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Search Results (31)
  • 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 >

  • Open Access


    Transcriptome analysis reveals potential genes associated with plant height in rice


    BIOCELL, Vol.47, No.2, pp. 409-421, 2023, DOI:10.32604/biocell.2023.023543

    Abstract Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects crop yield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified and described. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been well studied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified the differentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored the key pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of 2,184 DEGs,… More >

  • Open Access


    De Novo Transcriptome Analysis in Hevea brasiliensis to Unveil Genes Involved in Low Temperature Stress Response

    Bingsong Yang1,2,#, Xiaomeng Shi2,#, Tingting Guo1,2, Meixia Liang1,2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 559-575, 2023, DOI:10.32604/phyton.2022.024266

    Abstract Low temperature is one of the adversities threatening the growth and development and reduces the yield of rubber trees. However, molecular mechanisms toward rubber trees in response to low temperature are largely unclear. In this study, 7,159 and 7,600 differentially expressed genes (DEGs) were identified in ‘Reyan 73397’ rubber trees. Through GO analysis, the catalytic activity was the representative of the GO term in the only DEGs at the two studied temperatures (room temperature and 4°C, respectively), while KEGG analysis showed that carbon metabolism was the most important grouping under the comparison of these two temperatures. In addition, expression of… More >

  • Open Access


    Transcriptome Analysis of a Wild Eggplant Germplasm M239 in Response to Verticillium dahliae Infection

    Liyan Wu1, Jie Cheng1,2, Yaju Gong1, Rui Bao1, Zhibin Li1, Min Gui1,*, Guanghui Du2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 591-609, 2023, DOI:10.32604/phyton.2022.023481

    Abstract In this study, wild eggplant germplasm No. M239, which is highly susceptible to Verticillium wilt, was used as the experimental material. The physiological and biochemical indices (SOD, PAL, MDA and soluble protein) of M239 roots were measured at different times (0, 12, 24, 36, 48, 60 and 72 h) post inoculation with Verticillium dahliae, and the key time points for the M239 response to Verticillium wilt infection were screened. Then, RNA-Seq technology was used to screen the differentially expressed genes (DEGs) in M239 roots at 0, 12 and 48 h post-inoculation (hpi). The transcriptional results of M239 were also compared… More >

  • Open Access


    Full-Length Transcriptome Analysis of Cultivated and Wild Tetraploid Peanut

    Danlei Song#, Xiaona Yu#, Yaoyao Li, Xianheng Wang, Xinyuan Cui, Tong Si, Xiaoxia Zou, Yuefu Wang, Minglun Wang, Xiaojun Zhang*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 439-453, 2023, DOI:10.32604/phyton.2022.023165

    Abstract The high-quality genomes and large-scale full-length cDNA sequences of allotetraploid peanuts have been sequenced and released, which has accelerated the functional genomics and molecular breeding research of peanut. In order to understand the difference in the transcriptional levels of wild and cultivated peanuts. In this study, we integrated of second- and third-generation sequencing technologies to sequence full-length transcriptomes in peanut cv. Pingdu9616 and its putative ancestor Arachis monticola. The RNA extracted from six different tissues (i.e., roots, stems, leaves, flowers, needles and pods) were sampled at 20 days after flowering. A total of 31,764 and 33,981 high-quality transcripts were obtained… More >

  • Open Access


    The transcriptome analysis of cleft lip/palate-related PTCH1 variants in GMSM-K cells show carcinogenic potential


    BIOCELL, Vol.47, No.1, pp. 205-214, 2023, DOI:10.32604/biocell.2022.022572

    Abstract Cancer progression involves the sonic hedgehog (SHH) pathway, in which the receptor PTCH1 actives the downstream pathways. Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome (NBCCs) including neoplastic disease and congenital disorder. To evaluate the relationship between PTCH1 and cancer, we applied the CRISPR/Cas9 system to knock out PTCH1 in oral nontumorous epithelial cells (GMSM-K). Then we screened six PTCH1 variants associated with cleft lip/palate (CL/P), one of the congenital disorders in NBCCs, and generated PTCH1 variant and wild-type recombinant PTCH1−/− GMSM-K cell lines. Transcriptome sequencing was conducted in these cell lines. The results revealed that differentially… More >

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