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学者姓名：牛小平
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Abstract ：
Nitrogen (N) is crucial for plant growth and stress resistance and is primarily absorbed and transported by nitrate transporters (NRT). Suaeda glauca, known for its strong salt-alkali stress resistance, and SgNRT genes have rarely been reported. This study aims to identify and analyze the SgNRT gene family to understand its composition, evolutionary patterns, and roles in salt stress responses. We identified 212 SgNRTs, which were categorized into three branches, with SgNRT1/SgNPF and SgNRT2 as the major families. Structural analysis, conserved domains, chromosomal localization, and collinearity were also examined. Spatiotemporal expression characteristics of SgNRT genes were analyzed, revealing specific expression across 13 organs or tissues and dynamic responses to salt treatment over 48 h. Notably, SgNRT1.185, SgNRT2.25, and SgNRT2.2 exhibited rapid salt induction in leaves (activated within 0.5 h, peaking at 2 h), with SgNRT1.185 showing relatively high upregulation. SgNRT1.185 and SgNRT2.35 were induced by high salt concentrations (200 mM) in both roots and leaves. SgNRT2.35 exhibited higher basal and stress-induced levels than the other genes. Bioinformatics analysis suggests spatially specific expression of SgNRT genes, potentially involved in nitrogen absorption and transport across various developmental stages and organs/tissues of Suaeda glauca. These findings offer a theoretical basis for understanding the adaptive strategies of Suaeda glauca under saline-alkali stress and provide insights into the functional evolution of plant NRT genes, aiding in the development of stress-resistant crops.
Keyword ：
bioinformatics bioinformatics gene expression analysis gene expression analysis NRT gene family NRT gene family soil salinization soil salinization Suaeda glauca Suaeda glauca
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| GB/T 7714 | Ou, Zitong , Sun, Jin , Li, Xueli et al. Genome-Wide Identification, Characterization, and Expression Analysis of NRT Gene Family in Suaeda glauca [J]. | BIOLOGY-BASEL , 2025 , 14 (8) . |
| MLA | Ou, Zitong et al. "Genome-Wide Identification, Characterization, and Expression Analysis of NRT Gene Family in Suaeda glauca" . | BIOLOGY-BASEL 14 . 8 (2025) . |
| APA | Ou, Zitong , Sun, Jin , Li, Xueli , Feng, Haoran , Chen, Xingguang , Liang, Sisi et al. Genome-Wide Identification, Characterization, and Expression Analysis of NRT Gene Family in Suaeda glauca . | BIOLOGY-BASEL , 2025 , 14 (8) . |
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The cell cycle is a fundamental process of plant growth, development, and reproduction, in which cyclin-dependent kinases (CDKs) and cyclins (CYCs) play central roles in regulating the progression through various stages. These proteins are coordinated with multiple interacting partners to ensure the accurate execution of essential biological events such as DNA replication, chromosome segregation, and cell division. Marchantia polymorpha, one of the earliest diverging land plant species, has emerged as a key model for exploring fundamental mechanisms in plant biology and evolution. However, compared with other model plants, such as Arabidopsis thaliana and Oryza sativa, the core cell cycle genes in M. polymorpha remain relatively uncharacterized. In this study, we identified 31 core cell cycle genes in M. polymorpha through genome-wide analysis, including 13 CDKs, 8 CYCs, 5 E2F/DPs, 1 ICK, 1 RB, 1 CKS, and 2 Wee1 genes. We further analyzed their physicochemical properties, gene structures, and conserved domains, along with evolutionary pressures assessed via Ka/Ks and 4DTv analyses. Comparative genomic analysis revealed patterns of gene contraction and expansion. Additionally, we predicted cis-acting regulatory elements and performed differential expression analysis under various stress conditions to explore their potential functions and expression profiles. Finally, a protein-protein interaction (PPI) network was constructed, and key genes were experimentally validated. These findings provide valuable insights into the core cell cycle gene family in M. polymorpha, contributing to an enhanced understanding of cell cycle regulation and its evolutionary significance in plants.
