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  • Open Access


    Growth and Transcriptomics Analysis of Michelia macclurei Dandy Plantlets with Different LED Quality Treatments

    Zhaoli Chen, Ying Liu*, Bingshan Zeng, Qingbin Jiang, Shengkun Wang, Xiangyang Li

    Phyton-International Journal of Experimental Botany, Vol.92, No.10, pp. 2891-2906, 2023, DOI:10.32604/phyton.2023.030664

    Abstract Michelia macclurei Dandy is a significant tree species that has extensive cultivation for forestry and horticulture purposes in southern China, owing to its economic and practical importance. Light quality influences plantlet growth and development during tissue culture. However, the growth characteristic and molecular regulation of M. macclurei under different light quality conditions are not well understood yet. In this study, we investigated the morphological, chlorophyll content, and transcriptomic responses of M. macclurei plantlets under different light-emitting diode (LED) qualities, including white, blue, and red light. The results showed that blue light significantly increased plant height (21.29%) and leaf number (18.65%),… More >

  • Open Access


    Transcriptome and Metabolome Revealed the Mechanism of NtBRL3 Overexpression Tobacco (Nicotiana tabacum L. K326) in Response to Drought Stress

    Jing Yang, Tianxiunan Pu, Ke Wan, Linqi Wang, Yuanshuai Shi, Xu Luo, Jie Tan, Dongmei Wang, Yang Liu*

    Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2555-2576, 2023, DOI:10.32604/phyton.2023.030301

    Abstract Drought has severely affected the yield and quality of commercial crops. The BRI1 family plays an important role in plant response to drought stress, and BRL3 gene plays an important role in the study of drought in Arabidopsis thaliana. In this study, NtBRL3 was constructed as a vector and genetically transformed to obtain ‘N. Tobacco K326’ overexpression of NtBRL3. The enzyme activities of transgenic tobacco and wild-type tobacco were measured and transcriptome and metabolome analyses were performed. The results showed that the antioxidant enzymes of transgenic tobacco were more active under drought conditions, and 85 significantly differentially metabolites and 106… More >

  • Open Access


    Comparative Transcriptome Analysis of Seed Germination of a Cotton Variety with High Tolerance to Low Temperature

    Genhai Hu1,*, Maoni Chao1, Xiuren Zhou2, Yuanzhi Fu2

    Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2535-2554, 2023, DOI:10.32604/phyton.2023.030163

    Abstract Gossypium hirsutum L. is an important cash crop native to the subtropics and is widely cultivated around the world. Low temperature is an important stress that seriously affects seed germination and emergence during planting. In this study, transcriptomic profiles of low-temperature- and normal-temperature-germinated seeds of Xinluzao 25, a variety with low-temperature tolerance and high germination rates, were analyzed and compared. The following results were obtained. (1) A total of 81.06 Gb of clean data were obtained after transcriptome sequencing and assembly, and 76,931 non-redundant Unigene sequences were obtained after data consolidation and concatenation; of these, 69,883 Unigene sequences were annotated.… More >

  • Open Access


    Transcriptome Profiling of the Salt-Stress Response in Paper Mulberry

    Jie Zhang1, Yingwei Zhao2, Hongying Li3, Jianwei Ni4,*, Dongmei Wang1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2591-2610, 2023, DOI:10.32604/phyton.2023.028338

    Abstract Paper mulberry is a high-quality woody feed resource plant with high crude protein content. It is widely distributed in China and has excellent characteristics of salt and alkali tolerance. Paper mulberry has ecological and economic importance. Salt stress has become a critical factor with the increasing degree of soil salinity that restricts plant growth. In the saline-alkali environments, transcriptome expression is altered leading to phenotypic defects in most plants. However, the regulatory mechanism related to paper mulberry’s salt-stress (SS) response is not clearly understood. In the present study de novo transcriptomic assembly was performed, and gene expression levels were measured… More >

  • Open Access


    Comprehensive analysis of the role of immune-related PANoptosis lncRNA model in renal clear cell carcinoma based on RNA transcriptome and single-cell sequencing


    Oncology Research, Vol.31, No.4, pp. 543-567, 2023, DOI:10.32604/or.2023.029563

    Abstract The high immune infiltration and heterogeneity of the microenvironment in clear cell renal cell carcinoma (ccRCC) result in the variability of prognosis and clinical response. While PANoptosis has strong immunogenicity and is worthy of further study. In this study, data from The Cancer Genome Atlas database was used to obtain immune-related PANoptosis lncRNAs with prognostic value. Subsequently, the role of these lncRNAs in cancer immunity, progression and the therapeutic response was analyzed, and a new prediction model was constructed. Additionally, we further explored the biological value of PANoptosis-related lncRNAs using single-cell data from the Gene Expression Omnibus database. PANoptosis-associated lncRNAs… More >

