduced (E)-nerolidol and indole in withered leaves, which were not conducive to the formation of floral and fruity aroma compounds. In general, an appropriate amount of N fertilizer (225 kg/hm2) balanced tea yield and quality. These results not only provide essential information on how N application affects tea quality, but also provide detailed experimental data for field fertilization.

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Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China

Che,

Zhang,

et al. 2024

Ecology and Evolution

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Geological events can strongly affect the genetic structures and differentiation of fish populations. Especially, as an endemic fish of the genus Sinocyclocheilus in the Yunnan‐Guizhou Plateau, the effects of key geological events on the distributions and genetic structures remain poorly understood. Examining the phylogeographic patterns of Sinocyclocheilus fishes can be useful for elucidating the spatio‐temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used single nucleotide polymorphisms (SNP) method to investigate the phylogeographic patterns of Sinocyclocheilus fishes. Our analysis supports the endemicity of Sinocyclocheilus, but the samples of different regions of Sinocyclocheilus contain multiple ancestral components, which displayed more admixed and diversified genetic components, this may be due to the polymorphism of the ancestors themselves, or gene infiltration caused by hybridization between adjacent species of Sinocyclocheilus. We estimate that the most recent common ancestor (MRCA) of Sinocyclocheilus fish in the Central Yunnan Basin at approximately 3.75~3.11 Ma, and infer that the evolution of Sinocyclocheilus in the central Yunnan Basin is closely related to the formation of plateau lakes (around 4.0~0.02 Ma), and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping Sinocyclocheilus population structure. It is also the first time to prove that the altitude change has a great influence on the genetic variation among the populations of Sinocyclocheilus.

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Population sequencing enhances understanding of tea plant evolution

Cited by 131 publications

References 57 publications

Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome

Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome

Effects of Long-Term Nitrogen Fertilization on the Formation of Metabolites Related to Tea Quality in Subtropical China

Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China

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