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 Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of JAZ Family Genes in Camellia Sinensis

2020 ◽  
Vol 21 (7) ◽  
pp. 2433 ◽  
Author(s):  
Jiazhi Shen ◽  
Zhongwei Zou ◽  
Hongqing Xing ◽  
Yu Duan ◽  
Xujun Zhu ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Abiotic Stresses ◽  
Synergistic Effects ◽  
Tea Plant ◽  
Plant Genome ◽  
Pcr Analysis ◽  
Limited Information ◽  
Genome Database ◽  
Recombinant Cells ◽  
Genome Wide

JAZ (Jasmonate ZIM-domain) proteins play pervasive roles in plant development and defense reaction. However, limited information is known about the JAZ family in Camellia sinensis. In this study, 12 non-redundant JAZ genes were identified from the tea plant genome database. Phylogenetic analysis showed that the 12 JAZ proteins belong to three groups. The cis-elements in promoters of CsJAZ genes and CsJAZ proteins interaction networks were also analyzed. Quantitative RT–PCR analysis showed that 7 CsJAZ genes were preferentially expressed in roots. Furthermore, the CsJAZ expressions were differentially induced by cold, heat, polyethylene glycol (PEG), methyl jasmonate (MeJA), and gibberellin (GA) stimuli. The Pearson correlations analysis based on expression levels showed that the CsJAZ gene pairs were differentially expressed under different stresses, indicating that CsJAZs might exhibit synergistic effects in response to various stresses. Subcellular localization assay demonstrated that CsJAZ3, CsJAZ10, and CsJAZ11 fused proteins were localized in the cell nucleus. Additionally, the overexpression of CsJAZ3, CsJAZ10, and CsJAZ11 in E. coli enhanced the growth of recombinant cells under abiotic stresses. In summary, this study will facilitate the understanding of the CsJAZ family in Camellia sinensis and provide new insights into the molecular mechanism of tea plant response to abiotic stresses and hormonal stimuli.

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 Genome-Wide Identification of the Tify Gene Family and Their Expression Profiles in Response to Biotic and Abiotic Stresses in Tea Plants (Camellia sinensis)

2020 ◽  
Vol 21 (21) ◽  
pp. 8316
Author(s):  
Xin Zhang ◽  
Wei Ran ◽  
Jin Zhang ◽  
Meng Ye ◽  
Songbo Lin ◽  
...  
Keyword(s):  
Gene Family ◽  
Camellia Sinensis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Defense Responses ◽  
Tea Plant ◽  
Specific Gene ◽  
Mechanical Wounding ◽  
Genome Wide

The TIFY family is a plant-specific gene family that is involved in regulating a variety of plant processes, including developmental and defense responses. The chromosome-level genome of the tea plant (Camellia sinensis) has recently been released, but a comprehensive view of the TIFY family in C. sinensis (the CsTIFY genes) is lacking. The current study performed an extensive genome-wide identification of CsTIFY genes. The phylogenetics, chromosome location, exon/intron structure, and conserved domains of these genes were analyzed to characterize the members of the CsTIFY family. The expression profiles of the CsTIFY genes in four organs were analyzed, and they showed different spatial expression patterns. All CsJAZ genes were observed to be induced by jasmonate acid (JA) and exhibited different responses to abiotic and biotic stresses. Six of seven CsJAZ genes (CsJAZ1, CsJAZ2, CsJAZ3, CsJAZ4, CsJAZ7, and CsJAZ8) were upregulated by mechanical wounding and infestation with the tea geometrid (Ectropis obliqua), while infection with tea anthracnose (Colletotrichum camelliae) primarily upregulated the expression levels of CsJAZ1 and CsJAZ10. In addition, CsJAZs were observed to interact with CsMYC2 and AtMYC2. Therefore, the results of this study may contribute to the functional characterization of the CsTIFY genes, especially the members of the JAZ subfamily, as regulators of the JA-mediated defense response in tea plant.

scholarly journals NHX Gene Family in Camellia sinensis: In-silico Genome-Wide Identification, Expression Profiles, and Regulatory Network Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Abhirup Paul ◽  
Archita Chatterjee ◽  
Shreya Subrahmanya ◽  
Guoxin Shen ◽  
Neelam Mishra
Keyword(s):  
Camellia Sinensis ◽  
Regulatory Network ◽  
Expression Profiles ◽  
Abiotic Factors ◽  
Purifying Selection ◽  
Tea Plant ◽  
Functional Study ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants, such as Arabidopsis thaliana and cotton; however, not much is known about NHXs in tea plant. In the present study, NHX genes of tea were obtained through a genome-wide search using A. thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER; CsNHX8) and plasma membrane (PM; CsNHX9), respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location, and protein-conserved motifs and domains were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes is subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in Camellia sinensis based on the orthologous genes in A. thaliana. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.

scholarly journals Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Liangbin Zeng ◽  
Airong Shen ◽  
Jia Chen ◽  
Zhun Yan ◽  
Touming Liu ◽  
...  
Keyword(s):  
Protein Function ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Natural Fiber ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Cdna Libraries ◽  
Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

scholarly journals De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

2021 ◽  
Vol 22 (18) ◽  
pp. 9874
Author(s):  
Matin Miryeganeh ◽  
Hidetoshi Saze
Keyword(s):  
Stress Tolerance ◽  
Molecular Mechanisms ◽  
High Salinity ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Natural Habitats ◽  
Mangrove Species ◽  
Mangrove Tree ◽  
Bruguiera Gymnorhiza

Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

2020 ◽  
Author(s):  
Yuxin Pan ◽  
Jinpeng Wang ◽  
Zhenyi Wang ◽  
Hengwei Liu ◽  
Lan Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Cotton Species ◽  
Expressional Analysis ◽  
Significant Positive Selection

Abstract Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton fibers. Here, we performed evolutionary, phylogenetic, and expressional analysis of UXS genes from cottons and other selected plants. Results: By exploring the sequenced cotton genomes, we identified 10, 10, 18, and 20 UXSs genes in Gossypium raimondii , Gossypium arboretum , Gossypium hirsutum and Gossypium barbadense , and retrieved their homologs from other representative plants, including 5 dicots, 1 monocot, 5 green alga, 1 moss, and 1 lycophyte. Phylogenetic analysis suggested that UXS genes could be divided into four subgroups and members within each subgroup shared similar exon-intron structures, motif and subcellular location. Notably, gene colinearity information indicates 100% constructed trees to have aberrant topology, and helps determine and use corrected phylogeny. In spite of conservative nature of UXS, during the evolution of Gossypium , UXS genes were subjected to significant positive selection on key evolutionary nodes. Expression profiles derived from RNA-seq data showed distinct expression patterns of GhUXS genes in various tissues and different development. Most of GhUXS gene expressed highly at 10, 20 and 25 DPA (day post anthesis) of fibers. Real-time quantitative PCR analysis GhUXS genes expressed highly at 20 DPA or 25 DPA. Conclusions: UXS is relatively conserved in plants and significant positive selection affects cotton UXS evolution. The comparative genome-wide identification and expression profiling would lay an important foundation to understanding the biological functions of UXS gene family in cotton species and other plants.

Comparative transcriptomic analysis of flowering induction in pitaya induced by supplementary lighting

2019 ◽  
Author(s):  
Rui Xiong ◽  
Liu Chengli ◽  
Min Xu ◽  
Shuang-Shuang Wei ◽  
Hua Tang
Keyword(s):  
Time Course ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Floral Induction ◽  
Transcriptomic Analysis ◽  
Pcr Analysis ◽  
Reverse Transcription Pcr ◽  
Transcription Factor Genes ◽  
Supplementary Lighting ◽  
Transcriptomic Level

Abstract Background Pitayas are currently attracting considerable interest as a fruit with many health benefits. However, the lack of natural light after November in Hainan, China, severely restricts the production of pitaya in winter. To further explore the molecular mechanisms regulating flowering in pitaya, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya subjected to light induction. Results We assembled 68113 unigenes in total, comprising 29782 unigenes with functional annotations in the NR database, 20716 annotations in SwissProt, 18088 annotations in KOG, and 11059 annotations in KEGG. Comparison between different samples revealed different numbers of significantly differentially expressed genes (DEGs). A number of DEGs involved in energy metabolism-related processes and plant hormones were detected. Moreover, we discovered many CONSTANS-LIKE, FLOWERING LOCUS T and other DEGs involved in direct regulation of flowering, along with CDF and TCP, which function as typical transcription factor genes in the flowering process. At the transcriptomic level, we confirmed 13 DEGs with different functions in the time-course response to light-induced flowering by quantitative reverse-transcription PCR analysis. Conclusions These DEGs may include some key genes that control the floral-induction network, increasing our understanding of the molecular mechanism of floral regulation in pitaya. These findings will also aid the development of biotechnologies aimed at creating a variant of pitaya that is less sensitive to light conditions and blooms throughout the year.

scholarly journals Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 172
Author(s):  
Boyin Jia ◽  
Yuan Liu ◽  
Qining Li ◽  
Jiali Zhang ◽  
Chenxia Ge ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Growth And Development ◽  
Molecular Mechanisms ◽  
Muscle Development ◽  
Sika Deer ◽  
De Novo ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Growth Development ◽  
Development And Aging

Studies of the gene and miRNA expression profiles associated with the postnatal late growth, development, and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA sequencing (RNA-seq) and microRNA sequencing (miRNA-seq) analyses to determine the differentially expressed (DE) unigenes and miRNAs from skeletal muscle tissues at 1, 3, 5, and 10 years in sika deer. A total of 51,716 unigenes, 171 known miRNAs, and 60 novel miRNAs were identified based on four mRNA and small RNA libraries. A total of 2,044 unigenes and 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 1,946 unigenes and 4 miRNAs were differentially expressed between adult and adolescent sika deer, and 2,209 unigenes and 1 miRNAs were differentially expressed between aged and adult sika deer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DE unigenes and miRNA were mainly related to energy and substance metabolism, processes that are closely associate with the growth, development, and aging of skeletal muscle. We also constructed mRNA–mRNA and miRNA–mRNA interaction networks related to the growth, development, and aging of skeletal muscle. The results show that mRNA (Myh1, Myh2, Myh7, ACTN3, etc.) and miRNAs (miR-133a, miR-133c, miR-192, miR-151-3p, etc.) may play important roles in muscle growth and development, and mRNA (WWP1, DEK, UCP3, FUS, etc.) and miRNAs (miR-17-5p, miR-378b, miR-199a-5p, miR-7, etc.) may have key roles in muscle aging. In this study, we determined the dynamic miRNA and unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent miRNAs and unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth, and maintenance and will also provide valuable information for sika deer genetic breeding.

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