Plant Gene最新文献_第5页

Temporal and spatial expression analysis of AtbZIP9 during seed and silique development in Arabidopsis thaliana (L.) Heynh 拟南芥种子和果实发育过程中AtbZIP9的时空表达分析Heynh

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-12 DOI: 10.1016/j.plgene.2025.100536

Jonatan Illescas-Miranda , Victoria Llanos-Casado , Estefanía Contreras, Néstor Carrillo-Barral, Raquel Iglesias-Fernández

In Arabidopsis thaliana, seed dispersal is mediated by the silique, a specialized fruit that undergoes a complex developmental program involving cell division, expansion, and programmed cell death. Transcription factors (TFs) from the bZIP family are key regulators of these transitions. In this study, we focused on the C-group bZIP TF AtbZIP9 to characterize its expression, potential regulatory roles, and functional relevance during silique development and early seedling growth. Promoter-reporter assays and qPCR analyses revealed that AtbZIP9 is broadly expressed, with strong activity in vascular tissues and the funiculus during early and mid-stages of silique development. AtbZIP9 physically interacts with the S1-group member AtbZIP44, as shown by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays, supporting the formation of heterodimeric complexes. Despite the lack of major phenotypic alterations in AtbZIP9 knockout mutants during germination and early development—even under salt stress conditions—its co-expression with AtbZIP44 and the CW-modifying gene AtMAN7 suggests a role in transcriptional regulation during silique development. Recent evidence further links AtbZIP9 to ABA-responsive gene expression and identifies it as a likely component of redundant regulatory networks involving other C-group bZIPs. These findings highlight AtbZIP9 as a candidate transcriptional modulator of silique and seed developmental processes, potentially acting in coordination with AtbZIP44 and other factors.

在拟南芥中，种子的传播是由核介导的，核是一种特殊的果实，经历了一个复杂的发育过程，包括细胞分裂、扩增和程序性细胞死亡。来自bZIP家族的转录因子（TFs）是这些转变的关键调节因子。在这项研究中，我们重点研究了c组bZIP TF AtbZIP9，以表征其在硅酸发育和早期幼苗生长中的表达、潜在的调控作用和功能相关性。启动子报告子分析和qPCR分析显示，AtbZIP9广泛表达，在丝质发育早期和中期的维管组织和索细胞中具有较强的活性。酵母双杂交和双分子荧光互补（BiFC）实验表明，AtbZIP9与s1基团成员AtbZIP44相互作用，支持异二聚体复合物的形成。尽管AtbZIP9基因敲除突变体在萌发和早期发育过程中（甚至在盐胁迫条件下）缺乏主要的表型改变，但它与AtbZIP44和cw修饰基因AtMAN7的共表达表明，在硅藻发育过程中，AtbZIP9基因敲除突变体在转录调控中发挥作用。最近的证据进一步将AtbZIP9与aba反应性基因表达联系起来，并确定它可能是涉及其他c组bzip9的冗余调控网络的组成部分。这些研究结果表明，AtbZIP9可能与AtbZIP44和其他因子协同作用，是硅油和种子发育过程的候选转录调节剂。

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引用次数: 0

Evolutionary and functional insights into ascorbate oxidase genes in the Fabaceae plant family 豆科植物抗坏血酸氧化酶基因的进化和功能研究

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-09 DOI: 10.1016/j.plgene.2025.100538

Vitória Hirdes Glenzel , João Pedro Carmo Filgueiras , Andreia Carina Turchetto Zolet , Franceli Rodrigues Kulcheski