Keyword ：
core cell cycle genes core cell cycle genes evolutionary analysis evolutionary analysis gene redundancy gene redundancy genome analysis genome analysis Marchantia polymorpha Marchantia polymorpha
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| GB/T 7714 | Chen, Xingguang , Feng, Haoran , Liu, Mengjuan et al. Genome-Wide Identification and Evolution of Core Cell Cycle Genes in Marchantia polymorpha: Insights Into Redundancy, Stress, and Functional Evolution [J]. | PHYSIOLOGIA PLANTARUM , 2025 , 177 (5) . |
| MLA | Chen, Xingguang et al. "Genome-Wide Identification and Evolution of Core Cell Cycle Genes in Marchantia polymorpha: Insights Into Redundancy, Stress, and Functional Evolution" . | PHYSIOLOGIA PLANTARUM 177 . 5 (2025) . |
| APA | Chen, Xingguang , Feng, Haoran , Liu, Mengjuan , Cai, Jiahao , Sarwar, Rabia , Li, Xueli et al. Genome-Wide Identification and Evolution of Core Cell Cycle Genes in Marchantia polymorpha: Insights Into Redundancy, Stress, and Functional Evolution . | PHYSIOLOGIA PLANTARUM , 2025 , 177 (5) . |
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Passion fruit (Passiflora edulis), a tropical crop of significant economic value, exhibits temperature-sensitive floral development. Here, we identified 23 TALE transcription factors (PeTALEs) and characterized their roles in floral organogenesis and thermal adaptation. Phylogenetic analysis classified PeTALEs into KNOX and BELL subfamilies, with conserved domain architectures and cis-regulatory elements linked to stress and hormone signaling. Spatiotemporal expression profiling revealed PeTALE21 as a key regulator of corona initiation, while PeTALE17 dominated in later floral stages. Temperature stress assays demonstrated cold-induced upregulation of PeTALE15/16/19/22 and heat-mediated suppression of PeTALE10/18/21. Yeast two-hybrid assays uncovered functional interactions between PeTALE3/16/18/22/23, highlighting a network governing floral thermoresilience. This study provides the first genome-wide analysis of PeTALEs, offering insights for breeding climate-resilient passion fruit varieties.
Keyword ：
evolutionary analysis evolutionary analysis floral organogenesis floral organogenesis heat/cold stress heat/cold stress TALE gene TALE gene
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| GB/T 7714 | Jiang, Xinni , Miao, Jie , Zu, Weifan et al. Functional Characterization of KNOX and BELL Genes in Temperature-Responsive Floral Morphogenesis of Passion Fruit (Passiflora edulis) [J]. | PLANTS-BASEL , 2025 , 14 (10) . |
| MLA | Jiang, Xinni et al. "Functional Characterization of KNOX and BELL Genes in Temperature-Responsive Floral Morphogenesis of Passion Fruit (Passiflora edulis)" . | PLANTS-BASEL 14 . 10 (2025) . |
| APA | Jiang, Xinni , Miao, Jie , Zu, Weifan , Zhou, Ruohan , Zheng, Lexin , Wei, Ying et al. Functional Characterization of KNOX and BELL Genes in Temperature-Responsive Floral Morphogenesis of Passion Fruit (Passiflora edulis) . | PLANTS-BASEL , 2025 , 14 (10) . |
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Stress-associated proteins (SAPs), characterized by zinc finger domains, play a crucial role in regulating plant responses to various stresses. These proteins modulate stress-related gene expression and are integral to enhancing plant immunity, development, cell proliferation, and hormone regulation. In this study, we conducted a genome-wide analysis of the SAP gene family in Suaeda glauca (S. glauca), identifying 15 SAP genes encoding A20/AN1 zinc finger proteins. Functional analyses of three candidate genes under salinity stress were performed, examining phenotypic and physiological responses to better understand their role in stress tolerance. Sequence alignment, conserved domain analysis, and gene structure analysis revealed high conservation among S. glauca SAPs. Phylogenetic analysis identified two major groups within the gene family, providing insights into their evolutionary relationships. Transcription profiling analysis demonstrated significant expression of most SAP genes in response to salt stress, with qPCR validation confirming the upregulation of specific genes. Notably, transgenic Arabidopsis lines heterologously overexpressing the candidate genes SgSAP4, SgSAP5, and SgSAP7 demonstrated enhanced tolerance to salinity stress. This was evident from improved seed germination, root elongation, and reduced levels of stress markers, including malondialdehyde and free proline, compared to wildtype plants. These findings highlight the potential of these SAP genes in breeding programs aimed at improving salinity tolerance in crops.
