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Plant Omics in Challenging Environment

Submission Deadline: 01 March 2022 (closed) View: 175

Guest Editors

Dr. Khalid Rehman Hakeem, King Abdulaziz University, Saudi Arabia
Dr. Munir Ozturk, Ege University, Turkey
Dr. Peerzada Yasir Yousuf, Department of Higher Education, Jammu and Kashmir, India

Summary

The changing environment is one of the predominant stressors that negatively influence plant growth, development, quality, and productivity. This is a wide-ranging topic on which numerous studies have been conducted globally to comprehend the physiological, biochemical, and molecular dynamisms operative in plants under challenging conditions. Despite all these efforts, various adaptive mechanisms of plants under the challenging environment remain to be uncovered. Therefore, modern tools and methods for the identification and application of genes, RNAs, and proteins responsible for increased yield and desirable agronomical traits in plants under challenging environments are needed. In the past few decades, plant omics tools are used to understand the deeper molecular tolerance networks in plants in a challenging environment.

 

This special issue intends to integrate recent omics approaches such as phenomics, genomics, transcriptomics, proteomics, metabolomics, cytomics and interactomics, to make novel advancements in defining the molecular aspects of plant response to the challenging environmental conditions.


Keywords

Phenomics; Genomics; Proteomics; Transcriptomics; Metabolomics; Resistance; Regulations; Environment

Published Papers

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  • Open Access

    ARTICLE

    Intron Retention Fine-Tunes the Resistance of the Rice Mutant pls4 to Rice Sheath Blight (Rhizotonia solani AG I.1a)

    Shaochun Liu, Jiamin Hu, Haohua He, Junru Fu, Xu Jie, Dahu Zhou, Haihui Fu
    Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2035-2049, 2023, DOI:10.32604/phyton.2023.028296
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract OsPLS4 encodes a β-ketoacyl carrier protein reductase (KAR). The role of OsPLS4 in rice sheath blight (Rhizoctonia solani) remains unclear. Our preliminary studies showed that premature leaf senescence mutants (pls4) were highly susceptive to sheath blight in the early stage of rice development. To explore the role of this gene in the development of rice sheath blight, the transcriptome profiles of the rice pls4 mutant and wild type were compared by RNA-seq. The results revealed 2,569 differentially expressed genes (DEGs). The down-regulated genes were significantly enriched in the defense response-related biological processes. These down-regulated genes included the chitinase… More >

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    615

  • Open Access

    ARTICLE

    Global and Comparative Proteome Analysis of Nitrogen-Stress Responsive Proteins in the Root, Stem and Leaf of Brassica napus

    Liang Chai, Cheng Cui, Benchuan Zheng, Jinfang Zhang, Jun Jiang, Haojie Li, Liangcai Jiang
    Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 645-663, 2023, DOI:10.32604/phyton.2023.024717
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Nitrogen (N) is one of the basic nutrients and signals for plant development and deficiency of it would always limit the productions of crops in the field. Quantitative research on expression of N-stress responsive proteins on a proteome level remains elusive. In order to gain a deep insight into the proteins responding to nitrogen stress in rapeseed (Brassica napus L.), comparative proteomic analysis was performed to investigate changes of protein expression profiles from the root, stem and leaf under different N concentrations, respectively. More than 200 differential abundance proteins (DAPs) were detected and categorized into groups More >

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    692

  • Open Access

    ARTICLE

    Transcriptome Analysis and Physiological Responses of Economic Macroalga Gracilariopsis lemaneiformis under Sulfate Deficiency

    Haojie Jia, Hong Du, Muhmmad Aslam, Tangcheng Li, Canqi Zheng, Xihui Xie, Nan Huang, Honghao Liang, Pengbing Pei, Ping Li, Weizhou Chen, Xiaojuan Liu
    Phyton-International Journal of Experimental Botany, Vol.92, No.1, pp. 91-110, 2023, DOI:10.32604/phyton.2022.022663
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Sulfur is an essential macronutrient for the growth of all photosynthetic organisms and plays important roles in different metabolic pathways. However, sulfur metabolism and its related research on macroalgae with important ecological value is rather limited. In this study, marine ecological valued macroalga Gracilariopsis lemaneiformis was used to study the general physiological responses and transcriptome profiling under the sulfate deficiency. The relative growth rate of algae under sulfate deficiency was statistically significantly lower than that of control after 6 days. However, no significant differences were observed in the pigments content and Fv/Fm value, indicating that the… More >

