scholarly journals Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars

2015 ◽  
Vol 2015 ◽  
pp. 1-7
Author(s):  
Yan Wei ◽  
Wang Jing ◽  
Zhou Youxiang ◽  
Zhao Mingming ◽  
Gong Yan ◽  
...  
Keyword(s):  
Amino Acids ◽  
Camellia Sinensis ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
Tea Plant ◽  
Expression Data ◽  
Marker Assisted Breeding ◽  
Genome Wide ◽  
The World ◽  
Functional Analyses

Tea (Camellia sinensis) is a popular beverage all over the world and a number of studies have focused on the genetic uniqueness of tea and its cultivars. However, molecular mechanisms underlying these phenomena are largely undefined. In this report, based on expression data available from public databases, we performed a series of analyses to identify genes probably relevant to the uniqueness ofC. sinensisand two of its cultivars (LJ43 and ZH2). Evolutionary analyses showed that the evolutionary rates of genes involved in the pathways were not significantly different amongC. sinensis,C. oleifera, andC. azalea. Interestingly, a number of gene families, including genes involved in the pathways synthesizing iconic secondary metabolites of tea plant, were significantly upregulated, expressed inC. sinensis(LJ43) when compared toC. azalea, and this may partially explain its higher content of flavonoid, theanine, and caffeine. Further investigation showed that nonsynonymous mutations may partially contribute to the differences between the two cultivars ofC. sinensis, such as the chlorina and higher contents of amino acids in ZH2. Genes identified as candidates are probably relevant to the uniqueness ofC. sinensisand its cultivars should be good candidates for subsequent functional analyses and marker-assisted breeding.

scholarly journals Transcriptome and Expression Profiling Analysis of Recalcitrant Tea (Camellia sinensis L.) Seeds Sensitive to Dehydration

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Xiaofang Jin ◽  
Dandan Liu ◽  
Linlong Ma ◽  
Ziming Gong ◽  
Dan Cao ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Expression Profiles ◽  
Digital Gene Expression ◽  
Tea Plant ◽  
Pcr Analysis ◽  
Woody Perennial ◽  
Genome Wide ◽  
Mechanism Of Dehydration

The tea plant (Camellia sinensis (L.) O. Kuntze) is an economically important woody perennial nonalcoholic health beverage crop. Tea seeds are categorized as recalcitrant and are sensitive to dehydration treatment. However, the molecular basis of this phenomenon has not been investigated. Thus, we analyzed the genome-wide expression profiles of three dehydration stages using RNA-Seq and digital gene expression (DGE) technologies. We performed de novo assembly and obtained a total of 91,925 nonredundant unigenes, of which 58,472 were extensively annotated. By a hierarchical clustering of differentially expressed genes (DEGs), we found that 8929 DEGs were downregulated and 5875 DEGs were upregulated during dehydration treatment. A series of genes related to ABA biosynthesis and signal transduction, transcription factor, antioxidant enzyme, LEA protein, and proline metabolism that have been reported to function in dehydration process were found to be downregulated. Additionally, the expression profiles of 12 selected genes related to tea seed dehydration treatment were confirmed by qRT-PCR analysis. To our knowledge, this is the first genome-wide study elucidating the possible molecular mechanisms of sensitivity of recalcitrant tea seeds to dehydration. The results obtained in this study contribute to the preservation of tea seeds as genetic resources and can also be used to explore the mechanism of dehydration sensitivity of other recalcitrant seeds.

scholarly journals Discovery of Geranylgeranyl Pyrophosphate Synthase (GGPPS) Paralogs from Haematococcus pluvialis Based on Iso-Seq Analysis and Their Function on Astaxanthin Biosynthesis

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 696
Author(s):  
Danqiong Huang ◽  
Wenfu Liu ◽  
Anguo Li ◽  
Chaogang Wang ◽  
Zhangli Hu
Keyword(s):  
Amino Acids ◽  
Haematococcus Pluvialis ◽  
Enzymatic Reaction ◽  
Biosynthesis Pathway ◽  
Coding Region ◽  
Pantoea Ananatis ◽  
Geranylgeranyl Pyrophosphate ◽  
Geranylgeranyl Pyrophosphate Synthase ◽  
Genome Wide ◽  
The World