Ascorbate oxidase (AAO), a multicopper oxidase protein, plays a crucial role in catalyzing the oxidation of ascorbic acid (AA) in the apoplastic space. Despite the extensive attention on AAO functions, a significant gap remains in understanding its evolutionary trajectory and functional intricacies within the Fabaceae family that is recognized for its nutritional and economic importance. Our investigation revealed substantial conservation of the AAO gene family across all 21 studied Fabaceae species. Phylogenetic analysis consistently clustered Fabaceae AAO genes into two well-supported groups, indicating their shared and conserved origin. Similarly, gene structure analyses categorized sequences into two groups based on intronic sizes. Furthermore, motif analysis revealed ten conserved motifs in almost all of the AAO sequences. Notably, chromosomal localization data for Glycine max and Glycine soja AAO genes exhibited a highly similar gene distribution across the genome. Through comprehensive cis-regulatory analysis of G. max AAO genes, we identified binding motifs for transcription factors associated with various biological functions, including development, growth, and responses to biotic and abiotic stresses. Additionally, gene expression analyses unveiled significant variability in AAO gene expression profiles under different environmental stressors, highlighting the dynamic functional role of AAO in response to biotic and abiotic stresses. Our findings facilitated the identification of multiple AAO homologs in Fabaceae species, thereby enhancing our understanding of the functional roles of this gene family.

抗坏血酸氧化酶（AAO）是一种多铜氧化酶蛋白，在胞外空间催化抗坏血酸（AA）的氧化中起重要作用。尽管对AAO功能的广泛关注，但在了解其在豆科家族中的进化轨迹和功能复杂性方面仍存在显着差距，这是公认的营养和经济重要性。我们的研究发现，在所有21个被研究的豆科物种中，AAO基因家族都存在大量的保守性。系统发育分析一致将豆科AAO基因聚为两个支持良好的群体，表明它们具有共同和保守的起源。同样，基因结构分析根据内含子大小将序列分为两组。此外，基序分析在几乎所有的AAO序列中发现了10个保守基序。值得注意的是，甘氨酸max和甘氨酸大豆AAO基因的染色体定位数据显示，基因在基因组中的分布高度相似。通过对G. max AAO基因的全面顺式调控分析，我们确定了与多种生物学功能相关的转录因子的结合基序，包括发育、生长以及对生物和非生物胁迫的反应。此外，基因表达分析揭示了不同环境胁迫下AAO基因表达谱的显著差异，强调了AAO在生物和非生物胁迫下的动态功能作用。我们的发现促进了豆科植物中多个AAO同源物的鉴定，从而增强了我们对该基因家族功能作用的理解。

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引用次数: 0

In silico analysis and heterologous expression of OsNAC121 shed light on its structure and function in flowering and osmotic stress OsNAC121基因的硅晶分析和异源表达，揭示了其在开花和渗透胁迫中的结构和功能

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-06 DOI: 10.1016/j.plgene.2025.100537

Nazma Anjum, Ayushi Saini, Bina K. Singh, Amit K. Das, Mrinal K. Maiti

Plant-specific NAC transcription factors (TFs) are key master regulators in multiple vital physiological processes like development, organogenesis, stress tolerance and senescence. Identifying suitable TF is crucial for crop improvement program via biotechnological intervention. In rice (Oryza sativa L.) plant, only 38 out of 151 NAC TFs have been characterized till date. In this study, we have deciphered the in silico structure and in vivo function of OsNAC121 through heterologous expression in Escherichia coli and tobacco systems, and documented its potential role in flowering and osmotic stress. Like a typical NAC TF, OsNAC121 has a highly conserved NAC domain at the N-terminal half, featuring the subdomains A-E with the signature NAC fold comprising the twisted β-barrel between the two α-helices, and a highly variable C-terminal random coil. Analyses revealed that OsNAC121 binds to the consensus NAC binding DNA sequence (NACBS) in silico. In this study we have observed that the bacterially expressed truncated OsNAC121 protein forms tetramers in vitro, but structural modeling and DNA docking strongly support the dimeric form as the biologically relevant DNA-binding unit. Further bioinformatics analysis unravelled that R79 residue and the ⁸⁶WKAT⁸⁹ motif are pivotal for binding to the NACBS. Transgenic tobacco plants constitutively expressing OsNAC121 had elongated stem with reduced stem girth, grew faster, and flowered early, suggesting a role of OsNAC121 in determining the fate of meristematic cells. Transgenic tobacco plants also exhibited susceptibility to both drought and salinity stresses characterized by loss of chlorophyll, stunted height and smaller leaves. Therefore, we conclude that the OsNAC121 plays a crucial role in plant development, flowering time, and stress biology. Research in autologous host rice will elucidate the exact signalling pathway of OsNAC121 involving phytohormones and identify its interacting partners.

