scholarly journals TeaAS: a comprehensive database for alternative splicing in tea plants (Camellia sinensis)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaozeng Mi ◽  
Yi Yue ◽  
Mengsha Tang ◽  
Yanlin An ◽  
Hui Xie ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Camellia Sinensis ◽  
Tea Plant ◽  
Local Alignment ◽  
The Novel ◽  
Rna Seq ◽  
Expression Levels ◽  
Comprehensive Information ◽  
Search Tool ◽  
Tea Plants

AbstractAlternative splicing (AS) increases the diversity of transcripts and proteins through the selection of different splice sites and plays an important role in the growth, development and stress tolerance of plants. With the release of the reference genome of the tea plant (Camellia sinensis) and the development of transcriptome sequencing, researchers have reported the existence of AS in tea plants. However, there is a lack of a platform, centered on different RNA-seq datasets, that provides comprehensive information on AS.To facilitate access to information on AS and reveal the molecular function of AS in tea plants, we established the first comprehensive AS database for tea plants (TeaAS, http://www.teaas.cn/index.php). In this study, 3.96 Tb reads from 66 different RNA-seq datasets were collected to identify AS events. TeaAS supports four methods of retrieval of AS information based on gene ID, gene name, annotation (non-redundant/Kyoto encyclopedia of genes and genomes/gene ontology annotation or chromosomal location) and RNA-seq data. It integrates data pertaining to genome annotation, type of AS event, transcript sequence, and isoforms expression levels from 66 RNA-seq datasets. The AS events resulting from different environmental conditions and that occurring in varied tissue types, and the expression levels of specific transcripts can be clearly identified through this online database. Moreover, it also provides two useful tools, Basic Local Alignment Search Tool and Generic Genome Browser, for sequence alignment and visualization of gene structure.The features of the TeaAS database make it a comprehensive AS bioinformatics platform for researchers, as well as a reference for studying AS events in woody crops. It could also be helpful for revealing the novel biological functions of AS in gene regulation in tea plants.

scholarly journals Molecular Identification and Characterization of Hydroxycinnamoyl Transferase in Tea Plants (Camellia sinensis L.)

2018 ◽  
Vol 19 (12) ◽  
pp. 3938 ◽  
Author(s):  
Chi-Hui Sun ◽  
Chin-Ying Yang ◽  
Jason Tzen
Keyword(s):  
Abiotic Stress ◽  
Amino Acid ◽  
Camellia Sinensis ◽  
Polymerase Chain Reaction Analysis ◽  
Coffea Canephora ◽  
Tea Plant ◽  
Amino Acid Sequences ◽  
Hibiscus Cannabinus ◽  
Expression Level ◽  
Tea Plants

Tea (Camellia sinensis L.) contains abundant secondary metabolites, which are regulated by numerous enzymes. Hydroxycinnamoyl transferase (HCT) is involved in the biosynthesis pathways of polyphenols and flavonoids, and it can catalyze the transfer of hydroxyconnamoyl coenzyme A to substrates such as quinate, flavanol glycoside, or anthocyanins, thus resulting in the production of chlorogenic acid or acylated flavonol glycoside. In this study, the CsHCT gene was cloned from the Chin-Shin Oolong tea plant, and its protein functions and characteristics were analyzed. The full-length cDNA of CsHCT contains 1311 base pairs and encodes 436 amino acid sequences. Amino acid sequence was highly conserved with other HCTs from Arabidopsis thaliana, Populus trichocarpa, Hibiscus cannabinus, and Coffea canephora. Quantitative real-time polymerase chain reaction analysis showed that CsHCT is highly expressed in the stem tissues of both tea plants and seedlings. The CsHCT expression level was relatively high at high altitudes. The abiotic stress experiment suggested that low temperature, drought, and high salinity induced CsHCT transcription. Furthermore, the results of hormone treatments indicated that abscisic acid (ABA) induced a considerable increase in the CsHCT expression level. This may be attributed to CsHCT involvement in abiotic stress and ABA signaling pathways.

scholarly journals Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis)

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0125031 ◽  
Author(s):  
Chao Zheng ◽  
Lei Zhao ◽  
Yu Wang ◽  
Jiazhi Shen ◽  
Yinfei Zhang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Tea Plant ◽  
Rna Seq

scholarly journals Effects of Exogenous 6-Benzyladenine on Dwarfing, Shoot Branching, and Yield of Tea Plant (Camellia sinensis)