Keyword ：
Salinity stress Salinity stress SAP family SAP family Suaeda glauca Suaeda glauca Transgenic lines Transgenic lines
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| GB/T 7714 | Mohammadi, Mohammad Aqa , Wang, Yining , Zhang, Chunyin et al. Heterologous overexpression of the Suaeda glauca stress-associated protein (SAP) family genes enhanced salt tolerance in Arabidopsis transgenic lines [J]. | PLANT PHYSIOLOGY AND BIOCHEMISTRY , 2025 , 224 . |
| MLA | Mohammadi, Mohammad Aqa et al. "Heterologous overexpression of the Suaeda glauca stress-associated protein (SAP) family genes enhanced salt tolerance in Arabidopsis transgenic lines" . | PLANT PHYSIOLOGY AND BIOCHEMISTRY 224 (2025) . |
| APA | Mohammadi, Mohammad Aqa , Wang, Yining , Zhang, Chunyin , Ma, Haifeng , Sun, Jin , Wang, Lulu et al. Heterologous overexpression of the Suaeda glauca stress-associated protein (SAP) family genes enhanced salt tolerance in Arabidopsis transgenic lines . | PLANT PHYSIOLOGY AND BIOCHEMISTRY , 2025 , 224 . |
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Caffeic acid O-methyltransferase (COMT) catalyzes the penultimate methylation in monolignol biosynthesis, controlling lignin composition and abiotic-stress tolerance. Kenaf (Hibiscus cannabinus L.), a fast bast-fiber crop rich in lignin, is valued for its mechanical strength and resilience to salinity. However, the COMT gene family has not yet been systematically characterized in this species. Here, we integrated phylogenetics, synteny, promoter and transcriptome analyses to create a comprehensive profile of kenaf COMT genes. Genome-wide screening identified 81 HcCOMT genes. Phylogenetic reconstruction with COMTs from Arabidopsis thaliana and Gossypium hirsutum resolved 10 distinct clades. Synteny analysis revealed 2 collinear blocks with Arabidopsis and 14 with cotton, whereas intraspecific duplication events indicated recent lineage-specific expansion. Promoter analysis identified numerous cis-elements responsive to light, phytohormones and abiotic stress, suggesting complex transcriptional regulation. Transcriptome mining uncovered 6 candidate genes with pronounced tissue specificity and salt responsiveness; qRT-PCR confirmed these patterns in root, stem and leaf tissues under 200 mM NaCl: HcCOMT28 and HcCOMT29 were repressed in the leaf, whereas HcCOMT11, HcCOMT12, HcCOMT13, and HcCOMT17 were up-regulated, consistent with altered lignin deposition patterns. Our findings provide a comprehensive genomic resource delineating the structure, evolution, and salt-responsive expression of the kenaf COMT family, and establish a foundation for elucidating the molecular mechanisms underlying lignin-mediated salt tolerance and for breeding elite kenaf cultivars with tailored fiber properties.