植物特异性NAC转录因子（TFs）是植物发育、器官发生、抗逆性和衰老等重要生理过程的主要调控因子。通过生物技术干预确定合适的TF对作物改良计划至关重要。在水稻（Oryza sativa L.）植株中，151个NAC TFs中只有38个已被鉴定。在这项研究中，我们通过在大肠杆菌和烟草系统中的异源表达，破译了OsNAC121的硅结构和体内功能，并记录了其在开花和渗透胁迫中的潜在作用。与典型的NAC TF一样，OsNAC121在n端具有高度保守的NAC结构域，其子结构域a - e具有NAC褶皱特征，NAC褶皱由两个α-螺旋之间的扭曲β-桶组成，c端具有高度可变的随机线圈。分析结果表明，OsNAC121在硅片上与一致的NAC结合DNA序列（NACBS）结合。在本研究中，我们观察到细菌表达的截断的OsNAC121蛋白在体外形成四聚体，但结构建模和DNA对接强烈支持二聚体形式作为生物学相关的DNA结合单元。进一步的生物信息学分析揭示了R79残基和86WKAT89基序是与NACBS结合的关键。组成性表达OsNAC121的转基因烟草植株茎长、茎周缩短、生长更快、开花早，表明OsNAC121在决定分生组织细胞的命运中起着重要作用。转基因烟草还表现出对干旱和盐胁迫的敏感性，其特征是叶绿素丧失、身高发育不良和叶片变小。因此，我们认为OsNAC121在植物发育、开花时间和胁迫生物学中起着至关重要的作用。在自体寄主水稻上的研究将有助于阐明OsNAC121涉及植物激素的确切信号通路，并确定其相互作用的伙伴。

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引用次数: 0

Molecular marker assisted confirmation of a hybrid between Ascocentrum ampullaceum var. auranticum and Rhynchostylis retusa. 分子标记辅助鉴定了壶形散囊草与黄纹花的杂种关系。

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-08-05 DOI: 10.1016/j.plgene.2025.100533

Kangabam Soneja Devi , Nandeibam Samarjit Singh , Heisnam Haripriyari Devi , Haobam Sharmila Devi , Huidrom Sunitibala Devi

Two rare and endangered orchids, Rhynchostylis retusa, and Ascocentrum ampullaceum var. auranticum, a narrowly endemic orchid from Manipur, were used for the present study. These two orchids were selected as parents because they have desirable traits like dense and floriferous, colorful, and long-lasting flowers. Our goal is to develop a hybrid species that is intermediate and improved over its parents in terms of floral characteristics by the F1 generation. When A. ampullaceum var. auranticum was the female parent, a 90 % crossability success rate was attained. Half-strength Murashige and Skoog (MS) basal medium with no phytohormones was used for seed germination in vitro and protocorm development of the putative hybrid. The basal medium containing 1 mg/L BAP and 0.5 mg/L NAA showed the highest growth response with 7.57 shoots/explant, 5.90 leaves/explant, and 57.19 PLBs/explant, while the medium enriched with 1 mg/L NAA produced the maximum number of roots (4.95) after 150 days of inoculation. The assessment for rapid determination of genetic purity of the developed hybrid (F1 plants) between A. ampullaceum var. auranticum and R. retusa was carried out by using the molecular markers, SCoT and SSR. The F1 plants' complementing banding patterns, which they inherited from their parents, confirmed that they were pure hybrids. These PCR-based molecular markers could be used for the early assessment of hybridity.

本研究以两种珍稀濒危兰花——蛇纹兰（Rhynchostylis retusa）和曼尼普尔（Manipur）特有的壶形兰（Ascocentrum ampullaceum var. aururanticum）为研究对象。这两种兰花之所以被选为亲本，是因为它们具有致密、多花、色彩鲜艳、开花时间长等令人满意的特点。我们的目标是开发一个杂交物种，是中间和改进其亲本方面的花卉特征的F1代。当壶叶金莲为母本时，杂交成功率达90%。用不含激素的半强度Murashige和Skoog （MS）基础培养基进行离体种子萌发和原球茎发育。BAP含量为1 mg/L、NAA含量为0.5 mg/L的基础培养基在接种150 d后生根数最多，达到7.57根/外植体、5.90叶/外植体和57.19根/外植体；NAA含量为1 mg/L的基础培养基在接种150 d后生根数最多，达到4.95根。利用分子标记、SCoT和SSR等方法，对ampullaceum var. aururanticum和r.r etusa杂交后代（F1植株）的遗传纯度进行了快速鉴定。这些F1植株的互补带状模式从它们的亲本遗传而来，证实了它们是纯杂交种。这些基于pcr的分子标记可用于杂交的早期评估。