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 651-655 ◽  
Author(s):  
Liping Zhang ◽  
Chen Shen ◽  
Jipeng Wei ◽  
Wenyan Han
Keyword(s):  
Plant Height ◽  
Camellia Sinensis ◽  
Photosynthetic Rate ◽  
Tea Plant ◽  
Shoot Branching ◽  
Tea Plants ◽  
Lateral Branches ◽  
Spring Yield

6-Benzyladenine (6-BA) is a safe and efficient cytokinin. The adult tea plants of the cv. Longjing 43 were used in this study. The foliar portion of tea bushes were sprayed with different concentrations (50, 100, 200, or 400 mg·L−1) of 6-BA after heavy pruning, when three to four leaves grew out in late May. The effects of 6-BA application on the growth of the new shoots and lateral branches were quantified. After 5 months, treatments with 50, 100, 200, or 400 mg·L−1 6-BA suppressed plant height by 11.0%, 18.0%, 21.0%, or 22.0%, respectively; 6-BA at 100, 200, or 400 mg·L−1 decreased the number of lateral branches by 20.0%, 23.0%, or 18.0%, respectively. Meanwhile, treatments with 50, 200, or 400 mg·L−1 6-BA increased the length of lateral branches by 38.0%, 79.0%, or 81.0% respectively; 200 mg·L−1 6-BA increased the diameter of lateral branches by 8.0%. In addition, after 2 months, 50 or 200 mg·L−1 6-BA did not significantly affect the growth of functional leaves, 50, 100, or 200 mg·L−1 6-BA did not significantly affect photosynthetic rate (Pn) as compared with the control. Furthermore, 200 or 400 mg·L−1 6-BA significantly increased spring tea yield by 28.9% or 13.3%, respectively as compared with the control. In conclusion, 6-BA at the four concentrations promoted dwarfing and the formation of productive lateral branches and increased the spring yield, and 200 mg·L−1 6-BA exerted the best comprehensive effect.

scholarly journals Low Caffeine Content in Novel Grafted Tea with Camellia sinensis as Scions and Camellia oleifera as Stocks

2015 ◽  
Vol 10 (5) ◽  
pp. 1934578X1501000 ◽  
Author(s):  
Wei-Wei Deng ◽  
Min Li ◽  
Chen-Chen Gu ◽  
Da-Xiang Li ◽  
Lin-Long Ma ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Expression Patterns ◽  
Tea Plant ◽  
Protein Accumulation ◽  
Tea Leaves ◽  
Qrt Pcr ◽  
Caffeine Content ◽  
Caffeine Synthase ◽  
Specificity And Sensitivity ◽  
Tea Plants

Caffeine, a purine alkaloid, is a major secondary metabolite in tea leaves. The demand for low caffeine tea is increasing in recent years, especially for health reasons. We report a novel grafted tea material with low caffeine content. The grafted tea plant had Camellia sinensis as scions and C. oleifera as stocks. The content of purine alkaloids was determined in the leaves of one-year-old grafted tea plants by HPLC. We also characterized caffeine synthase (CS), a key enzyme involved in caffeine biosynthesis in tea plants, at the expression level. The expression patterns of CS were examined in grafted and control leaves by Western blot, using a self-prepared polyclonal antibody with high specificity and sensitivity. The expression of related genes ( TCS1, tea caffeine synthase gene, GenBank accession No. AB031280; sAMS, SAM synthetase gene, AJ277206; TIDH, IMP dehydrogenase gene, EU106658) in the caffeine biosynthetic pathway was investigated by qRT-PCR. HPLC showed that the caffeine content was only 38% as compared with the non-grafted tea leaves. Immunoblotting analysis showed that CS protein decreased by half in the leaves of grafted tea plants. qRT-PCR revealed no significant changes in the expression of two genes in the upstream pathway ( sAMS and TIDH), while the expression of TCS1 was greatly decreased (50%). Taken together, these data revealed that the low caffeine content in the grafted tea leaves is due to low TCS1 expression and CS protein accumulation.

scholarly journals Metabolism of Gallic Acid and Its Distributions in Tea (Camellia sinensis) Plants at the Tissue and Subcellular Levels

