scholarly journals Tea plant genomics: achievements, challenges and perspectives

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
En-Hua Xia ◽  
Wei Tong ◽  
Qiong Wu ◽  
Shu Wei ◽  
Jian Zhao ◽  
...  
Keyword(s):  
Cultural Values ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Plant Genome ◽  
Alcoholic Beverages ◽  
Plant Genomics ◽  
Breeding Programs ◽  
Tea Quality ◽  
Genomic Studies ◽  
Tea Plants

AbstractTea is among the world’s most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.

scholarly journals Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Fang-Dong Li ◽  
Wei Tong ◽  
En-Hua Xia ◽  
Chao-Ling Wei
Keyword(s):  
Cultural Values ◽  
Plant Species ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Tea Plant ◽  
Sequencing Depth ◽  
Alcoholic Beverages ◽  
Sequencing Data ◽  
Tea Plants

Abstract Background Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. Results We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS. Conclusions The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.

scholarly journals Plant Availability of Magnesium in Typical Tea Plantation Soils 

2020 ◽  
Author(s):  
Qunfeng Zhang ◽  
Dandan Tang ◽  
Xiangde Yang ◽  
Saipan Geng ◽  
Ying He ◽  
...  
Keyword(s):  
Quality Improvement ◽  
Tea Plant ◽  
Tea Plantation ◽  
Fertilizer Use Efficiency ◽  
Fertilizer Use ◽  
Plant Cultivation ◽  
Yield And Quality ◽  
Tea Quality ◽  
Use Efficiency ◽  
Tea Plants

Abstract Background and aims: Magnesium (Mg) plays important roles in improving the yield and quality of tea. However, Mg deficiency frequently occurs in acidic tea plantation soil. Methods: Tea plants were pot-cultivated in 12 typical tea plantations soils amended with and without Mg fertilizer. Exchangeable Mg (Ex-Mg) concentration in soils were quantitatively extracted using four extraction solutions (Mehlich-3, BaCl2, CaCl2 and NH4OAC). Plant availability of Mg was evaluated by Mg uptake and use efficiency, as well as its association with quality-components in tea plants.Results: Ex-Mg in soils were extracted most efficiently by Mehlich-3, while Mg concentrations in tea plant tissue higher correlated with Ex-Mg extracted by CaCl2 than other extraction solutions. Mg fertilizer use efficiency in tea plant varied from 6.08% to 29.56 %, and Mg fertilization significantly improve green tea quality by decreasing the ratio of total polyphenol to amino acid in tea leaves (24-60%). Moreover, the effect of Mg application on tea quality improvement and the use efficiency of Mg fertilizer both negatively correlated with total Mg concentration (r = -0.94 and -0.63, respectively) and nitrogen (N) level (r = -0.61 and -0.51, respectively) in soils prior to tea plant cultivation.Conclusions: CaCl2 could be recommended for plant-available Mg extraction in tea plantation soil, and Mg fertilizer use efficiency could be affected and predicted by total N and Mg status in soils prior to tea plant cultivation, providing a potential theoretical for guidance of Mg fertilization for tea yield and quality improvement in tea plantation management.

scholarly journals Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

2020 ◽  
Author(s):  
Huan Wang ◽  
ZhaoTang Ding ◽  
Mengjie Gou ◽  
Jianhui Hu ◽  
Yu Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Future Research ◽  
Specific Expression ◽  
Genome Wide ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Tea Plants

Abstract Background: Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants.Results: In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency.Conclusions: We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

scholarly journals Identification of CBF Transcription Factors in Tea Plants and a Survey of Potential CBF Target Genes under Low Temperature

2019 ◽  
Vol 20 (20) ◽  
pp. 5137 ◽  
Author(s):  
Pengjie Wang ◽  
Xuejin Chen ◽  
Yongchun Guo ◽  
Yucheng Zheng ◽  
Chuan Yue ◽  
...  
Keyword(s):  
Low Temperature ◽  
Target Genes ◽  
Expression Profiles ◽  
Temperature Treatment ◽  
Vital Role ◽  
Tea Plant ◽  
Plant Genome ◽  
Cell Wall Modification ◽  
Low Temperature Treatment ◽  
Tea Plants