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引用次数: 0

Harnessing genome editing for the advancement of underutilized crops: A critical review highlighting current progress, challenges and future prospects 利用基因组编辑促进未充分利用的作物：一篇强调当前进展、挑战和未来前景的批判性综述

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-07-30 DOI: 10.1016/j.plgene.2025.100534

Sunandan Swain , Sadhan Debnath , Khalil Khamassi , Kajal Samantara , Parsa Ram , Amarjeet Kumar , Ashok Kumar Mahawer , Tanushri Kaul

Underutilized cereals and legumes are the rich source of important minerals, essential amino acids, vitamins and phytochemicals. These crops possess valuable agronomic and physiological traits, including resilience to harsh climates and the ability to thrive in low-input farming systems. Such characteristics make them vital for agricultural diversification in the face of climate change and biodiversity loss, and they hold significant potential for strengthening global food security and promoting sustainable agriculture. As they possess exceptional nutritional properties, there is a huge need for specific attention to these crops. However, they have been marginalized due to the dominance of high-yielding commercial varieties of major staple food crops, limited adaptability to diverse climatic conditions, insufficient investment, lack of awareness, and monoculture practices. In recent years, advancements in genomics and high throughput sequencing technologies have paved the ways for implementing cutting-edge genomics technologies, like RNA-guided nucleases and other advanced genome editing tools to improve traits such as yield and quality, stress tolerance, nutritional properties and antinutritional factors (ANFs) in these crops. This review mainly focusses on the importance of various underutilized crops, latest progress in gene-editing applications in these crops, major challenges in the implementation of this precise technology for crop improvement including regulatory restrictions and the need for tailored gene-editing approaches to unlock the full potential of these neglected crops. Additionally, it explores strategies to address technical hurdles, such as off-target effects and delivery methods, to enhance the effectiveness of these technologies in agricultural and crop improvement.

未充分利用的谷物和豆类是重要矿物质、必需氨基酸、维生素和植物化学物质的丰富来源。这些作物具有宝贵的农艺和生理特性，包括对恶劣气候的适应能力和在低投入农业系统中茁壮成长的能力。面对气候变化和生物多样性丧失，这些特征对农业多样化至关重要，在加强全球粮食安全和促进可持续农业方面具有巨大潜力。由于它们具有特殊的营养特性，因此非常需要对这些作物进行特别关注。然而，由于主要粮食作物的高产商业品种占主导地位，对多种气候条件的适应性有限，投资不足，缺乏认识和单一栽培做法，它们已被边缘化。近年来，基因组学和高通量测序技术的进步为实施尖端基因组学技术铺平了道路，如rna引导核酸酶和其他先进的基因组编辑工具，以提高这些作物的产量和质量、耐受性、营养特性和抗营养因子（ANFs）等性状。这篇综述主要集中在各种未充分利用的作物的重要性、基因编辑在这些作物中的应用的最新进展、实施这种精确技术进行作物改良的主要挑战，包括监管限制和定制基因编辑方法的需求，以释放这些被忽视的作物的全部潜力。此外，它还探讨了解决技术障碍的战略，如脱靶效应和交付方法，以提高这些技术在农业和作物改良中的有效性。

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引用次数: 0

Genome-wide identification and expression analysis of the OVATE gene family in melon (Cucumis melo L.) 甜瓜（Cucumis melo L.） OVATE基因家族全基因组鉴定及表达分析

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-07-20 DOI: 10.1016/j.plgene.2025.100532

Zixuan Li , Shuaidong Wu , Wenxi Liu , Jiyuan Wang , Yanliang Guo , Congsheng Yan , Yan Wang , Huijun Zhang , Jie Liu