2020 ◽  
Vol 21 (16) ◽  
pp. 5684 ◽  
Author(s):  
Xiaochen Zhou ◽  
Lanting Zeng ◽  
Yingjuan Chen ◽  
Xuewen Wang ◽  
Yinyin Liao ◽  
...  
Keyword(s):  
Gallic Acid ◽  
Camellia Sinensis ◽  
Tea Plant ◽  
Plant Diseases ◽  
Tea Leaves ◽  
Specialized Metabolites ◽  
Tea Plants ◽  
Mg Content ◽  
Ga Content

In tea (Camellia sinensis) plants, polyphenols are the representative metabolites and play important roles during their growth. Among tea polyphenols, catechins are extensively studied, while very little attention has been paid to other polyphenols such as gallic acid (GA) that occur in tea leaves with relatively high content. In this study, GA was able to be transformed into methyl gallate (MG), suggesting that GA is not only a precursor of catechins, but also can be transformed into other metabolites in tea plants. GA content in tea leaves was higher than MG content—regardless of the cultivar, plucking month or leaf position. These two metabolites occurred with higher amounts in tender leaves. Using nonaqueous fractionation techniques, it was found that GA and MG were abundantly accumulated in peroxisome. In addition, GA and MG were found to have strong antifungal activity against two main tea plant diseases, Colletotrichum camelliae and Pseudopestalotiopsis camelliae-sinensis. The information will advance our understanding on formation and biologic functions of polyphenols in tea plants and also provide a good reference for studying in vivo occurrence of specialized metabolites in economic plants.

scholarly journals Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis

2018 ◽  
Author(s):  
Jin Li ◽  
Peng Yu
Keyword(s):  
Alternative Splicing ◽  
Computational Analysis ◽  
Potential Role ◽  
Exon Skipping ◽  
Chronic Inflammatory Disease ◽  
Splicing Factors ◽  
The Novel ◽  
Rna Seq ◽  
Genome Wide

AbstractPsoriasis is a chronic inflammatory disease that affects the skin, nails, and joints. For understanding the mechanism of psoriasis, though, alternative splicing analysis has received relatively little attention in the field. Here, we developed and applied several computational analysis methods to study psoriasis. Using psoriasis mouse and human datasets, our differential alternative splicing analyses detected hundreds of differential alternative splicing changes. Our analysis of conservation revealed many exon-skipping events conserved between mice and humans. In addition, our splicing signature comparison analysis using the psoriasis datasets and our curated splicing factor perturbation RNA-Seq database, SFMetaDB, identified nine candidate splicing factors that may be important in regulating splicing in the psoriasis mouse model dataset. Three of the nine splicing factors were confirmed upon analyzing the human data. Our computational methods have generated predictions for the potential role of splicing in psoriasis. Future experiments on the novel candidates predicted by our computational analysis are expected to provide a better understanding of the molecular mechanism of psoriasis and to pave the way for new therapeutic treatments.

scholarly journals Transcriptome Analysis, Marker Discovery and Pigment Biosynthesis of Red-leaf Juglans regia

2017 ◽  
Vol 5 (2) ◽  
pp. 20
Author(s):  
Xin Chen ◽  
Li Xu ◽  
Xiao-juan Zong ◽  
Hai-rong Wei ◽  
Jia-wei Wang ◽  
...  
Keyword(s):  
Juglans Regia ◽  
Local Alignment ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Leaf Trait ◽  
Search Tool ◽  
Pigment Biosynthesis ◽  
Marker Discovery ◽  
Insight Into

Red-leaf trait rarely occurs in Juglans regia, and the genetic mechanism underlying this phenomenon is still unknown. In this study, we attempted to provide insight into the comprehensive transcriptome of red-leaf J. regia by RNA-Seq using Illumina SeqTM2000 platform. A total of 33,488,602 high-quality reads (3.35G cleans bases) were obtained and assembled into 53,782 unigenes. A total of 3,683 unigenes were annotated by using basic local alignment search tool to search against protein databases, All the matched unigenes were categorized by gene ontology analysis, and 3,466 were assigned to metabolism, among which 74 were mapped to anthocyanin, carotenoid, and betalain biosynthetic pathways by Kyoto Encyclopedia of Genes and Genomes analysis. Approximately 656 transcription factors were isolated including MYB, NAC, and bHLH. Additionally, a total of 13,981 simple sequence repeats, 41,088 single nucleotide polymorphisms, and 5,860 insertions and deletions were determined from J. regia transcriptome. Therefore, the current J. regia transcriptome provides deep insight into the molecular basis of red-leaf breeding of J. regia.

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