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  • Open Access

    ARTICLE

    Transcriptome Analysis of Inflorescence Development at the Five-Leaf Stage in Castor (Ricinus communis L.)

    Yong Zhao1,#, Yaxuan Jiang3,#, Li Wen1, Rui Luo2, Guorui Li2, Jianjun Di2, Mingda Yin2, Zhiyan Wang2, Fenglan Huang2,4,5,6,7,*, Fanjuan Meng3,*

    Phyton-International Journal of Experimental Botany, Vol.93, No.4, pp. 713-723, 2024, DOI:10.32604/phyton.2024.047657

    Abstract The yield of castor is influenced by the type of inflorescence and the proportion of female flowers. However, there are few studies on the genetic mechanism involved in the development and differentiation of castor inflorescences. In this study, we performed transcriptomic analyses of three different phenotypes of inflorescences at the five-leaf stage. In comparison to the MI (complete pistil without willow leaves), 290 and 89 differentially expressed genes (DEGs) were found in the SFI (complete pistil with willow leaves) and the BI (monoecious inflorescence), respectively. Among the DEGs, 104 and 88 were upregulated in the SFI and BI, respectively, compared… More >

  • Open Access

    ARTICLE

    Antitumor effects of a novel photosensitizer-mediated photodynamic therapy and its influence on the cell transcriptome

    JINGJING CHEN1, DAN WANG2, ZEQUN WANG2, MENGYUAN HAN4, HOUQING YIN2, WENTING ZHOU4, RIBAI YAN5, YAN PAN2,3,*

    Oncology Research, Vol.32, No.5, pp. 911-923, 2024, DOI:10.32604/or.2023.042384

    Abstract Photodynamic therapy (PDT) is a promising cancer treatment. This study investigated the antitumor effects and mechanisms of a novel photosensitizer meso-5-[ρ-diethylene triamine pentaacetic acid-aminophenyl]−10,15,20-triphenyl-porphyrin (DTP) mediated PDT (DTP-PDT). Cell viability, reactive oxygen species (ROS), and apoptosis were measured with a Cell Counting Kit-8 assay, DCFH-DA fluorescent probe, and Hoechst staining, respectively. Cell apoptosis- and autophagy-related proteins were examined using western blotting. RNA sequencing was used to screen differentially expressed mRNAs (DERs), and bioinformatic analysis was performed to identify the major biological events after DTP-PDT. Our results show that DTP-PDT inhibited cell growth and induced ROS generation in MCF-7 and SGC7901… More > Graphic Abstract

    Antitumor effects of a novel photosensitizer-mediated photodynamic therapy and its influence on the cell transcriptome

  • Open Access

    ARTICLE

    Transcriptome-Wide Identification and Functional Analysis of PgSQE08-01 Gene in Ginsenoside Biosynthesis in Panax ginseng C. A. Mey.

    Lei Zhu1,#, Lihe Hou1,3,#, Yu Zhang1, Yang Jiang1, Yi Wang1,2, Meiping Zhang1,2, Mingzhu Zhao1,2,*, Kangyu Wang1,2,*

    Phyton-International Journal of Experimental Botany, Vol.93, No.2, pp. 313-327, 2024, DOI:10.32604/phyton.2024.047938

    Abstract Panax ginseng C. A. Mey. is an important plant species used in traditional Chinese medicine, whose primary active ingredient is a ginsenoside. Ginsenoside biosynthesis is not only regulated by transcription factors but also controlled by a variety of structural genes. Nonetheless, the molecular mechanism underlying ginsenoside biosynthesis has always been a topic in the discussion of ginseng secondary metabolites. Squalene epoxidase (SQE) is a key enzyme in the mevalonic acid pathway, which affects the biosynthesis of secondary metabolites such as terpenoid. Using ginseng transcriptome, expression, and ginsenoside content databases, this study employed bioinformatic methods to systematically analyze the genes encoding… More >

  • Open Access

    ARTICLE

    Differential Expression of Genes Related to Fruit Development and Capsaicinoids Synthesis in Habanero Pepper Plants Grown in Contrasting Soil Types

    Eduardo Burgos-Valencia1,#, Federico García-Laynes1,#, Ileana Echevarría-Machado1, Fatima Medina-Lara1, Miriam Monforte-González1, José Narváez-Zapata2,*, Manuel Martínez-Estévez1,*

    Phyton-International Journal of Experimental Botany, Vol.93, No.2, pp. 151-183, 2024, DOI:10.32604/phyton.2023.046943

    Abstract Habanero pepper (Capsicum chinense Jacq.) is a crop of economic relevance in the Peninsula of Yucatan. Its fruits have a high level of capsaicinoids compared to peppers grown in other regions of the world, which gives them industrial importance. Soil is an important factor that affects pepper development, nutritional quality, and capsaicinoid content. However, the effect of soil type on fruit development and capsaicinoid metabolism has been little understood. This work aimed to compare the effect of soils with contrasting characteristics, black soil (BS) and red soil (RS), on the expression of genes related to the development of fruits, and… More >

  • Open Access

    ARTICLE

    Physiological and Transcriptome Analysis Illuminates the Molecular Mechanisms of the Drought Resistance Improved by Alginate Oligosaccharides in Triticum aestivum L.