The OVATE gene family (OFP) is widely present in plants and plays a crucial role in regulating growth, development, and plant morphology, particularly in shaping fruit morphology. However, limited research has been conducted on the OFP gene in melon. In this study, we systematically identified and analyzed the entire OFP gene family in the melon genome. By comparing with 20 AtOFP protein sequences, 16 CmOFP genes were identified from the melon genome, and their physicochemical properties were characterized. Phylogenetic relationship analysis revealed that CmOFP and AtOFP could be classified into five subfamilies. Syntenic analysis demonstrated high synteny between Arabidopsis and melon OFP. Additionally, the gene structure and conserved domains of CmOFP were determined, and its predicted tertiary protein structure was elucidated. Through promoter analysis of CmOFP, a total of 30 regulatory elements were identified, showing significant differences in both number and classification among these elements. Expression pattern analysis indicated that the relative expression of CmOFP in the ovary was high and decreased post-pollination. Transcriptome analysis of different melon fruit pulps revealed that plant hormone signal transduction pathways were closely associated with fruit shape determination. Notably, four CmOFP genes exhibited significant differential expression across various fruit shapes, suggesting potential applications in fruit shape improvement. This study provides a theoretical foundation for further exploring the functional roles of CmOFP and their utilization in melon breeding programs.

OVATE基因家族（OFP）广泛存在于植物中，在调节植物的生长发育和形态，特别是果实形态的形成中起着至关重要的作用。然而，对甜瓜中OFP基因的研究有限。在这项研究中，我们系统地鉴定和分析了甜瓜基因组中的整个OFP基因家族。通过比对20个AtOFP蛋白序列，从甜瓜基因组中鉴定出16个CmOFP基因，并对其理化性质进行了分析。系统发育关系分析表明，CmOFP和AtOFP可划分为5个亚科。同源性分析表明拟南芥与甜瓜OFP具有较高的同源性。此外，还确定了CmOFP的基因结构和保守结构域，并对其预测的三级蛋白结构进行了阐释。通过对CmOFP的启动子分析，共鉴定出30个调控元件，这些元件在数量和分类上都存在显著差异。表达谱分析表明，CmOFP在子房中的相对表达量较高，授粉后相对表达量降低。对不同甜瓜果肉的转录组分析表明，植物激素信号转导途径与果实形状的决定密切相关。值得注意的是，4个CmOFP基因在不同果实形状中表现出显著的差异表达，这表明CmOFP基因在改善果实形状方面具有潜在的应用前景。该研究为进一步探索CmOFP的功能作用及其在甜瓜育种中的应用提供了理论基础。

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引用次数: 0

Computational interference of gene regulatory networks on the growth and development of millets 基因调控网络对谷子生长发育的计算干扰

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-07-15 DOI: 10.1016/j.plgene.2025.100531

Lipsa Leena Panigrahi , Gayatri Mishra , Dhaneswar Swain , Gyana Ranjan Rout

Millets are among the cereal crops cultivated for nutrient-rich food. They are generally considered as resilient crops in terms of growth requirements, as they can withstand harsh climatic factors such as unpredictable climate change and nutrient-depleted soils. The present review highlighted that gene regulatory networks are rewired to control the adaptable traits and to understand the transcriptional regulatory system against environmental stress. By combining machine learning, predictive modeling, and multi-omics data to unravel intricate regulatory relationships, computational methods have entirely changed the study of GRNs (gene regulatory networks), making and identifying important transcription factors, co-regulators, and signaling networks. Recent developments in artificial intelligence, systems biology, and bioinformatics have made reconstructing and analyzing millet GRNs, providing new information on blooming mechanisms, nutrient absorption,and drought resistance. Data scarcity, species-specific heterogeneity, and the requirement for high-throughput functional validation. Computational models incorporating transcriptomics, proteomics, and metabolomics help to improve crop improvement by enabling targeted genetic alterations and increasing predictive accuracy. This study discusses critical approaches, accessible datasets, and new developments in computational GRN investigations in millets. Deep learning, CRISPR-based gene editing, and synthetic biology in millet research are among the opportunities to develop new genotypes. By using computational methods to gain a thorough understanding of millet GRNs, it will be possible to create millet varieties that are more nutritious and climate-robust, promoting sustainable agriculture.