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    906

  • Open Access

    ARTICLE

    Overexpression of Wheat TaELF3-1BL Delays Flowering in Arabidopsis

    Junsheng Sun, Haozhen Zhang, Mingxia Zhang, Sishen Li, Yanrong An
    Phyton-International Journal of Experimental Botany, Vol.92, No.1, pp. 79-90, 2023, DOI:10.32604/phyton.2022.022225
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract EARLY FLOWERING 3 (ELF3), a light zeitnehmer (time-taker) gene, regulates circadian rhythm and photoperiodic flowering in Arabidopsis, rice, and barley. The three orthologs of ELF3 (TaELF3-1AL, TaELF3-1BL, and TaELF3-1DL) have been identified in wheat too, and one gene, TaELF3-1DL, has been associated with heading date. However, the basic characteristics of these three genes and the roles of the other two genes, TaELF3-1BL and, TaELF3-1AL, remain unknown. Therefore, the present study obtained the coding sequences of the three orthologs (TaELF3-1AL, TaELF3-1BL, and TaELF3-1DL) of ELF3 from bread wheat and characterized them and investigated the role of TaELF3-1BL in Arabidopsis. Protein sequence comparison revealed similarities… More >

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    829

  • Open Access

    ARTICLE

    Wheat Lysin-Motif-Containing Proteins Characterization and Gene Expression Patterns under Abiotic and Biotic Stress

    Minjie Liu, Na Gao, Yaqiong Zhao, Yingpeng Wu, Zongying Yuan
    Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2367-2382, 2022, DOI:10.32604/phyton.2022.021406
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Lysin motif (LysM)-containing proteins (LYPs) are important pattern recognition receptors in plants. However, the evolutionary history and characteristics of LYP genes remain largely unclear in wheat. In this study, 62 LYPs were identified at genome wide in wheat. Based on phylogenetic and domain analysis, wheat LYPs were classified into 6 subgroups (group LysMe, LysMn, LYP, LYK, LysMFbox). Syntenic analysis showed the evolution of LYP genes in wheat. RNA-seq data showed that 22 genes were not expressed at any tissue or stress stimulation period. Some LYP and LYK genes were tissue- or stage- specific. The majority of TaLYK5s, More >

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  • Open Access

    ARTICLE

    Selection and Verification of Reference Genes for qRT-PCR Analysis in Iris domestica under Drought

    Qiang Ai, Cuijing Liu, Mei Han, Limin Yang
    Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2537-2548, 2022, DOI:10.32604/phyton.2022.021889
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Iris domestica is a plant of the Iridaceae family and is drought-tolerant, but its drought-resistance mechanism is not yet clear. Analysing the gene expression changes of I. domestica by qRT-PCR is an important mean to understand its drought resistance characteristics. Nevertheless, a lack of reference genes greatly hinders investigation and research on the adaptation of I. domestica to drought at the molecular and genetic levels. In this study, we assessed the expression stability of 11 candidate gene in I. domestica under drought stress conditions and different tissues using geNorm, NormFinder, BestKeeper and RefFinder tools. The results showed that EF1β was More >

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    914

  • Open Access

    ARTICLE

    Genome-Wide Identification and Expression Profiling of the Shaker K+ Channel and HAK/KUP/KT Transporter Gene Families in Grape (Vitis vinifera L.)

    Han Lei, Junlin Li, Zhizhong Song
    Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2519-2536, 2022, DOI:10.32604/phyton.2022.021268
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Potassium (K+) is an essential macronutrient for plants to maintain normal growth and development. Shaker-like K+ channels and HAK/KUP/KT transporters are critical components in the K+ acquisition and translocation. In this study, we identified 9 Shaker-like K+ channel (VvK) and 18 HAK/KUP/KT transporter (VvKUP) genes in grape, which were renamed according to their distributions in the genome and relative linear orders among the distinct chromosomes. Similar structure organizations were found within each group according to the exon/intron structure and protein motif analysis. Chromosomal distribution analysis showed that 9 VvK genes and 18 VvKUP genes were unevenly distributed on 7… More >

