Plant Gene最新文献

{"title":"Integrating AI in plant science: A review of applications and future prospects","authors":"Imran Khan,&nbsp;Brajesh Kumar Khare","doi":"10.1016/j.plgene.2025.100542","DOIUrl":"10.1016/j.plgene.2025.100542","url":null,"abstract":"<div><div>Plant science, which includes crop biology, genetics, and agronomy, is crucial for ensuring food security and enhancing agricultural productivity. As global food demand increases, the field is evolving by incorporating advanced technologies to address challenges such as climate change, disease resistance, and yield improvement. Artificial Intelligence is a key technology driving this transformation, offering new opportunities for innovation and progress in plant science. This review provides a comprehensive overview of the current and future applications of AI in plant science, with a special focus on areas where conventional techniques fall short. Unlike traditional methods that often rely on manual, time-intensive analysis, AI-driven models can learn complex patterns from high-dimensional biological and phenotypic data, automate decision-making, and scale rapidly. It begins with a discussion of the core principles of plant science, followed by an examination of AI technologies and their potential. The paper explores AI's role in plant genomics and breeding, focusing on key areas like genome sequencing, genetic marker identification, and the development of improved crop varieties. Special attention is given to AI-driven approaches in crop improvement, where machine learning models are increasingly used to optimize breeding programs, enhance yield predictions, support phenotypic selection, and address challenges like disease resistance. The review also discusses the challenges of applying AI in plant science, including issues with data quality, model interpretability, and integrating AI into large-scale agricultural practices. Finally, the paper looks ahead to the future of AI in plant science, suggesting directions for further research and development.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100542"},"PeriodicalIF":1.6,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144879786","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}

{"title":"Genome-wide identification and expression analysis of UDP-glycosyltransferases genes associated with secondary metabolism during grain development in pearl millet (Pennisetum glaucum)","authors":"Adarsh Kumar,&nbsp;Theint Theint Tun,&nbsp;Vinay Kumar","doi":"10.1016/j.plgene.2025.100541","DOIUrl":"10.1016/j.plgene.2025.100541","url":null,"abstract":"<div><div>This study focused on analysing the UDP-glycosyltransferase gene family in <em>Pennisetum glaucum,</em> which plays an essential role in plant metabolism and glycosylation of the secondary metabolites. We identified 191 UGTs by performing a BLASTp search against the available pearl millet genome, utilizing amino acid sequences of the conserved plant secondary product glycosyltransferase (PSPG) motif and already reported <em>UGT</em> genes from <em>Arabidopsis</em> and maize. Phylogenetic analysis categorized these genes into 18 groups (A–R), and their genomic distribution was mapped across 10 pearl millet chromosomes. Subcellular localization analysis showed that PglUGT proteins localized to the cytoplasm, chloroplast, and nucleus. Functional annotation was carried out by Gene Ontology (GO) analysis of all the <em>PglUGT</em> genes for biological processes, cellular components, and molecular functions. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that a particular set of <em>PglUGT</em> genes are directly linked with secondary metabolite biosynthesis during seed development. Further, TLC analysis documented the presence of glycoside flavonoids (vitexin and orientin) during different grain development stages: just before milky stage (S1), milky stage (S2–3) and physiological mature (S4). Expression profiling of 20 randomly selected <em>PglUGT</em> genes across different grain developmental stages also showed the elevated expression during these stages, underscoring their potential roles in plant growth and grain development. In conclusion, this study documented the identification and characterization of <em>UGT</em> genes in genome of pearl millet and proposed the potential role of UGTs during seed development.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100541"},"PeriodicalIF":1.6,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144879785","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}

{"title":"Temporal and spatial expression analysis of AtbZIP9 during seed and silique development in Arabidopsis thaliana (L.) Heynh","authors":"Jonatan Illescas-Miranda ,&nbsp;Victoria Llanos-Casado ,&nbsp;Estefanía Contreras,&nbsp;Néstor Carrillo-Barral,&nbsp;Raquel Iglesias-Fernández","doi":"10.1016/j.plgene.2025.100536","DOIUrl":"10.1016/j.plgene.2025.100536","url":null,"abstract":"<div><div>In <em>Arabidopsis thaliana</em>, 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 <em>AtbZIP9</em> knockout mutants during germination and early development—even under salt stress conditions—its co-expression with <em>AtbZIP44</em> and the CW-modifying gene <em>AtMAN7</em> 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.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100536"},"PeriodicalIF":1.6,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841494","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}

{"title":"Evolutionary and functional insights into ascorbate oxidase genes in the Fabaceae plant family","authors":"Vitória Hirdes Glenzel ,&nbsp;João Pedro Carmo Filgueiras ,&nbsp;Andreia Carina Turchetto Zolet ,&nbsp;Franceli Rodrigues Kulcheski","doi":"10.1016/j.plgene.2025.100538","DOIUrl":"10.1016/j.plgene.2025.100538","url":null,"abstract":"<div><div>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 <em>AAO</em> gene family across all 21 studied Fabaceae species. Phylogenetic analysis consistently clustered Fabaceae <em>AAO</em> 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 <em>Glycine</em> max and <em>Glycine soja AAO</em> genes exhibited a highly similar gene distribution across the genome. Through comprehensive <em>cis</em>-regulatory analysis of <em>G.</em> max <em>AAO</em> 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 <em>AAO</em> 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 <em>AAO</em> homologs in Fabaceae species, thereby enhancing our understanding of the functional roles of this gene family.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100538"},"PeriodicalIF":1.6,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810166","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}