小米是一种营养丰富的谷类作物。就生长需求而言，它们通常被认为是适应力强的作物，因为它们可以承受恶劣的气候因素，如不可预测的气候变化和营养枯竭的土壤。本文综述了基因调控网络的重新布线，以控制适应性性状，并了解对环境胁迫的转录调控系统。通过结合机器学习、预测建模和多组学数据来揭示复杂的调控关系，计算方法完全改变了grn（基因调控网络）的研究，制造和识别重要的转录因子、协同调控因子和信号网络。近年来，人工智能、系统生物学和生物信息学的发展使谷子grn得以重构和分析，为谷子开花机制、养分吸收和抗旱性提供了新的信息。数据稀缺性、物种特异性异质性以及对高通量功能验证的需求。结合转录组学、蛋白质组学和代谢组学的计算模型通过实现靶向遗传改变和提高预测准确性来帮助改善作物改良。本研究讨论了小米计算GRN研究的关键方法、可访问的数据集和新发展。小米研究中的深度学习、基于crispr的基因编辑和合成生物学都是开发新基因型的机会。通过使用计算方法来全面了解谷子grn，将有可能创造出更有营养、更适应气候变化的谷子品种，从而促进可持续农业。

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引用次数: 0

Chloroplast genomes of six Aloe species: Insights into genetic variation and evolutionary patterns 六种芦荟的叶绿体基因组：遗传变异和进化模式的见解

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-07-13 DOI: 10.1016/j.plgene.2025.100530

Dede Kurniawan , Linzhou Li , Min Liu , Jose Marie Wynne Aquavita , Martha Britany Napitupulu , Manik Prabhu Narsing Rao , Turhadi Turhadi , Shouzhou Zhang , Tong Wei , Sunil Kumar Sahu

Aloe is a highly diverse genus of succulent plants with important pharmacological, medicinal, and commercial importance. However, the limited availability of genomic resources has constrained evolutionary and comparative genomics studies of this genus. To address this problem, we sequenced and assembled the first comprehensive chloroplast genome sequences of six Aloe species (Aloe barberae, Aloe excelsa, Aloe marlothii, Aloe perfoliata, Aloe glauca, and Aloe tenuifolia) using a high-throughput whole-genome sequencing approach. The total length of the assembled chloroplast genomes varied from 152,383 to 154,127 bp, exhibiting a conserved quadripartite structure comprising 131 genes. Comparative genomic analyses revealed the loss of the rpl32 and infA genes across all the sampled species except for Aloe arborescens, suggesting lineage-specific gene retention. Furthermore, we identified eight protein-coding genes under positive selection and five intergenic regions with significant variability, which hold potential for molecular species identification (DNA barcoding) and phylogenetic studies. Phylogenetic reconstruction revealed robust branch support values, validating the monophyletic status of the Aloe genus and updating the sister clade of Aloe vera, which was previously close to Aloe maculata. These findings offer insights into genetic variation, gene loss, and potential evolutionary patterns, contributing to future phylogenetic and conservation research.

芦荟是一种高度多样化的多肉植物属，具有重要的药理、药用和商业意义。然而，有限的基因组资源限制了该属的进化和比较基因组学研究。为了解决这个问题，我们使用高通量全基因组测序方法对6种芦荟（芦荟，芦荟excelsa，芦荟marlothii，芦荟perfoliata，芦荟glauca和芦荟tenuifolia）进行了首次全面的叶绿体基因组测序和组装。叶绿体基因组总长度在152,383 ~ 154,127 bp之间，呈现由131个基因组成的保守四部结构。比较基因组分析显示，除了芦荟外，所有样本物种的rpl32和infA基因都缺失，这表明谱系特异性基因保留。此外，我们还发现了8个正选择的蛋白质编码基因和5个具有显著变异的基因间区，这些基因具有分子物种鉴定（DNA条形码）和系统发育研究的潜力。系统发育重建显示了强大的分支支持值，验证了芦荟属的单系地位，并更新了芦荟的姐妹分支，该分支此前与芦荟接近。这些发现提供了对遗传变异、基因丢失和潜在进化模式的见解，有助于未来的系统发育和保护研究。