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    1527

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    803

  • Open Access

    ARTICLE

    Transcriptome Analysis and Morphological Changes in Response to Waterlogging in Iris pseudacorus

    Xiaofang Yu, Linjie Yue, Qing Wu, Liu Yang, Chunyu Fan, Zhiwen Wang, Jiani Hu
    Phyton-International Journal of Experimental Botany, Vol.91, No.10, pp. 2135-2162, 2022, DOI:10.32604/phyton.2022.020139
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Iris pseudacorus is a widely cultivated and studied ornamental plant with a large biomass, strong adaptability and extensive management. Moreover, it has the ability to decontaminate and enrich heavy metals. However, few studies have been conducted on its submergence tolerance with little known about the molecular response of I. pseudacorus to flooding. Morphologically, I. pseudacorus had strong adaptability to waterlogging, the aerenchyma was gradually enlarged and adventitious roots developed between 0 and 14 d. The transcriptome data showed that the differentially expressed genes counts in plants flooded for 2 h, 4 h, 12 h and 24 h compared… More >

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    1398

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    926

  • Open Access

    ARTICLE

    Genome-Wide Characterization of the Cellulose Synthase Gene Superfamily in Tea Plants (Camellia sinensis)

    Qianqian Li, Qi Zhao, Xinzhuan Yao, Baohui Zhang, Litang Lu
    Phyton-International Journal of Experimental Botany, Vol.91, No.10, pp. 2163-2189, 2022, DOI:10.32604/phyton.2022.021530
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract The cellulose synthase gene superfamily, including Cellulose synthase A (CesA) and cellulose synthase-like (Csl) gene families, is responsible for the synthesis of cellulose and hemicellulose, respectively. The CesA/Csl genes are vital for abiotic stress resistance and shoot tenderness regulation of tea plants (Camellia sinensis). However, the CesA/Csl gene family has not been extensively studied in tea plants. Here, we identified 53 CsCesA/Csl genes in tea plants. These genes were grouped into five subfamilies (CsCesA, CsCslB, CsCslD, CsCslE, CsCslG) based on the phylogenetic relationships with Arabidopsis and rice. The analysis of chromosome distribution, gene structure, protein domain and motif revealed that most genes in CsCesA,… More >

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    1755

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    882

  • Open Access

    ARTICLE

    Identification of Suitable Reference Genes for qRT-PCR Normalization in Tilia miqueliana Maxim

    Huanli Wang, Lingjun Yan, Xi Huang, Zhongwei Wang, Yuanhao Yue, Shijie Tang
    Phyton-International Journal of Experimental Botany, Vol.91, No.10, pp. 2191-2210, 2022, DOI:10.32604/phyton.2022.020735
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Quantitative real-time polymerase chain reaction (qRT-PCR) is a rapid and effective approach toward detecting the expression patterns of target genes. The selection of a stable reference gene under specific test condition is essential for expressing levels of target genes accurately. Tilia miqueliana, considered endangered, is a prominent native ornamental and honey tree in East China. No study has evaluated the optimal endogenous reference gene for qRT-PCR analysis in T. miqueliana systematically. In this study, fifteen commonly used reference genes were selected as candidate genes, and the stabilities of their expressions were assessed using four algorithms (GeNorm, NormFiner,… More >

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    1561

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    709

  • Open Access

    ARTICLE

    Analysis of Seed Phenotypic and Metabolic Characteristics of Diploid and Tetraploid Tartary Buckwheat

    Xiaodong Shi, Cong Wang, Wenjian Li, Hanlei Xiao, Yanjie Li, Bei Niu
    Phyton-International Journal of Experimental Botany, Vol.91, No.9, pp. 1973-1986, 2022, DOI:10.32604/phyton.2022.020065
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Polyploid plants grow well, are stress tolerant, and are rich in nutrients and bioactive compounds. Thus, they are useful for improving crop quality and yield. In this study, we compared the seed characteristics and metabolite profiles of diploid and tetraploid tartary buckwheat, which was developed via an artificially induced chromosome doubling event. The length, width, area, and thousand-grain weight were greater for the tetraploid seeds than for the diploid seeds. However, the germination rate decreased for the tetraploid seeds. Additionally, there was a gap between the shell and kernel of the tetraploid seeds. Moreover, the… More >

