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  • Open Access


    Identification and Expression Analysis of Abscisic Acid Signal Transduction Genes in Hemp Seeds

    Cong Hou1, Kang Ning1, Xiuye Wei1, Yufei Cheng1, Huatao Yu1, Haibin Yu2, Xia Liu1,*, Linlin Dong1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2087-2103, 2023, DOI:10.32604/phyton.2023.029041

    Abstract Abscisic acid (ABA) is involved in regulating diverse biological processes, but its signal transduction genes and roles in hemp seed germination are not well known. Here, the ABA signaling pathway members, PYL, PP2C and SnRK2 gene families, were identified from the hemp reference genome, including 7 CsPYL (pyrab-actin resistance1-like, ABA receptor), 8 CsPP2CA (group A protein phosphatase 2c), and 7 CsSnRK2 (sucrose nonfermenting1-related protein kinase 2). The content of ABA in hemp seeds in germination stage is lower than that in non-germination stage. Exogenous ABA (1 or 10 μM) treatment had a significant regulatory effect on the selected PYL, PP2C,… More >

  • Open Access


    Genome-Wide Identification and Expression Analysis of the Phytocyanin Gene Family in Nicotiana tabacum

    Peiling Wang1,#, Xiaohong Xu2,#, Yong Li2, Hecui Zhang1, Xuejie Zhang3, Siru Zhou1, Yimei Liu1, Yunyan Feng1, Tonghong Zuo1, Liquan Zhu1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1469-1492, 2023, DOI:10.32604/phyton.2023.027133

    Abstract Phytocyanin (PC) is a class of plant-specific blue copper proteins involved in electron transport, plant growth, development, and stress resistance. However, PC proteins have not been systematically evaluated in tobacco plants. We determined the whole-genome sequences of the PC family in the tobacco cultivar ‘K326.’ The transcriptome data were used to analyze the expression of the NtPC family at different development stages and tissue-specific genes. Real-time fluorescence quantitative analysis was used to analyze the expression of the NtPC gene family under low temperature and methyl jasmonate stress. The tobacco NtPC family contained 110 members and was divided into four subfamilies:… More >

  • Open Access


    Correlating Transcriptional Networks to Papillary Renal Cell Carcinoma Survival: A Large-Scale Coexpression Analysis and Clinical Validation

    Xingliang Feng*1, Meng Zhang*†1, Jialin Meng*, Yongqiang Wang, Yi Liu*, Chaozhao Liang*, Song Fan*

    Oncology Research, Vol.28, No.3, pp. 285-297, 2020, DOI:10.3727/096504020X15791676105394

    Abstract We aimed to investigate the potential mechanisms of progression and identify novel prognosis-related biomarkers for papillary renal cell carcinoma (PRCC) patients. The related data were derived from The Cancer Genome Atlas (TCGA) and then analyzed by weighted gene coexpression network analysis (WGCNA). The correlation between each module and the clinical traits were analyzed by Pearson’s correlation analysis. Pathway analysis was conducted to reveal potential mechanisms. Hub genes within each module were screened by intramodule analysis, and visualized by Cytoscape software. Furthermore, important hub genes were validated in an external dataset and clinical samples. A total of 5,839 differentially expressed genes… More >

  • Open Access


    Genome-wide identification of NAC gene family and expression analysis under abiotic stresses in Salvia miltiorrhiza


    BIOCELL, Vol.46, No.8, pp. 1947-1958, 2022, DOI:10.32604/biocell.2022.019806

    Abstract NAC (NAM, ATAF, CUC) is a class of transcription factors involved in plant growth regulation, abiotic stress responses, morphogenesis and metabolism. Salvia miltiorrhiza is an important Chinese medicinal herb, but the characterization of NAC genes in this species is limited. In this study, based on the Salvia miltiorrhiza genomic databases, 82 NAC transcription factors were identified, which were divided into 14 groups. Meanwhile, phylogenetic analysis, gene structure, chromosomal localization and potential role of SmNACs in abiotic stress conditions were also studied. The results revealed that some SmNACs had different structures than others, which advised that these genes may have multiple/distinct… More >

  • Open Access


    Genome-wide identification of U-box gene family and expression analysis under abiotic stresses in Salvia miltiorrhiza


    BIOCELL, Vol.46, No.7, pp. 1751-1762, 2022, DOI:10.32604/biocell.2022.019455

    Abstract Plant U-box (PUB) E3 ubiquitin ligases play important roles in hormone signaling pathways and in response to different abiotic stresses, but little is known about U-box genes in Danshen (root of Salvia miltiorrhiza Bunge). Here, we identified and characterized 70 SmPUB genes based on its genome sequence. Phylogenetic analysis of U-box genes from S. miltiorrhiza and Arabidopsis suggested that they can be clustered into seven subgroups (I–VII). Typical U-box domains were found in all identified SmPUB genes through the analysis of conserved motifs. Moreover, qRT-PCR was applied to analyze the relative expression levels of U-box genes in S. miltiorrhiza roots… More >