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引用次数: 0

Structural and functional insights into Jasmonate ZIM-domain 2 (GhJAZ2) interactions in cotton fiber development via Jasmonic acid signaling 通过茉莉酸信号传导，茉莉酸zim -结构域2 （GhJAZ2）在棉纤维发育中的相互作用的结构和功能研究

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-06-28 DOI: 10.1016/j.plgene.2025.100528

Muhammad Sulyman Saleem , Sultan Habibullah Khan , Zunaira Afzal Naveed

Cotton is one of the world's most vital fiber crops, and enhancing its fiber quality continues to be a major priority for the textile sector. The protein GhJAZ2, belonging to the Jasmonate ZIM-domain (JAZ) family, functions as a transcriptional repressor that influences fiber initiation by interacting with proteins such as GhMYB25-like, GhWD40, GhMYC2, GhGL1, and GhJI1, all of which participate in jasmonic acid (JA) signaling pathways. Despite their known involvement, detailed insights into their interactions and precise three-dimensional structures remain elusive.

In this research, we aimed to characterize the functional roles of GhJAZ2 and its interacting partners, and to model their structural interactions computationally. We utilized homology-based modeling to construct 3D models and applied HADDOCK software for protein-protein docking to accurately pinpoint interaction sites and assess binding affinities. Our findings indicated that the ZIM domain of GhJAZ2 serves as the central interaction region. Specifically, key residues within the TIFY motif, particularly ILE126 and TYR128, play a significant role in binding GhWD40, GhMYC2, GhGL1, and GhJI1 proteins. These results underscore the critical role of the TIFY motif in enabling GhJAZ2 to act as a repressor during fiber development.

This study provides valuable new insights into the molecular processes involved in JA-driven fiber development in cotton, identifying potential genetic targets that could be manipulated to significantly improve fiber quality.

棉花是世界上最重要的纤维作物之一，提高其纤维质量仍然是纺织部门的一个主要优先事项。GhJAZ2蛋白属于茉莉酸zm结构域（JAZ）家族，作为一种转录抑制因子，通过与ghmyb25样蛋白、GhWD40、GhMYC2、GhGL1和GhJI1等蛋白相互作用来影响纤维的起始，这些蛋白都参与茉莉酸（JA）信号通路。尽管已知它们的参与，但对它们的相互作用和精确的三维结构的详细见解仍然难以捉摸。在本研究中，我们旨在表征GhJAZ2及其相互作用伙伴的功能角色，并通过计算模拟它们的结构相互作用。我们利用同源性建模技术构建三维模型，并应用HADDOCK软件进行蛋白-蛋白对接，精确定位相互作用位点，评估结合亲和力。我们的研究结果表明GhJAZ2的ZIM结构域是中心相互作用区。具体来说，TIFY基序中的关键残基，特别是ILE126和TYR128，在结合GhWD40、GhMYC2、GhGL1和GhJI1蛋白中发挥重要作用。这些结果强调了TIFY基序在使GhJAZ2在纤维发育过程中发挥抑制作用的关键作用。这项研究为棉花中ja驱动纤维发育的分子过程提供了有价值的新见解，确定了潜在的基因靶点，可以通过操纵来显着提高纤维质量。

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引用次数: 0

Genome-wide identification of HD-Zip transcription factor family in Artemisia argyi and functional analysis of AaHDZ64 in trichome development 艾蒿HD-Zip转录因子家族的全基因组鉴定及AaHDZ64在毛状体发育中的功能分析

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-06-27 DOI: 10.1016/j.plgene.2025.100529

Zhanhu Cui , Chunyan Miao , Heyang Shang , Qian Zhao , Shujiao Li , Zhongyi Zhang , Yuqing Wang , Xianzhang Huang