  • Open Access


    Transcriptome analysis reveals tumor antigen and immune subtypes of melanoma


    Oncology Research, Vol.31, No.3, pp. 389-403, 2023, DOI:10.32604/or.2023.029274

    Abstract Purpose: To screen potential tumor antigens for melanoma vaccine development and identify different immune subtypes. Methods: Transcriptional data (HTSEQ-FPKM) and clinical information of a 472 Melanoma cohort GDC TCGA Melanoma (SKCM) were downloaded from the UCSC XENA website (). Subsequently, transcriptome data and clinical information of 210 melanoma cohort GSE65904 were downloaded from Gene Expression Omnibus (GEO), a large global public database. All the transcriptome expression data matrices were log2 transformed for subsequent analysis. GEPIA, TIMER, and IMMPORT databases are also used for analysis. Cell function experiments were performed to validate the role of the IDO1 gene in melanoma cell… More >

  • Open Access


    Transcriptome Analysis of Auxin Drives Cone Size Regulation in Fokienia hodginsii

    Shunde Su1,2,#, Huan Chang3,#, Xiangyang Kang1,*, Renhua Zheng2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1713-1723, 2023, DOI:10.32604/phyton.2023.027586

    Abstract As the reproductive organ of the endangered species Fokienia hodginsii, the size of the cones is a constraint on the reproductive renewal of the population. In this study, the molecular basis of the influence of cone size on F. hodginsii was elucidated by comparing the phenotype, biochemistry, and transcriptome of two cultivars of F. hodginsii (‘FJ431’ and ‘FJ415’). The two cultivars differed significantly in cone size, with FJ431 having a significantly larger cone size and weight than FJ415, 1.32 and 1.90 times that of FJ415, respectively. RNA-Seq analysis of both cultivars retrieved 75,940 genes whose approximate functions were classified as… More >

  • Open Access


    Integrated Transcriptome and Small RNA Sequencing Analyses Reveals Insights into the Molecular Mechanism of Seed Germination in Mung Bean

    Yanyan Pu1,#, Liwen Wang2,#, Leilei Li3, Yujun Si4, Shubin Xie2, Yunzhe Cong1, Dong Wang1, Yongchao Gong1, Rumei Tian1, Xue Chen3, Xiaoyan Zhang1, Min Liu1, Hanfeng Ding1,3,*, Nana Li1,3,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1793-1812, 2023, DOI:10.32604/phyton.2023.026822

    Abstract During the life cycle of a plant, seed germination is crucial. Upon ingestion of water, the dry seeds resumed energy metabolism and cellular repair. To dissect the complex mechanisms at the very beginning of seed germination, two approaches including transcriptome and small RNA sequencing were conducted during the water imbibition process of mung bean seeds compared with dry seed. The transcriptome sequencing analysis identified 10,108 differentially expressed genes (DEGs) between dry and imbibed mung bean seeds. KEGG enrichment analyses demonstrated numerous DEGs involved in hormone signaling pathways, carbohydrate, and energy metabolism. Out of the total DEGs, 129 genes were investigated… More >

  • Open Access


    Comparative Non Participating Transcriptome Analysis Response to Low Phosphorus by CmPht1;2 in Chrysanthemum

    Chen Liu1,2 , Xiaowei Tang1,2, Xiaohui Qu1,2 , Fadi Chen1, Jiafu Jiang1 and Sumei Chen1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1391-1404, 2023, DOI:10.32604/phyton.2023.027231

    Abstract Chrysanthemum morifolium Ramat is one of the four major cut flowers in the world. Pht1 family is focus on the uptake and transport of phosphate in plants. In our previous studies, CmPht1;2 overexpression line (Oe1) had higher phosphate contents both in roots and shoots, and its root development was significantly enhanced than wild type (WT) at low phosphorus conditions in chrysanthemum. Metabolomics analysis showed that several metabolites had a change in pyruvate metabolism and tricarboxylic acid (TCA) cycle pathway. To explore the gene difference expression and the change of metabolic pathway between CmPht1;2-Oe1 and WT, we conducted the transcriptome analysis.… More >

  • Open Access


    Comparative Transcriptome Analyses Reveal Genes Related to Spine Development in Cucumber (Cucumis sativus)

    Yue Chen1,2,#, Huan Wang1,#, Taibai Xu1, Peng Zhou1, Junsong Pan2, Weiwei She1,*, Weiwei Zhang1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1059-1070, 2023, DOI:10.32604/phyton.2023.026486

    Abstract Fruit spine is an important quality trait of cucumber. To better understand the molecular basis of cucumber spine development and function, RNA-Seq was performed to identify differentially expressed genes (DEGs) in fruit spines of different development stages, namely, 8 days before anthesis (SpBA8), anthesis (SpA) and 8 days after anthesis (SpAA8). Stage-wise comparisons obtained 2,259 (SpBA8 vs. SpA), 4,551 (SpA vs. SpAA8), and 5,290 (SpBA8 vs. SpAA8) DEGs. All the DEGs were classified into eight expression clusters by trend analysis. Among these DEGs, in addition to the Mict, Tril, CsTTG1, CsMYB6, NS, and Tu genes that have been reported to… More >

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