Keyword ：
COMT COMT expression pattern expression pattern kenaf kenaf lignin synthesis lignin synthesis salt stress salt stress
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| GB/T 7714 | Xu, Jiantang , Liu, Tianjin , Lin, Hui et al. Comprehensive analysis of the Caffeic acid O-methyltransferase gene family in kenaf (Hibiscus cannabinus L.) and their expression characteristics in response to salinity stress [J]. | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
| MLA | Xu, Jiantang et al. "Comprehensive analysis of the Caffeic acid O-methyltransferase gene family in kenaf (Hibiscus cannabinus L.) and their expression characteristics in response to salinity stress" . | FRONTIERS IN PLANT SCIENCE 16 (2025) . |
| APA | Xu, Jiantang , Liu, Tianjin , Lin, Hui , Huang, Rong , Chen, Meixia , Fang, Pingping et al. Comprehensive analysis of the Caffeic acid O-methyltransferase gene family in kenaf (Hibiscus cannabinus L.) and their expression characteristics in response to salinity stress . | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
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TALE (Three Amino acid Loop Extension) homeodomain transcription factors are key conserved elements in eukaryotic developmental patterning. In plants, this superclass divides into the KNOX and BELL families, which are essential for regulating meristem maintenance, organogenesis, and tissue identity. Recent advances show that TALE proteins are intricately involved in plant reproductive processes, including gametophyte differentiation, embryonic axis formation, and floral organogenesis. They function as molecular scaffolds, integrating spatiotemporal signals and hormonal signaling like auxin, cytokinin, and gibberellin to control phase transitions and reproductive cell fate determination. The lineage-specific expansions and domain rearrangements of TALE genes across bryophytes, gymnosperms, and angiosperms indicate repeated co-option and neofunctionalization throughout land plant evolution. Emerging insights from epigenomics and protein interactomes reveal that TALE complexes modulate cell type-specific transcriptional responses. This review synthesizes current understanding of TALE-mediated regulatory networks during plant reproductive development and presents a conceptual framework for investigating their roles in developmental plasticity and stress-responsive fertility. We also highlight opportunities to utilize TALE-based regulatory modules to develop climate-resilient crops through multi-omics and genome editing approaches. Decoding the reproductive logic embedded in TALE networks offers transformative potential for reprogramming plant development in an era of agricultural and ecological uncertainty.
Keyword ：
BELL BELL KNOX KNOX meristem identity meristem identity reproduction development reproduction development TALE homeodomain TALE homeodomain
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| GB/T 7714 | Niu, Xiaoping , Jiang, Xinni , Li, Haoran et al. TALE Homeodomain Proteins in Plant Reproductive Development and Environmental Stress Resilience [J]. | PLANT CELL AND ENVIRONMENT , 2025 . |
| MLA | Niu, Xiaoping et al. "TALE Homeodomain Proteins in Plant Reproductive Development and Environmental Stress Resilience" . | PLANT CELL AND ENVIRONMENT (2025) . |
| APA | Niu, Xiaoping , Jiang, Xinni , Li, Haoran , Qin, Rongjuan , Qin, Yuan . TALE Homeodomain Proteins in Plant Reproductive Development and Environmental Stress Resilience . | PLANT CELL AND ENVIRONMENT , 2025 . |
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Anthracnose of the tea plant (Camellia sinensis), caused by Colletotrichum spp., poses a significant threat to both the yield and quality of tea production. To address this challenge, researchers have looked to the application of endophytic bacteria as a natural alternative to the use chemical pesticides, offering potential for enhancing disease resistance and abiotic stress tolerance in tea plants. This study focused on identifying effective microbial agents to combat tea anthracnose caused by Colletotrichum fructicola. A total of 38 Bacillus-like strains were isolated from the tea rhizosphere, with 8 isolates showing substantial inhibitory effects against the mycelial growth of C. fructicola, achieving an average inhibition rate of 60.68%. Among these, strain T3 was particularly effective, with a 69.86% inhibition rate. Through morphological, physiological, and biochemical characterization, along with 16S rRNA gene phylogenetics analysis, these strains were identified as B. inaquosorum (T1 and T2), B. tequilensis (T3, T5, T7, T8, and T19), and B. spizizenii (T6). Biological and molecular assays confirmed that these strains could induce the expression of genes associated with antimicrobial compounds like iturin, fengycin, subtilosin, and alkaline protease, which effectively reduced the disease index of tea anthracnose and enhanced tea plant growth. In conclusion, this study demonstrates that B. inaquosorum, B. tequilensis, and B. spizizenii strains are promising biocontrol agents for managing tea anthracnose.