C-repeat binding factors (CBFs) are key signaling genes that can be rapidly induced by cold and bind to the C-repeat/dehydration-responsive motif (CRT/DRE) in the promoter region of the downstream cold-responsive (COR) genes, which play a vital role in the plant response to low temperature. However, the CBF family in tea plants has not yet been elucidated, and the possible target genes regulated by this family under low temperature are still unclear. In this study, we identified five CsCBF family genes in the tea plant genome and analyzed their phylogenetic tree, conserved domains and motifs, and cis-elements. These results indicate that CsCBF3 may be unique in the CsCBF family. This is further supported by our findings from the low-temperature treatment: all the CsCBF genes except CsCBF3 were significantly induced after treatment at 4 °C. The expression profiles of eight tea plant tissues showed that CsCBFs were mainly expressed in winter mature leaves, roots and fruits. Furthermore, 685 potential target genes were identified by transcriptome data and CRT/DRE element information. These target genes play a functional role under the low temperatures of winter through multiple pathways, including carbohydrate metabolism, lipid metabolism, cell wall modification, circadian rhythm, calcium signaling, transcriptional cascade, and hormone signaling pathways. Our findings will further the understanding of the stress regulatory network of CsCBFs in tea plants.

scholarly journals An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ya Wang ◽  
Fei Chen ◽  
Yuanchun Ma ◽  
Taikui Zhang ◽  
Pengchuan Sun ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Tea Plant ◽  
Plant Evolution ◽  
Plant Genome ◽  
Whole Genome ◽  
Biosynthesis Pathway ◽  
Duplicated Genes ◽  
Tandem Gene Duplication ◽  
Tea Plants

AbstractTea, coffee, and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value. The genomes of four tea plant varieties have recently been sequenced, but there is some debate regarding the characterization of a whole-genome duplication (WGD) event in tea plants. Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered. Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication (WGT) event. This WGD was shared by the Polemonioids-Primuloids-Core Ericales (PPC) sections, encompassing at least 17 families in the order Ericales. In addition, our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway, four pairs of duplicated genes in the theanine biosynthesis pathway, and one pair of genes in the caffeine biosynthesis pathway, which were expanded and retained following this WGD. Nearly all these gene pairs were expressed in tea plants, implying the contribution of the WGD. This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes, the WGD may have been another main factor driving the evolution of tea flavor.

scholarly journals Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6385 ◽  
Author(s):  
Zi-wei Zhou ◽  
Hui-li Deng ◽  
Qing-yang Wu ◽  
Bin-bin Liu ◽  
Chuan Yue ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Economic Value ◽  
Tea Plant ◽  
Alcoholic Beverages ◽  
Post Harvest ◽  
Tea Plants ◽  
Suitable Reference ◽  
Turn Over ◽  
Selection Of

Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none has been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms—GeNorm, Normfinder, and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and withering treatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the five best reference genes in the withering group. The expression level of lipoxygenase genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.

scholarly journals Validation of reference genes for gene expression studies in post-harvest leaves of tea plant (Camellia sinensis)

2018 ◽  
Author(s):  
Ziwei Zhou ◽  
Huili Deng ◽  
Qingyang Wu ◽  
Binbin Liu ◽  
Chuan Yue ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Economic Value ◽  
Tea Plant ◽  
Alcoholic Beverages ◽  
Post Harvest ◽  
Tea Plants ◽  
Suitable Reference ◽  
Turn Over ◽  
Selection Of

Tea is one of three major non-alcoholic beverages that are popular all around the world. The economic value of the final tea product largely depends on the post-harvest physiology of tea leaves. The utilization of quantitative reverse transcription polymerase chain reaction (RT-qPCR) is a widely accepted and precise approach to determine the target gene expression of tea plants, and the reliability of results hinges on the selection of suitable reference genes. A few reliable reference genes have been documented using various treatments and different tissues of tea plants, but none have been done on post-harvest leaves during the tea manufacturing process. The present study selected and analyzed 15 candidate reference genes: Cs18SrRNA, CsGADPH, CsACT, CsEF-1α, CsUbi, CsTUA, Cs26SrRNA, CsRuBP, CsCYP, CselF-4α, CsMON1, CsPCS1, CsSAND, CsPPA2, CsTBP. This study made an assessment on the expression stability under two kinds of post-harvest treatment, turn over and withering, using three algorithms—geNorm, Normfinder and Bestkeeper. The results indicated that the three commonly used reference genes, CsTUA, Cs18SrRNA, CsRuBP, together with Cs26SrRNA, were the most unstable genes in both the turn over and witheringtreatments. CsACT, CsEF-1α, CsPPA2, and CsTBP were the top four reference genes in the turn over treatment, while CsTBP, CsPCS1, CsPPA2, CselF-4α, and CsACT were the four best reference genes in the witheringgroup. The expression level of lipoxygenase (LOX) genes, which were involved in a number of diverse aspects of plant physiology, including wounding, was evaluated to validate the findings. To conclude, we found a basis for the selection of reference genes for accurate transcription normalization in post-harvest leaves of tea plants.