Haematococcus pluvialis is widely distributed in the world and well known as the richest natural source of astaxanthin that is a strong antioxidant with excellent commercial value. The pathway of astaxanthin biosynthesis in H. pluvialis has been documented as an enzymatic reaction. Several enzymes have been reported, but their isoforms or homologs have not been investigated genome-wide. To better understand the astaxanthin biosynthesis pathway in H. pluvialis, eight candidates of the geranylgeranyl pyrophosphate synthase gene (HpGGPPS) predicted from Iso-seq data were isolated in this study. The length of coding region of these candidates varied from 960 bp to 1272 bp, composing of 7–9 exons. The putative amino acids of all candidates composed the signature domain of GGPPS gene. However, the motifs in the domain region are varied, indicating different bio-functions. Phylogenetic analysis revealed eight candidates can be clustered into three groups. Only two candidates in Group1 encode the synthase participating in the astaxanthin formation. The yield of astaxanthin from these two candidates, 7.1 mg/g (DW) and 6.5 mg/g (DW) respectively, is significant higher than that from CrtE (2.4 mg/g DW), a GGPPS gene from Pantoea ananatis. This study provides a potential productive pathway for astaxanthin synthesis.

scholarly journals Population sequencing enhances understanding of tea plant evolution

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinchao Wang ◽  
Hu Feng ◽  
Yuxiao Chang ◽  
Chunlei Ma ◽  
Liyuan Wang ◽  
...  
Keyword(s):  
Population Genetic ◽  
Tea Plant ◽  
Plant Evolution ◽  
Marker Assisted Breeding ◽  
High Quality ◽  
Domestication Selection ◽  
The World ◽  
High Species Diversity ◽  
Selection For ◽  
Genomic Resequencing

Abstract Tea is an economically important plant characterized by a large genome, high heterozygosity, and high species diversity. In this study, we assemble a 3.26-Gb high-quality chromosome-scale genome for the ‘Longjing 43’ cultivar of Camellia sinensis var. sinensis. Genomic resequencing of 139 tea accessions from around the world is used to investigate the evolution and phylogenetic relationships of tea accessions. We find that hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations with the spread of tea cultivation. Population genetic and transcriptomic analyses reveal that during domestication, selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. This study provides resources for marker-assisted breeding of tea and sets the foundation for further research on tea genetics and evolution.

scholarly journals Genome-Wide Identification of CsATGs in Tea Plant and the Involvement of CsATG8e in Nitrogen Utilization

2020 ◽  
Vol 21 (19) ◽  
pp. 7043
Author(s):  
Wei Huang ◽  
Dan-Ni Ma ◽  
Hong-Ling Liu ◽  
Jie Luo ◽  
Pu Wang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Woody Species ◽  
Nutrient Utilization ◽  
Tea Plant ◽  
Plant Genome ◽  
Wild Type ◽  
Genome Wide ◽  
A Genome ◽  
Phosphorus And Potassium ◽  
Stage 1

Nitrogen (N) is a macroelement with an indispensable role in the growth and development of plants, and tea plant (Camellia sinensis) is an evergreen perennial woody species with young shoots for harvest. During senescence or upon N stress, autophagy has been shown to be induced in leaves, involving a variety of autophagy-related genes (ATGs), which have not been characterized in tea plant yet. In this study, a genome-wide survey in tea plant genome identified a total of 80 Camellia Sinensis autophagy-related genes, CsATGs. The expression of CsATG8s in the tea plant showed an obvious increase from S1 (stage 1) to S4 (stage 4), especially for CsATG8e. The expression levels of AtATGs (Arabidopsis thaliana) and genes involved in N transport and assimilation were greatly improved in CsATG8e-overexpressed Arabidopsis. Compared with wild type, the overexpression plants showed earlier bolting, an increase in amino N content, as well as a decrease in biomass and the levels of N, phosphorus and potassium. However, the N level was found significantly higher in APER (aerial part excluding rosette) in the overexpression plants relative to wild type. All these results demonstrated a convincing function of CsATG8e in N remobilization and plant development, indicating CsATG8e as a potential gene for modifying plant nutrient utilization.

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 Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea Plant Camellia sinensis

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhizhu Zhao ◽  
Dongna Ma
Keyword(s):  
Camellia Sinensis ◽  
Function Analysis ◽  
Gc Content ◽  
Tea Plant ◽  
Pentose Phosphate ◽  
Specific Expression ◽  
Phenotypic Alteration ◽  
Genome Wide ◽  
The Rich ◽  
Lineage Specific Genes

Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

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