Keyword ：
16S rRNA 16S rRNA disease resistance disease resistance fengycin fengycin microbial agents microbial agents tea plant tea plant
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| GB/T 7714 | Chen, Meixia , Lin, Hui , Zu, Weifan et al. Evaluating Native Bacillus Strains as Potential Biocontrol Agents against Tea Anthracnose Caused by Colletotrichum fructicola [J]. | PLANTS-BASEL , 2024 , 13 (20) . |
| MLA | Chen, Meixia et al. "Evaluating Native Bacillus Strains as Potential Biocontrol Agents against Tea Anthracnose Caused by Colletotrichum fructicola" . | PLANTS-BASEL 13 . 20 (2024) . |
| APA | Chen, Meixia , Lin, Hui , Zu, Weifan , Wang, Lulu , Dai, Wenbo , Xiao, Yulin et al. Evaluating Native Bacillus Strains as Potential Biocontrol Agents against Tea Anthracnose Caused by Colletotrichum fructicola . | PLANTS-BASEL , 2024 , 13 (20) . |
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In plants, sexual reproduction relies on the proper development of floral organs that facilitate the successful development of fruits and seeds. Auxin responsive small auxin-up RNA (SAUR) genes play essential roles in floral organ formation and fruit development. However, little is known about the role of SAUR genes in pineapple floral organ formation and fruit development as well as stress responses. In this study, based on genome information and transcriptome datasets, 52 AcoSAUR genes were identified and grouped into 12 groups. The gene structure analysis revealed that most AcoSAUR genes did not have introns, although auxin-acting elements were abundant in the promoter region of AcoSAUR members. The expression analysis across the multiple flower and fruit development stages revealed differential expression of AcoSAUR genes, indicating a tissue and stage-specific function of AcoSAURs. Correlation analysis and pairwise comparisons between gene expression and tissue specificity identified stamen-, petal-, ovule-, and fruit-specific AcoSAURs involved in pineapple floral organs (AcoSAUR4/5/15/17/19) and fruit development (AcoSAUR6/11/36/50). RT-qPCR analysis revealed that Aco-SAUR12/24/50 played positive roles in response to the salinity and drought treatment. This work provides an abundant genomic resource for functional analysis of AcoSAUR genes during the pineapple floral organs and fruit development stages. It also highlights the role of auxin signaling involved in pineapple reproductive organ growth.
Keyword ：
Ananas comosus L Ananas comosus L Auxin Auxin Expression profiles Expression profiles Phylogenetic analysis Phylogenetic analysis SAUR SAUR
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| GB/T 7714 | Zhang, Yunfei , Ye, Tao , She, Zeyuan et al. Small Auxin Up RNA (SAUR) gene family identification and functional genes exploration during the floral organ and fruit developmental stages in pineapple (Ananas comosus L.) and its response to salinity and drought stresses [J]. | INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES , 2023 , 237 . |
| MLA | Zhang, Yunfei et al. "Small Auxin Up RNA (SAUR) gene family identification and functional genes exploration during the floral organ and fruit developmental stages in pineapple (Ananas comosus L.) and its response to salinity and drought stresses" . | INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 237 (2023) . |
| APA | Zhang, Yunfei , Ye, Tao , She, Zeyuan , Huang, Shupeng , Wang, Lulu , Aslam, Mohammad et al. Small Auxin Up RNA (SAUR) gene family identification and functional genes exploration during the floral organ and fruit developmental stages in pineapple (Ananas comosus L.) and its response to salinity and drought stresses . | INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES , 2023 , 237 . |
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Heat stress transcription factors (HSFs) are the major regulators of plant response to environmental stress, especially heat and drought stress. To gain a deeper understanding of the mechanisms underlying HSFs in the abiotic stress response of passion fruit, we conducted an in silico analysis of the HSF gene family. Through bioinformatics and phylogenetic analyses, we identified 18 PeHSF members and classified them into A, B, and C groups. Collinearity analysis results revealed that the expansion of the PeHSF gene family was due to the presence of segmental duplication. Furthermore, gene structure and protein domain analysis illustrated that PeHSFs in the same subgroup are relatively conserved. Conserved motif and function domain analysis suggested that PeHSF proteins possess typical conserved functional domains of the HSF family. A protein interaction network and 3D structure prediction were used to study the potential regulatory relationship of PeHSFs. Additionally, the sub -cellular localization results of PeHSF-A6a, PeHSF-B4b, and PeHSF-C1a were consistent with the predictions. RNA-seq and RT-qPCR analysis revealed the expression patterns of PeHSFs in different tissues of passion fruit floral organs. Promoter analysis and the expression patterns of the PeHSFs under different treatments demonstrated their involvement in various abiotic stress processes. Notably, overexpression of PeHSF-C1a consistently enhanced tolerance to drought and heat stress in Arabidopsis. Overall, our findings provide a scientific basis for further functional studies of PeHSFs that could contribute to improvement of passion fruit breeding.
