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  • Open Access

    ARTICLE

    Genome-Wide Exploration of the Grape GLR Gene Family and Differential Responses of VvGLR3.1 and VvGLR3.2 to Low Temperature and Salt Stress

    Honghui Sun1,2,#, Ruichao Liu1,2,#, Yueting Qi1, Hongsheng Gao1, Xueting Wang1, Ning Jiang1,2, Xiaotong Guo1,2, Hongxia Zhang1, Chunyan Yu1,2,*

    Phyton-International Journal of Experimental Botany, Vol.93, No.3, pp. 533-549, 2024, DOI:10.32604/phyton.2024.049417

    Abstract Grapes, one of the oldest tree species globally, are rich in vitamins. However, environmental conditions such as low temperature and soil salinization significantly affect grape yield and quality. The glutamate receptor (GLR) family, comprising highly conserved ligand-gated ion channels, regulates plant growth and development in response to stress. In this study, 11 members of the VvGLR gene family in grapes were identified using whole-genome sequence analysis. Bioinformatic methods were employed to analyze the basic physical and chemical properties, phylogenetic trees, conserved domains, motifs, expression patterns, and evolutionary relationships. Phylogenetic and collinear analyses revealed that the VvGLRs were divided into three… More >

  • Open Access

    ARTICLE

    Systematic analysis of DNA polymerases as therapeutic targets in pan-cancers

    ZHENHUA LI1, HUILAI LV1, FAN ZHANG1, ZIMING ZHU2, QIANG GUO3, MINGBO WANG1, CHAO HUANG1, LIJUAN CHEN4, WENPAN ZHANG4, YUN LI5,*, ZIQIANG TIAN1,*

    BIOCELL, Vol.48, No.1, pp. 123-138, 2024, DOI:10.32604/biocell.2023.031568

    Abstract Introduction: DNA polymerases are crucial for maintaining genome stability and influencing tumorigenesis. However, the clinical implications of DNA polymerases in tumorigenesis and their potential as anti-cancer therapy targets are not well understood. Methods: We conducted a systematic analysis using TCGA Pan-Cancer Atlas data and Gene Set Cancer Analysis results to examine the expression profiles of 15 DNA polymerases (POLYs) and their clinical correlations. We also evaluated the prognostic value of POLYs by analyzing their expression levels in relation to overall survival time (OS) using Kaplan-Meier survival curves. Additionally, we investigated the correlations between POLY expression and immune cells, DNA damage… More >

  • Open Access

    ARTICLE

    Genetic Diversity, Population Structure, and Genome-Wide Association Study of Seven Agronomic Traits in 273 Diverse Upload Cotton Accessions

    Yajun Liang1,2,#, Juyun Zheng1,#, Junduo Wang1,#, Zhaolong Gong1, Zhiqiang Li3, Ling Min4, Zeliang Zhang2, Zhiwei Sang2, Yanying Qu2, Xueyuan Li1,*, Quanjia Chen2,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.12, pp. 3345-3357, 2023, DOI:10.32604/phyton.2023.028755

    Abstract Upland cotton (Gossypium hirsutum) is the most important plant producing natural fibers for the textile industry. In this study, we first investigated the phenotypic variation of seven agronomic traits of 273 diverse cotton accessions in the years 2017 and 2018, which were from 18 geographical regions. We found large variations among the traits in different geographical regions and only half of the traits in either years 2017 or 2018 followed a normal distribution. We then genotyped the collection with 81,612 high quality SNPs. Phylogenetic tree and population structure revealed a diverse genetic structure of the core collection, and geographical diversification… More >

  • Open Access

    ARTICLE

    The whole-genome survey of Acer griseum, its polymorphic simple sequence repeats development and application

    XIAO-JUN ZHOU1,*, YU-WEI TIAN1, RUI-HAN LI2

    BIOCELL, Vol.47, No.8, pp. 1907-1913, 2023, DOI:10.32604/biocell.2023.030191

    Abstract Background: Acer griseum Pax is an endangered species endemic to China with both ornamental and economic value. However, the lack of information on its genome size and characteristics hinders further work at the genome level. Methods: This paper applied bioinformatics methods to predict the characteristics and patterns of the A. griseum genome, providing an important basis for formulating its whole-genome sequencing scheme. This study also characterized the simple sequence repeats (SSRs) of A. griseum, laying the foundation for the development and application of genome-wide SSR markers. In this study, PE150 sequencing was performed by the BGI MGISEQ platform, and the… More >