    Yunhong Zhang1,2,*, Yonghui Yang1,2, Jiawei Mao1,2

    Phyton-International Journal of Experimental Botany, Vol.93, No.2, pp. 185-212, 2024, DOI:10.32604/phyton.2023.046811

    Abstract Alginate oligosaccharides (AOS) enhance drought resistance in wheat (Triticum aestivum L.), but the definite mechanisms remain largely unknown. The physiological and transcriptome responses of wheat seedlings treated with AOS were analyzed under drought stress simulated with polyethylene glycol-6000. The results showed that AOS promoted the growth of wheat seedlings and reduced oxidative damage by improving peroxidase and superoxide dismutase activities under drought stress. A total of 10,064 and 15,208 differentially expressed unigenes (DEGs) obtained from the AOS treatment and control samples at 24 and 72 h after dehydration, respectively, were mainly enriched in the biosynthesis of secondary metabolites (phenylpropanoid biosynthesis,… More >

  • Open Access

    ARTICLE

    CHDTEPDB: Transcriptome Expression Profile Database and Interactive Analysis Platform for Congenital Heart Disease

    Ziguang Song1,2, Jiangbo Yu1, Mengmeng Wang3, Weitao Shen4, Chengcheng Wang1, Tianyi Lu1, Gaojun Shan1, Guo Dong1, Yiru Wang1, Jiyi Zhao1,*

    Congenital Heart Disease, Vol.18, No.6, pp. 693-701, 2023, DOI:10.32604/chd.2024.048081

    Abstract CHDTEPDB (URL: ) is a manually integrated database for congenital heart disease (CHD) that stores the expression profiling data of CHD derived from published papers, aiming to provide rich resources for investigating a deeper correlation between human CHD and aberrant transcriptome expression. The development of human diseases involves important regulatory roles of RNAs, and expression profiling data can reflect the underlying etiology of inherited diseases. Hence, collecting and compiling expression profiling data is of critical significance for a comprehensive understanding of the mechanisms and functions that underpin genetic diseases. CHDTEPDB stores the expression profiles of over 200 sets of 7… More >

  • Open Access

    ARTICLE

    Physiological Dynamics and Transcriptomic Analysis of Cut Roses ‘Carola’ Treated with KNO

    Songmei Liu, Yuheng Wu, Hongmei Li, Dongli Cai, Huiling Liang, Changchun Ye, Shenggen He*

    Phyton-International Journal of Experimental Botany, Vol.92, No.12, pp. 3267-3290, 2023, DOI:10.32604/phyton.2023.045453

    Abstract

    The consumption of cut roses (Rosa hybrida) has always ranked first in the world. However, it is vulnerable to rapid petal and leaf wilting due to leaf stomatal water loss, which seriously affects its ornamental quality and economic value. Stomatal movement, a key in plant physiological processes, is influenced by potassium and nitrate. Advancing comprehension of its physiological and molecular mechanism holds promise for preserving the freshness of cut roses. This study observed the impacts of different concentrations of KNO3 vase treatments on stomatal opening and water loss in cut rose ‘Carola’ leaves, as well as their transcriptional responses to… More >

  • Open Access

    ARTICLE

    Analysis of differentially expressed genes in Verruca vulgaris vs. adjacent normal skin by RNA-sequencing

    QINGQING GUO1,2, JIAYUE QI1,2, XIAOQIANG LIANG2, ZIGANG ZHAO2, JIA BAI2, FANG XIE2,#,*, CHENGXIN LI1,2,#,*

    BIOCELL, Vol.47, No.11, pp. 2435-2443, 2023, DOI:10.32604/biocell.2023.043126

    Abstract Introduction: Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes. Currently, very little genetic information is available regarding verruca vulgaris in the Chinese population. This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing. Methods: High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform. The transcriptomes were analyzed using bioinformatics and the differentially expressed genes (DEGs) were verified by immunohistochemistry. Verruca vulgaris exhibited a unique molecular signature. Results: In total, 1,643 DEGs were identified in verruca… More >

  • Open Access

    EDITORIAL

    Editorial: Transcriptome analysis in tumor microenvironment and tumor heterogeneity

    JINHUI LIU1,*, JIAHENG XIE2,*, PEIXIN DONG3

    Oncology Research, Vol.32, No.1, pp. 99-100, 2024, DOI:10.32604/or.2023.045719

    Abstract This article has no abstract. More >

  • Open Access

    ARTICLE

    Transcriptomic Responses of Garlic (Allium sativum L.) to Heat and Drought Stresses

    Seung Hee Eom, Tae Kyung Hyun*

    Phyton-International Journal of Experimental Botany, Vol.92, No.11, pp. 3077-3090, 2023, DOI:10.32604/phyton.2023.044032

    Abstract Heat and drought are prominent abiotic stressors that limit crop productivity and yield, particularly concerning climate change; therefore, understanding the molecular mechanisms underlying plant stress responses is crucial for stress-tolerant crop production. This study conducted a transcriptomic analysis to elucidate how garlic (Allium sativum L.) responds to drought and heat stress conditions. Transcriptome libraries were generated to identify differentially expressed genes (DEGs) induced by drought and heat stresses. Functional classification and clustering analysis of DEGs revealed stress-specific gene expression patterns. Notably, cell wall-related genes were implicated in the drought response, whereas heat stress was associated with heat stress transcription factors… More >

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