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  • 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

    ARTICLE

    ScRNA-seq reveals the correlation between M2 phenotype of tumor-associated macrophages and lymph node metastasis of breast cancer

    JUN SHEN1,#, HONGFANG MA2,#, YONGXIA CHEN3, JIANGUO SHEN1,*

    Oncology Research, Vol.31, No.6, pp. 955-966, 2023, DOI:10.32604/or.2023.029638

    Abstract The process of lymphatic metastasis was proved to be associated with podoplanin-expressing macrophages in breast cancer (BC). This study aimed to investigate the role of the M2 phenotype of tumor-associated macrophages and mine the key M2 macrophages-related genes for lymph node metastasis in BC. We downloaded the GSE158399 dataset from the Gene Expression Omnibus (GEO) database, which includes transcriptomic profiles of individual cells from primary tumors, negative lymph nodes (NLNs), and positive lymph nodes (PLNs) of breast cancer patients. The cell subsets were identified by clustering analysis after quality control of the scRNA-seq using Seurat. The activation and migration capability… More >

  • 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

    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 genes and… More >

  • Open Access

    ARTICLE

    Exploring Splicing Variants and Novel Genes in Sacred Lotus Based on RNA-seq Data

    Xinyi Zhang, Zimeng Yu, Pingfang Yang*

    Phyton-International Journal of Experimental Botany, Vol.92, No.6, pp. 1665-1679, 2023, DOI:10.32604/phyton.2023.029482

    Abstract Sacred lotus (Nelumbo nucifera) is a typical aquatic plant, belonging to basal eudicot plant, which is ideal for genome and genetic evolutionary study. Understanding lotus gene diversity is important for the study of molecular genetics and breeding. In this research, public RNA-seq data and the annotated reference genome were used to identify the genes in lotus. A total of 26,819 consensus and 1,081 novel genes were identified. Meanwhile, a comprehensive analysis of gene alternative splicing events was conducted, and a total of 19,983 “internal” alternative splicing (AS) events and 14,070 “complete” AS events were detected in 5,878 and 5,881 multi-exon… More >

  • Open Access

    ARTICLE

    HD-Zip Transcription Factor is Responsible for No-Lobed Leaf in Watermelon (Citrullus lanatus L.)

    Shixiang Duan1,#, Yaomiao Guo1,#, Yinping Wang1, Muhammad Jawad Umer2, Dongming Liu1, Sen Yang1, Huanhuan Niu1, Shouru Sun1, Luming Yang1, Junling Dou1,*, Huayu Zhu1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1311-1328, 2023, DOI:10.32604/phyton.2023.026928

    Abstract Leaf is a vital organ of plants that plays an essential role in photosynthesis and respiration. As an important agronomic trait in leaf development, leaf shape is classified into lobed, entire (no-lobed), and serrated in most crops. In this study, two-lobed leaf watermelon inbred lines WT2 and WCZ, and a no-lobed leaf watermelon inbred line WT20 were used to create two F2 populations. Segregation analysis suggested that lobed leaves were dominant over the no-lobed leaves, and it was controlled by a signal gene. A locus on watermelon chromosome 4 controlling watermelon lobed/no-lobed leaves was identified through BSA-seq strategy combined with… More >

  • Open Access

    ARTICLE

    Genome-Wide Identification and Characterisation of Abiotic Stress Responsive mTERF Gene Family in Amaranthus hypochondriacus

    Mortaza Hajyzadeh*

    Phyton-International Journal of Experimental Botany, Vol.92, No.5, pp. 1649-1664, 2023, DOI:10.32604/phyton.2023.028028

    Abstract Abiotic stresses at different growth stages in the life of plants negatively affect yield productivity. Therefore, plants, including Amaranthus hypochondriacus, develop adaptive strategies to face the stresses and expand functional diversification. In plants, the mitochondrial transcription termination factors (mTERF) are essential functions in regulation, and organelles (mitochondria and chloroplasts) control gene expression (OGE) under several stress conditions. Based on the in-silico-wide genome and transcriptome analysis, twenty-four mTERF genes were detected in the main targeted mitochondria organelles clustered into three different main groups. The chromosomal location and gene duplication analysis indicated one segmental and one tandem duplication in the genome. The… More >