Keyword ：
Abiotic stress Abiotic stress Gene expression Gene expression HSF genes HSF genes Passiflora edulis Passiflora edulis Transcription factor Transcription factor
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| GB/T 7714 | Wang, Lulu , Liu, Yanhui , Chai, Gaifeng et al. Identification of passion fruit HSF gene family and the functional analysis of PeHSF-C1a in response to heat and osmotic stress [J]. | PLANT PHYSIOLOGY AND BIOCHEMISTRY , 2023 , 200 . |
| MLA | Wang, Lulu et al. "Identification of passion fruit HSF gene family and the functional analysis of PeHSF-C1a in response to heat and osmotic stress" . | PLANT PHYSIOLOGY AND BIOCHEMISTRY 200 (2023) . |
| APA | Wang, Lulu , Liu, Yanhui , Chai, Gaifeng , Zhang, Dan , Fang, Yunying , Deng, Kao et al. Identification of passion fruit HSF gene family and the functional analysis of PeHSF-C1a in response to heat and osmotic stress . | PLANT PHYSIOLOGY AND BIOCHEMISTRY , 2023 , 200 . |
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Background Cell polarity establishment and maintenance is indispensable for plant growth and development. In plants, the YABBY transcription factor family has a distinct role in leaf asymmetric polarity establishment and lateral organ initiation. However, for the important sugar crop Saccharum, little information on YABBY genes is available. Results In this study, a total of 20 sequences for 7 SsYABBY genes were identified in the sugarcane genome, designated as SsYABBY1-7 based on their chromosome locations, and characterized by phylogenetic analysis. We provided a high-resolution map of SsYABBYs' global expression dynamics during vegetative and reproductive organ morphogenesis and revealed that SsYABBY3/4/5 are predominately expressed at the seedling stage of stem and leaf basal zone; SsYABBY2/5/7 are highly expressed in ovules. Besides, cross-species overexpression and/or complementation verified the conserved function of SsYABBY2 in establishing leaf adaxial-abaxial polarity and ovules development. We found that the SsYABBY2 could successfully rescue the leaves curling, carpel dehiscence, and ovule abortion defects in Arabidopsis crc mutant. Conclusions Collectively, our study demonstrates that SsYABBY genes retained a conserved function in establishing and preserving leaf adaxial-abaxial polarity and lateral organ development during evolution.
Keyword ：
Expression analysis Expression analysis Polarity establishment Polarity establishment Sugarcane Sugarcane YABBY genes YABBY genes
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| GB/T 7714 | She, Zeyuan , Huang, Xiaoyi , Aslam, Mohammad et al. Expression characterization and cross-species complementation uncover the functional conservation of YABBY genes for leaf abaxial polarity and carpel polarity establishment in Saccharum spontaneum [J]. | BMC PLANT BIOLOGY , 2022 , 22 (1) . |
| MLA | She, Zeyuan et al. "Expression characterization and cross-species complementation uncover the functional conservation of YABBY genes for leaf abaxial polarity and carpel polarity establishment in Saccharum spontaneum" . | BMC PLANT BIOLOGY 22 . 1 (2022) . |
| APA | She, Zeyuan , Huang, Xiaoyi , Aslam, Mohammad , Wang, Lulu , Yan, Maokai , Qin, Rongjuan et al. Expression characterization and cross-species complementation uncover the functional conservation of YABBY genes for leaf abaxial polarity and carpel polarity establishment in Saccharum spontaneum . | BMC PLANT BIOLOGY , 2022 , 22 (1) . |
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