The homeodomain-leucine zipper (HD-Zip) family of transcription factor is a unique and vital gene family in plants, involved in various processes including organ development, stress responses, and regulation of secondary metabolite biosynthesis. This study aimed to investigate the role of HD-Zip family transcription factors in the development of Artemisia argyi trichomes. By utilizing the whole genome data of A. argyi, we identified 69 AaHDZ transcription factors and systematically characterized their structural and physicochemical properties. The predicted amino acid sequence lengths range from 188 to 854 residues, with relative molecular masses of 22.2–94.6 kDa, theoretical isoelectric points of 4.65–9.31, and lipid solubility indices of 52.08–89.14. All of these proteins were hydrophilic. The results of subcellular localization predictions indicated that most AaHDZ proteins are localized in the nucleus, while a few are located in the cytoplasm and chloroplasts. Based on the classification of the HD-Zip family in Arabidopsis thaliana, the 69 AaHDZ proteins were divided into four subfamilies, with similar gene structures observed within each subfamily. Heterologous overexpression of AaHDZ64 gene significantly increased trichome density in A. thaliana. The results confirmed that AaHDZ64 is a positive regulatory factor for the growth and development of trichomes. This study provides a theoretical foundation for understanding the molecular regulatory mechanisms underlying trichome development in A. argyi leaves and offers insights for the precision breeding of A. argyi.

同源域-亮氨酸拉链（HD-Zip）转录因子家族是植物中一个独特而重要的基因家族，参与了器官发育、逆境反应和次生代谢产物生物合成的调控等多种过程。本研究旨在探讨HD-Zip家族转录因子在艾叶毛状体发育中的作用。利用艾叶的全基因组数据，鉴定出69个AaHDZ转录因子，并对其结构和理化性质进行了系统表征。预测氨基酸序列长度为188 ~ 854个残基，相对分子质量为22.2 ~ 94.6 kDa，理论等电点为4.65 ~ 9.31，脂溶性指数为52.08 ~ 89.14。所有这些蛋白质都是亲水的。亚细胞定位预测结果表明，大多数AaHDZ蛋白定位于细胞核，少数位于细胞质和叶绿体中。根据拟南芥HD-Zip家族的分类，将69个AaHDZ蛋白划分为4个亚家族，每个亚家族中都有相似的基因结构。AaHDZ64基因的异源过表达显著增加了拟蓝藻的毛密度。结果证实，AaHDZ64是毛状体生长发育的正向调控因子。本研究为了解艾叶毛状体发育的分子调控机制提供了理论基础，并为艾叶精细育种提供了参考。

{"title":"Genome-wide identification of HD-Zip transcription factor family in Artemisia argyi and functional analysis of AaHDZ64 in trichome development","authors":"Zhanhu Cui , Chunyan Miao , Heyang Shang , Qian Zhao , Shujiao Li , Zhongyi Zhang , Yuqing Wang , Xianzhang Huang","doi":"10.1016/j.plgene.2025.100529","DOIUrl":"10.1016/j.plgene.2025.100529","url":null,"abstract":"<div><div>The homeodomain-leucine zipper (HD-Zip) family of transcription factor is a unique and vital gene family in plants, involved in various processes including organ development, stress responses, and regulation of secondary metabolite biosynthesis. This study aimed to investigate the role of HD-Zip family transcription factors in the development of <em>Artemisia argyi</em> trichomes. By utilizing the whole genome data of <em>A. argyi</em>, we identified 69 AaHDZ transcription factors and systematically characterized their structural and physicochemical properties. The predicted amino acid sequence lengths range from 188 to 854 residues, with relative molecular masses of 22.2–94.6 kDa, theoretical isoelectric points of 4.65–9.31, and lipid solubility indices of 52.08–89.14. All of these proteins were hydrophilic. The results of subcellular localization predictions indicated that most AaHDZ proteins are localized in the nucleus, while a few are located in the cytoplasm and chloroplasts. Based on the classification of the HD-Zip family in <em>Arabidopsis thaliana</em>, the 69 AaHDZ proteins were divided into four subfamilies, with similar gene structures observed within each subfamily. Heterologous overexpression of <em>AaHDZ64</em> gene significantly increased trichome density in <em>A. thaliana</em>. The results confirmed that <em>AaHDZ64</em> is a positive regulatory factor for the growth and development of trichomes. This study provides a theoretical foundation for understanding the molecular regulatory mechanisms underlying trichome development in <em>A. argyi</em> leaves and offers insights for the precision breeding of <em>A. argyi</em>.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100529"},"PeriodicalIF":2.2,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144523420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0