{"title":"In silico analysis and heterologous expression of OsNAC121 shed light on its structure and function in flowering and osmotic stress","authors":"Nazma Anjum,&nbsp;Ayushi Saini,&nbsp;Bina K. Singh,&nbsp;Amit K. Das,&nbsp;Mrinal K. Maiti","doi":"10.1016/j.plgene.2025.100537","DOIUrl":"10.1016/j.plgene.2025.100537","url":null,"abstract":"<div><div>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 <em>via</em> biotechnological intervention. In rice (<em>Oryza sativa</em> L.) plant, only 38 out of 151 NAC TFs have been characterized till date. In this study, we have deciphered the <em>in silico</em> structure and <em>in vivo</em> function of OsNAC121 through heterologous expression in <em>Escherichia coli</em> 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) <em>in silico</em>. In this study we have observed that the bacterially expressed truncated OsNAC121 protein forms tetramers <em>in vitro,</em> 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.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100537"},"PeriodicalIF":1.6,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144828607","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}

{"title":"Molecular marker assisted confirmation of a hybrid between Ascocentrum ampullaceum var. auranticum and Rhynchostylis retusa.","authors":"Kangabam Soneja Devi ,&nbsp;Nandeibam Samarjit Singh ,&nbsp;Heisnam Haripriyari Devi ,&nbsp;Haobam Sharmila Devi ,&nbsp;Huidrom Sunitibala Devi","doi":"10.1016/j.plgene.2025.100533","DOIUrl":"10.1016/j.plgene.2025.100533","url":null,"abstract":"<div><div>Two rare and endangered orchids, <em>Rhynchostylis retusa</em>, and <em>Ascocentrum ampullaceum</em> var. <em>auranticum</em>, 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 <em>A. ampullaceum</em> var. <em>auranticum</em> 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 <em>in vitro</em> 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 <em>A. ampullaceum</em> var. <em>auranticum</em> and <em>R. retusa</em> 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.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100533"},"PeriodicalIF":1.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144772237","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}

{"title":"Harnessing genome editing for the advancement of underutilized crops: A critical review highlighting current progress, challenges and future prospects","authors":"Sunandan Swain ,&nbsp;Sadhan Debnath ,&nbsp;Khalil Khamassi ,&nbsp;Kajal Samantara ,&nbsp;Parsa Ram ,&nbsp;Amarjeet Kumar ,&nbsp;Ashok Kumar Mahawer ,&nbsp;Tanushri Kaul","doi":"10.1016/j.plgene.2025.100534","DOIUrl":"10.1016/j.plgene.2025.100534","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"44 ","pages":"Article 100534"},"PeriodicalIF":1.6,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810167","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}

{"title":"Genome-wide identification and expression analysis of the OVATE gene family in melon (Cucumis melo L.)","authors":"Zixuan Li ,&nbsp;Shuaidong Wu ,&nbsp;Wenxi Liu ,&nbsp;Jiyuan Wang ,&nbsp;Yanliang Guo ,&nbsp;Congsheng Yan ,&nbsp;Yan Wang ,&nbsp;Huijun Zhang ,&nbsp;Jie Liu","doi":"10.1016/j.plgene.2025.100532","DOIUrl":"10.1016/j.plgene.2025.100532","url":null,"abstract":"<div><div>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 <em>OFP</em> gene in melon. In this study, we systematically identified and analyzed the entire <em>OFP</em> gene family in the melon genome. By comparing with 20 AtOFP protein sequences, 16 <em>CmOFP</em> 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 <em>OFP</em>. Additionally, the gene structure and conserved domains of CmOFP were determined, and its predicted tertiary protein structure was elucidated. Through promoter analysis of <em>CmOFP</em>, 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 <em>CmOFP</em> 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 <em>CmOFP</em> 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 <em>CmOFP</em> and their utilization in melon breeding programs.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100532"},"PeriodicalIF":2.2,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144704123","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}

{"title":"Computational interference of gene regulatory networks on the growth and development of millets","authors":"Lipsa Leena Panigrahi ,&nbsp;Gayatri Mishra ,&nbsp;Dhaneswar Swain ,&nbsp;Gyana Ranjan Rout","doi":"10.1016/j.plgene.2025.100531","DOIUrl":"10.1016/j.plgene.2025.100531","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100531"},"PeriodicalIF":2.2,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655443","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}

{"title":"Chloroplast genomes of six Aloe species: Insights into genetic variation and evolutionary patterns","authors":"Dede Kurniawan ,&nbsp;Linzhou Li ,&nbsp;Min Liu ,&nbsp;Jose Marie Wynne Aquavita ,&nbsp;Martha Britany Napitupulu ,&nbsp;Manik Prabhu Narsing Rao ,&nbsp;Turhadi Turhadi ,&nbsp;Shouzhou Zhang ,&nbsp;Tong Wei ,&nbsp;Sunil Kumar Sahu","doi":"10.1016/j.plgene.2025.100530","DOIUrl":"10.1016/j.plgene.2025.100530","url":null,"abstract":"<div><div><em>Aloe</em> 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 <em>A</em><em>loe</em> species (<em>Aloe barberae, Aloe excelsa, Aloe marlothii, Aloe perfoliata, Aloe glauca</em>, and <em>Aloe tenuifolia</em>) 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 <em>rpl32</em> and <em>infA</em> genes across all the sampled species except for <em>Aloe arborescens</em>, 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 <em>Aloe</em> genus and updating the sister clade of <em>Aloe vera</em>, which was previously close to <em>Aloe maculata</em>. These findings offer insights into genetic variation, gene loss, and potential evolutionary patterns, contributing to future phylogenetic and conservation research.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100530"},"PeriodicalIF":2.2,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655442","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}