  • Open Access

    ARTICLE

    Genome-Wide Analysis of the F3′5′H Gene Family in Blueberry (Vaccinium corymbosum L.) Provides Insights into the Regulation of Anthocyanin Biosynthesis

    Xiaolan Guo1,2, Jinbin Hu3, Shimei Yang4, Delu Wang2,*, Jianbing Wang1

    Phyton-International Journal of Experimental Botany, Vol.92, No.9, pp. 2683-2697, 2023, DOI:10.32604/phyton.2023.029820

    Abstract The F3′5′H gene family plays an important role in regulating anthocyanin biosynthesis, abiotic stress, and hormone signaling. In this study, 14 F3′5′H genes were identified from the blueberry genome. The chromosomal distribution, physicochemical properties, F3′5′H domain, conserved motifs, cis-acting elements, and intron/exon compositions were analyzed. The functional prediction analysis of these VcF3′5′Hs indicated that their biological functions included light response and other secondary metabolites. The results of qRT-PCR showed that VcF3′5′Hs (especially VcF3′5′H4) were highly expressed at the ripening stage. Subcellular localization revealed that VcF3′5′H4 may be located in the endoplasmic reticulum. Co-expression analysis showed that the VcF3′5′H gene family… More >

  • Open Access

    ARTICLE

    Genome-Wide Analysis of the KANADI Gene Family and Its Expression Patterns under Different Nitrogen Concentrations Treatments in Populus trichocarpa

    Minghui Niu1,#, Heng Zhang1,#, Xiangyang Li1, Zhibao Hu1, Hongjiao Zhang2,3, Zhiru Xu2,3, Chunpu Qu1,4,*, Guanjun Liu1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2001-2015, 2023, DOI:10.32604/phyton.2023.029350

    Abstract KANADI (KAN) is a plant-specific gene that controlled the polarity development of lateral organs. It mainly acted on the abaxial characteristics of plants to make the lateral organs asymmetrical. However, it had been less identified in woody plants. In this study, the members of the KAN gene family in Populus trichocarpa were identified and analyzed using the bioinformatics method. The results showed that a total of 8 KAN family members were screened out, and each member contained the unique GARP domain and conserved region of the family proteins. Phylogenetic analysis and their gene structures revealed that all KAN genes from… More >

  • Open Access

    CASE REPORT

    Compound Heterozygous PLD1 Variants in Right-Sided Heart Malformations

    Cherith Somerville1,2, Kelsey Kalbfleisch1,2, Roozbeh Manshaei1,2, Qiliang Ding1,2, John B.A. Okello1,2,3, Rachel Silver4, David Chitayat2,4, Varsha Thakur5, Olivier Villemain5,6,7, Rebekah Jobling1,2,8,*

    Congenital Heart Disease, Vol.18, No.2, pp. 213-218, 2023, DOI:10.32604/chd.2023.023042

    Abstract We report a three-year-old male child who presented with congenital valvular defects, right ventricular malformation, and initial developmental delay. Genome sequencing showed rare deleterious biallelic missense variants in PLD1. In his parents’ second pregnancy, echocardiogram at 13 weeks gestation revealed right-sided cardiac malformations resembling the clinical presentation of the family’s first child. Targeted DNA analysis showed that the fetus carried the same biallelic PLD1 variants as their older sibling. This case helps to further delineate the clinical spectrum of PLD1-related defects and highlights the value of both genome sequencing in congenital heart disease and early fetal echocardiography to establish phenotype. More >

  • Open Access

    ARTICLE

    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

    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

    Structural characterization of four Rhododendron spp. chloroplast genomes and comparative analyses with other azaleas

    XIAOJUN ZHOU1,*, MENGXUE LIU1, LINLIN SONG2

    BIOCELL, Vol.47, No.3, pp. 657-668, 2023, DOI:10.32604/biocell.2023.026781

    Abstract Azalea is a general designation of Rhododendron in the Ericaceae family. Rhododendron not only has high ornamental value but also has application value in ecological protection, medicine, and scientific research. In this study, we used Illumina and PacBio sequencing to assemble and annotate the entire chloroplast genomes (cp genomes) of four Rhododendron species. The chloroplast genomes of R. concinnum, R. henanense subsp. lingbaoense, R. micranthum, and R. simsii were assembled into 207,236, 208,015, 207,233, and 206,912 bp, respectively. All chloroplast genomes contain eight rRNA genes, with either 88 or 89 protein-coding genes. The four cp genomes were compared and analyzed… More >

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