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    1569

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    697

  • Open Access

    ARTICLE

    Comparative Analysis of the Complete Chloroplast Genome Sequences of Four Origin Plants of Lonicerae Flos (Lonicera; Caprifoliaceae)

    Sisi Liu, Lisi Zhou, Jiaoli Huang, Huijie Zeng, Zhongquan Qiao, Yongxin Li, Gang Zhang
    Phyton-International Journal of Experimental Botany, Vol.91, No.7, pp. 1503-1516, 2022, DOI:10.32604/phyton.2022.020390
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Lonicerae Flos (LF) derived from the dried flower buds or opening flowers of four Lonicera plants (Lonicera macranthoides, L. hypoglauca, L. confusa, and L. fulvotnetosa), is a popular traditional Chinese medicine. Because the four origin plants are very similar in morphology, it is difficult to control the quality of LF in actual production. Over the past decade, many reports have pointed out the differences among them, including the botanical characteristics and active ingredients. However, there is still a lack of rapid methods that can be applied to the identification of the four origins. In this study, comparative analysis of the… More >

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    1765

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    1053

  • Open Access

    ARTICLE

    Comparative Transcriptome Analysis Reveals Different Mechanisms of Adaptation to Environment among Three Species of Saussurea DC.

    Weimin Zhao, Fengzhen Li, Guomin Shi, Jialei Guo, Guifang He, Tao He
    Phyton-International Journal of Experimental Botany, Vol.91, No.7, pp. 1517-1528, 2022, DOI:10.32604/phyton.2022.019630
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Saussurea medusa, Saussurea hypsipeta and Saussurea obvallata are typical alpine snowline plants growing in the Qinghai-Tibet plateau. They are characterized by a specialized morphology. S. medusa and S. hypsipeta have very dense trichomes on whole plant, whereas S. obvallata has transparent bracts covered inflorescences. The different forms reflect their adaptation to cold environments. To investigate the different mechanisms of adaptation of these species to cold temperatures, transcriptome sequencing was performed in three species of Saussurea DC. A total of 116394 137237 and 113879 Unigenes were identified from S. medusa, S. hypsipeta and S. obvallata, respectively. Of these, 55909 (48.03%), 65519 (47.74%) and 51889 (45.56%) Unigenes… More >

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    831

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  • Open Access

    ARTICLE

    Molecular Basis of Unique Branching Phenotypes in Salvia splendens and the Role of PSY

    Peipei Hong, Mei Wang, Liting Zhi, Hongwei Chen, Kefeng Liu, Hongli Wang
    Phyton-International Journal of Experimental Botany, Vol.91, No.6, pp. 1211-1226, 2022, DOI:10.32604/phyton.2022.018435
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract The branching system of higher plants plays a very important role in plant morphogenesis, and the number of branches can directly affect crop yield and the ornamental value of plants. It is a complicated development process involving complex molecular mechanisms. The ‘Cailinghong’ variety of Salvia splendens is characterized by its great branching ability with the ability to grow into a spherical form naturally, without pinching. To gain insight into the molecular events during the branching development of S. splendens, suppressive subtractive hybridization (SSH) technology was used to screen differentially expressed genes between the erect plant type (strain… More >

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    1792

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    974

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    ARTICLE

    Integrated Analysis of Metabolome and Transcriptome of Bambusa emeiensis Shoots in Response to Bamboo Snout Beetle Cyrtotrachelus buqueti (Coleoptera: Curculionidae)

    Hao Tang, Yuanqiu Li, Chaobing Luo
    Phyton-International Journal of Experimental Botany, Vol.91, No.6, pp. 1227-1244, 2022, DOI:10.32604/phyton.2022.019278
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Plants have evolved constitutive and inductive defense mechanisms to protect themselves from herbivorous insects. Metabolites in plants are thought to be involved in response to herbivores. Bambusa emeiensis is an important bamboo species widely distributed in Southwest China. It is easy to attract herbivores such as Cyrtotrachelus buqueti. Through the detection and analysis of metabolites in B. emeiensis metabolomic data, 35 differential metabolites (biomarkers) were finally identified from 206 detection peaks, mainly primary metabolites. Subsequently, we conducted an association analysis between 35 biomarkers that annotated to be involved in 71 metabolic pathways in the metabolome and 324 differentially… More >