  • Open Access


    Expression analysis of OsSERK, OsLEC1 and OsWOX4 genes in rice (Oryza sativa L.) callus during somatic embryo development


    BIOCELL, Vol.46, No.7, pp. 1633-1641, 2022, DOI: 10.32604/biocell.2022.019111

    Abstract Somatic embryogenesis is an asexual reproduction process that occurs in many plant species, including rice. This process contains several totipotency markers such as Somatic Embryogenesis Receptor-like Kinase (SERK), Leafy Cotyledon1 (LEC1) and WUSCHEL-Related Homeobox4 (WOX4) and also a helpful model for embryo development and clones and transformations. Here, we report the gene expression during somatic embryo development correlates with regeneration frequency in 14 Javanica rice (pigmented and non-pigmented) using modifified N6 media supplemented with Kinetin (2.0 mg/L) and NAA (1.0 mg/L). Although there have been advances in understanding the genetic basis of somatic embryogenesis in other varieties, rice is still… More >

  • Open Access


    Genome-wide identification, characterization, and expression analysis of aluminum-activated malate transporter genes (ALMTs) in Gossypium hirsutum L.


    BIOCELL, Vol.46, No.5, pp. 1347-1356, 2022, DOI:10.32604/biocell.2022.018254

    Abstract Aluminum-activated malate transporters (ALMT) are widely involved in plant growth and metabolic processes, including adaptation to acid soils, guard cell regulation, anion homeostasis, and seed development. Although ALMT genes have been identified in Arabidopsis, wheat, barley, and Lotus japonicus, little is known about its presence in Gossypium hirsutum L. In this study, ALMT gene recognition in diploid and tetraploid cotton were done using bioinformatics analysis that examined correlation between homology and evolution. Differentially regulated ALMT genetic profile in G. hirsutum was examined, using RNA sequencing and qRT-PCR, during six fiber developmental time-points, namely 5 d, 7 d, 10 d, 15… More >

  • Open Access


    Genome-Wide Identification, Expression Profiling and Protein-Protein Interaction Properties of the BEL-Like Homeodomain Gene Family in Apple

    Huifeng Li1, Qiang Zhao2, Hai Wang1, Qinglong Dong3,*, Yi Xu4,*

    Phyton-International Journal of Experimental Botany, Vol.91, No.2, pp. 315-331, 2022, DOI:10.32604/phyton.2022.016951

    Abstract BEL1-like homeodomain (BLH) family proteins are homeodomain transcription factors, which are found ubiquitously in plants and play important roles in regulating meristem and flower development. Although BLH proteins have been reported in some plant species, there is very little information available for plants in the Malus genus (e.g., apple tree:Malus domestica). In the present study, we identified 19 apple MdBLH genes. Phylogenetic analysis revealed that the MdBLH genes could be divided into five groups. Analysis of gene structure showed that MdBLH gene has four exons, and the third exon was 61 bp in length. Chromosomal location analysis suggested that the MdBLHMore >

  • Open Access


    Genome-wide identification and in silico gene expression analysis of the related to ABI3/VP1 (RAV) transcription factor family in barley (Hordeum vulgare L.)


    BIOCELL, Vol.45, No.6, pp. 1673-1685, 2021, DOI:10.32604/biocell.2021.016316

    Abstract RAV (Related to ABI3/VP1) transcription factors are unique members of the AP2-ERF superfamily with AP2 and B3 domains and play important roles in the regulation of seed germination, plant growth, and stress response. In the study, 7 RAV genes, named HvRAVs, were identified in barley based on the available genome sequences. While five of the seven HvRAVs were located on chromosome 3, HvRAV5 and HvRAV7 were located on chromosome 1 and 4, respectively. Six of the predicted HvRAVs were intron-less, except HvRAV2, which had one intron. HvRAV proteins have shown basic, instable, and hydrophilic properties. The AP2 domain specific RAYD… More >

  • Open Access


    Cloning and Bioinformatics Analysis of the GlROP6 gene in Glehnia littoralis

    Min Yan1, Han Wang1, Shaohua Liu1, Ye Xu1, Zizhuo Nie1, Yifeng Zhou2, Li Li2,*

    Phyton-International Journal of Experimental Botany, Vol.90, No.4, pp. 1293-1300, 2021, DOI:10.32604/phyton.2021.015601

    Abstract Rho-related GTPase from plants (ROP) proteins play an essential role in plant stress resistance. In this study, the full-length GlROP6 gene was cloned based on G. littoralis transcriptome sequencing data acquired in response to salt stress. The protein sequence, conserved domains, secondary structure, three-dimensional structure, phylogenetic relationships, and expression pattern of the GlROP6 gene were systematically analysed. Our results showed that the full-length GlROP6 gene had an open reading frame of 606 bp, which encoded 201 amino acid residues with a relative molecular weight of 22.23463 kDa and a theoretical isoelectric point of 9.06. Amino acid sequence analyses indicated that… More >

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