  • Open Access

    ARTICLE

    B Class Floral Homeotic Genes are Involved in the Petal Identity and Flower Meristem Determinations in Chrysanthemum morifolium

    Jiayou Liu, Lian Ding, Xue Zhang, Song Li, Yunxiao Guan, Diwen Jia, Aiping Song, Jiafu Jiang, Fadi Chen*

    Phyton-International Journal of Experimental Botany, Vol.92, No.2, pp. 311-331, 2023, DOI:10.32604/phyton.2022.023896

    Abstract Chrysanthemum morifolium, an ornamental crop with diverse forms of inflorescence, is a good model for studying flower development in Asteraceae. However, the genetic background is complex and the mechanisms of regulating flower development are still unclear. Here, we identified two natural mutant lines of chrysanthemum and named them M1 and M2 according to the severity of the phenotype. Both lines showed defects in petal identity, and the petals of the M1 line had a mild phenotype: partially loss of petal identity and conversion of petals into green, leaf-like organs. The M2 line had severe phenotypes: in addition to severe petal… More >

  • Open Access

    ARTICLE

    Comparative Transcriptome Analysis of Salt-Stress-Responsive Genes in Rice Roots

    Rui Song1, Yan Huang2, Xin Ji3, Yunfei Wei3, Qiuyuan Liu3, Shumei Li3, Juan Liu3,*, Pengfei Dong1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.1, pp. 237-250, 2023, DOI:10.32604/phyton.2022.023081

    Abstract Soil salinity greatly impairs plant growth and crop productivity. Rice (Oryza sativa L.) is a salt-sensitive crop. To better understand the molecular mechanisms of salt tolerance in roots, the BGISEQ-500 sequencing platform was employed to elucidate transcriptome changes in rice roots after 0, 3, 24, and 72 h of salt stress. The results showed that root K+ content decreased and Na+ content increased rapidly after the initial stage of salt stress, but that fresh and dry weight in root did not significantly reduce. Compared to the control (no salt stress), 1,292, 453, and 486 differentially expressed genes (DEGs) were upregulated,… More >

  • Open Access

    ARTICLE

    Transcriptome Analysis and Genes Function Verification of Root Development of Paeonia suffruticosa under Sandy Loam Cultivation

    Yinglong Song1,#, Wenqian Shang1,#, Zheng Wang1,*, Songlin He1,2,*, Xinya Meng3, Liyun Shi1, Yuxiao Shen1, Dan He1, Xueyuan Lou1, Yuke Sun1

    Phyton-International Journal of Experimental Botany, Vol.91, No.12, pp. 2791-2812, 2022, DOI:10.32604/phyton.2022.023572

    Abstract Relatively poor in vitro rooting has limited the large-scale commercial production of tree peony. In this study, on the basis of transcriptome sequencing, differentially expressed genes and the associated metabolic pathways were identified in tree peony roots at different stages of root formation under sandy loam cultivation. A total of 31.63 Gb raw data were generated and 120,188 unigenes (mean length of 911.98 bp) were annotated according to six databases (NR, NT, GO, KEGG, COG, and Swiss-Prot). Analyses of the ungerminated root primordium period, induced root primordium period, and root formation period detected 8,232, 6,907, and 10,687 differentially expressed genes related… More >

  • Open Access

    ARTICLE

    Transcriptome Analysis via RNA Sequencing Reveals the Molecular Mechanisms Underlying the Hedera helix Response to High Temperature

    Ting Zhang1,2, Ping Li3,*, Jiali Wei3,*

    Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2403-2417, 2022, DOI:10.32604/phyton.2022.022421

    Abstract Hedera helix is an evergreen ornamental plant that is resistant to cool but not high temperature and deserves to be further researched for improving its adaptability to heat stress. Two Hedera helix cultivars, heat-tolerant (HT) ‘Jessica’ and heat-sensitive (HS) ‘Shamrock’, were used for differences analyses of transcriptome. We detected 6179 differentially expressed genes (DEGs) and 5992 DEGs in ‘Jessica’ and ‘Shamrock’ to heat stress, respectively. Among these, 1983 upregulated DEGs and 1400 downregulated DEGs were shared between both varieties, resulting in enhancement of various pathways such as biosynthesis of secondary metabolites, glyoxylate dicarboxylate metabolism, and protein processing in endoplasmic reticulum… More >

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