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    1034

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    ARTICLE

    Identification of a Unique Germacrene A Oxidase from Xanthium strumarium

    Lifen Zheng, Fangfang Chen, Yuanjun Li, Changfu Li
    Phyton-International Journal of Experimental Botany, Vol.91, No.5, pp. 989-998, 2022, DOI:10.32604/phyton.2022.019219
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract 8,12-sesquiterpene lactones (STLs) are an important class of natural products with unique pharmaceutical activities. For years the pathway leading to 8,12-STLs remains an enigma. Xanthium strumarium accumulates abundant 8,12-STLs, and xanthatin is a characteristic 8,12-STL in it. Xanthatin has been previously postulated to be derived from germacrene A, but the steps from germacrene A to xanthatin are unknown. As part of an effort to understand the xanthatin biosynthetic pathway. This study reports the characterization of a unique germacrene A oxidase (XsGAO) from X. strumarium. Unlike a classical GAO enzyme, which is known to catalyze a three-step oxidation More >

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    ARTICLE

    Cloning and Characterization of EuGID1 in Eucommia ulmoides Oliver

    Yulu Chen, Fen Zhang, Ju Cai, Yichen Zhao, Jiaxue Cui, Yan Li
    Phyton-International Journal of Experimental Botany, Vol.91, No.5, pp. 999-1013, 2022, DOI:10.32604/phyton.2022.018984
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Gibberellic acid controlled the key developmental processes of the life cycle of landing plants, and regulated the growth and development of plants. In this study, a novel gibberellin receptor gene EuGID1 was obtained from Eucommia ulmoides Oliver. The cDNA of EuGID1 was 1556 bp, and the open reading frame was 1029 bp, which encoded 343 amino acids. EuGID1 had the homology sequence with the hormone-sensitive lipase family. Amino acid sequence alignment confirmed EuGID1 protein had the highest homology with the GID1 protein of Manihot esculenta. EuGID1 was located in the nucleus and cell membrane and had expression in four plant More >

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    1051

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    ARTICLE

    Proteomic Analysis of Chrysanthemum Lateral Buds after Removing Apical Dominance Based on Label-Free Technology

    Sicong Zheng, Jingjing Song, Cheng Luo, Xin Li, Qiqi Ma, Beibei Jiang, Qinglin Liu, Yuanzhi Pan
    Phyton-International Journal of Experimental Botany, Vol.91, No.3, pp. 525-539, 2022, DOI:10.32604/phyton.2022.017629
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Studying the genetic basis and regulatory mechanism of chrysanthemum lateral bud outgrowth is of great significance for reduction the production cost of cut chrysanthemum. To clarify the molecular basis of lateral bud elongation after removal of apical dominance in chrysanthemum, label-free quantification analysis was used to analyze the proteome changes after apical bud removal. Quantitative real-time PCR (qPCR) was used to analyze the changes in the expression of three plant hormone-related genes. A total of 440 differentially expressed proteins were successfully identified at three time points during the lateral bud elongation. The number of differentially… More >

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    1163

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    ARTICLE

    Identification of Genes Involved in Celastrol Biosynthesis by Comparative Transcriptome Analysis in Tripterygium wilfordii

    Yaru Zhu, Xiujun Zhang, Yansheng Zhang, Shiyou Lü, Changfu Li
    Phyton-International Journal of Experimental Botany, Vol.91, No.2, pp. 279-291, 2022, DOI:10.32604/phyton.2022.017625
    （This article belongs to the Special Issue: Plant Omics in Challenging Environment)
    Abstract Tripterygium wilfordii has been renowned mostly because of the anticancer effects of its root extracts, which is partly ascribed to the presence of celastrol, a pentacyclic triterpenoid, as one of the main active components. Celastrol also has recently been reported as an effective prodrug in the treatment of obesity. Despite the promising activities, the pathway leading to celastrol biosynthesis, especially cytochrome P450 (CYP) enzyme(s) that occur in its downstream steps, are largely unknown. This study conducted a comparative analysis of the T. wilfordii transcriptome derived from its root and leaf tissues. Differential gene expression analysis identified a More >

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