scholarly journals Identification and Expression Analyses of SBP-Box Genes Reveal Their Involvement in Abiotic Stress and Hormone Response in Tea Plant (Camellia sinensis)

2018 ◽  
Vol 19 (11) ◽  
pp. 3404 ◽  
Author(s):  
Pengjie Wang ◽  
Di Chen ◽  
Yucheng Zheng ◽  
Shan Jin ◽  
Jiangfan Yang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Tea Plant ◽  
Plant Genome ◽  
Plant Growth And Development ◽  
Comprehensive Understanding ◽  
Transcription Factor Family ◽  
Squamosa Promoter Binding Protein ◽  
Tea Plants

The SQUAMOSA promoter binding protein (SBP)-box gene family is a plant-specific transcription factor family. This family plays a crucial role in plant growth and development. In this study, 20 SBP-box genes were identified in the tea plant genome and classified into six groups. The genes in each group shared similar exon-intron structures and motif positions. Expression pattern analyses in five different tissues demonstrated that expression in the buds and leaves was higher than that in other tissues. The cis-elements and expression patterns of the CsSBP genes suggested that the CsSBP genes play active roles in abiotic stress responses; these responses may depend on the abscisic acid (ABA), gibberellic acid (GA), and methyl jasmonate (MeJA) signaling pathways. Our work provides a comprehensive understanding of the CsSBP family and will aid in genetically improving tea plants.

scholarly journals CsLAZY1 mediates shoot gravitropism and branch angle in tea plants (Camellia sinensis)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaobo Xia ◽  
Xiaozeng Mi ◽  
Ling Jin ◽  
Rui Guo ◽  
Junyan Zhu ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Tea Plant ◽  
Plant Genome ◽  
Gravity Inversion ◽  
High Sequence Similarity ◽  
Branch Angle ◽  
Shoot Gravitropism ◽  
Tea Plants

Abstract Background Branch angle is a pivotal component of tea plant architecture. Tea plant architecture not only affects tea quality and yield but also influences the efficiency of automatic tea plant pruning. However, the molecular mechanism controlling the branch angle, which is an important aspect of plant architecture, is poorly understood in tea plants. Results In the present study, three CsLAZY genes were identified from tea plant genome data through sequence homology analysis. Phylogenetic tree displayed that the CsLAZY genes had high sequence similarity with LAZY genes from other plant species, especially those in woody plants. The expression patterns of the three CsLAZYs were surveyed in eight tissues. We further verified the expression levels of the key CsLAZY1 transcript in different tissues among eight tea cultivars and found that CsLAZY1 was highly expressed in stem. Subcellular localization analysis showed that the CsLAZY1 protein was localized in the plasma membrane. CsLAZY1 was transferred into Arabidopsis thaliana to investigate its potential role in regulating shoot development. Remarkably, the CsLAZY1 overexpressed plants responded more effectively than the wild-type plants to a gravity inversion treatment under light and dark conditions. The results indicate that CsLAZY1 plays an important role in regulating shoot gravitropism in tea plants. Conclusions The results provide important evidence for understanding the functions of CsLAZY1 in regulating shoot gravitropism and influencing the stem branch angle in tea plants. This report identifies CsLAZY1 as a promising gene resource for the improvement of tea plant architecture.

scholarly journals Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huan Wang ◽  
Zhaotang Ding ◽  
Mengjie Gou ◽  
Jianhui Hu ◽  
Yu Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Future Research ◽  
Specific Expression ◽  
Genome Wide ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Tea Plants

Abstract Background Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants. Results In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency. Conclusions We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

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