Plant Gene最新文献

{"title":"Molecular identification of endemic plant species in Kars Province based on universal barcode gene regions","authors":"Asiye Uluğ ,&nbsp;Funda Özdemir Değirmenci ,&nbsp;Gül Esma Akdoğan","doi":"10.1016/j.plgene.2025.100514","DOIUrl":"10.1016/j.plgene.2025.100514","url":null,"abstract":"<div><div>Located in the highest and coldest region of north-eastern Türkiye, the province of Kars boasts a remarkable floral diversity, accounting for 16 % of the country's flora with 1615 plant species identified. This region represents the Caucasian lands of Türkiye and serves as a transition point between the Iranian-Turkish, European-Siberian and Mediterranean floral regions. Despite its considerable botanical wealth of the province, the flora of Kars Province remains poorly documented in the scientific literature. The aim of this research was to provide the molecular identity of 14 endemic plant species in the province using DNA-based methods. Three universal DNA barcode genes—<em>trnH-psbA</em> (non-coding spacer region), ribulose-1,5-bisphosphate carboxylase large subunit (<em>rbcL</em>), and maturase K (<em>matK</em>)—were sequenced to facilitate accurate identification. The endemic plant species were correctly identified to genus and species level based on the presence of the corresponding sequence of the investigated gene regions. By submitting 36 new barcodes to the NCBI database, this study contributes valuable genetic resources for future research in plant genetic studies. The findings highlight the potential of DNA barcoding to improve our understanding of plant diversity and to inform conservation efforts in the Caucasus region. The research not only contributes to our knowledge of Türkiye's plant diversity, but also advances the global discourse on genetic, taxonomic, ecological and biodiversity research dedicated to the conservation of endemic species in their natural habitats.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100514"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785384","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":"Somatic drought stress memory affects leaf morpho-physiological traits of plants via epigenetic mechanisms and phytohormonal signalling","authors":"Franklin Alongi ,&nbsp;Anja Petek-Petrik ,&nbsp;Mohammad Mukarram ,&nbsp;Hülya Torun ,&nbsp;Bernhard Schuldt ,&nbsp;Peter Petrík","doi":"10.1016/j.plgene.2025.100509","DOIUrl":"10.1016/j.plgene.2025.100509","url":null,"abstract":"<div><div>Drought stress memory in plants is an adaptive mechanism that enhances resilience to future water stress through physiological and molecular modifications triggered by previous drought events. This review explores somatic drought stress memory within a plant's lifespan, with a specific focus on leaf and stomatal morphology, minimum leaf conductance, photosynthetic efficiency, water-use efficiency, antioxidant capacity, and leaf senescence. We examine how epigenetic mechanisms—such as DNA methylation, histone modifications, and non-coding RNAs—regulate gene expression in coordination with hormonal signalling pathways. Phytohormones, including abscisic acid, jasmonic acid, ethylene, salicylic acid, auxins and cytokinins, are central to these processes, influencing key morphological and physiological adaptations, such as stomatal regulation, cuticle thickness, water retention, and improved water-use efficiency. The review synthesizes current knowledge on the molecular and hormonal networks underlying these adaptations and their impact on leaf architecture and metabolism. Despite advancements, critical gaps remain in identifying the specific genes and pathways involved, understanding the longevity of epigenetic marks, and elucidating the intricate cross-talk between phytohormones during drought stress memory. This review emphasizes the need for integrated -omics approaches to map epigenetic modifications and uncover their roles in developing drought-resistant plants through targeted stress priming strategies.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100509"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of sodium-inducible genes and efficient use of sodium ions determine the tolerance strategies of Cakile maritima and Brassica tournefortii in natural habitats","authors":"Abdel Hamid A. Khedr ,&nbsp;Mamdouh S. Serag ,&nbsp;Haneen A. Abdulsamad ,&nbsp;Reham M. Nada","doi":"10.1016/j.plgene.2025.100512","DOIUrl":"10.1016/j.plgene.2025.100512","url":null,"abstract":"<div><div>One of the potential routes for improving the stress tolerance of crops is discovering the tolerance mechanisms of halophytes. <em>Cakile maritima</em> and <em>Brassica tournefortii</em> were collected from four sites with different salinity levels. Two populations for each species were collected from each site. The populations of <em>C. maritima</em> had different phenotypic traits, especially at high salinity levels. Meanwhile, the populations of <em>B. tournefortii</em> had approximately similar phenotypic traits at all sites. The present study aimed to compare the tolerance strategies used by <em>C. maritima</em> and <em>B. tournefortii</em> by examining the responses of different populations of each species to high salinity levels in their natural habitats. The evolutionary relationship among the populations of each species was recorded. Growth performance, pigment concentration, Rubisco protein content, ion concentration and regulation of salt-inducible genes were evaluated. At high salinity levels, the biomass of most <em>C. maritima</em> populations increased, but the reverse was true for <em>B. tournefortii</em> populations. The acclimation of <em>B. tournefortii</em> to salt stress depends on Na⁺ extrusion mechanisms. Meanwhile, <em>C. maritima</em> acclimated by a regulated and controlled ion uptake, regulated salt-inducible genes and efficient use of Na⁺ in osmotic adjustment. Hierarchical analysis revealed that the expression pattern of Na⁺-inducible genes was not only species-dependent but also organ-dependent. The expression pattern did not correspond to the profiles of promoter regulatory motifs of the examined genes. The study concluded that the tolerance mechanisms are not static among halophytes, but they are dependent on the species and even on the population of a species.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100512"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835255","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":"Integrated metabolomic and transcriptomic insights into the role of anthocyanin and flavonoid biosynthesis in the pulp coloration mechanisms of Baccaurea ramiflora Lour. (Burmese grape)","authors":"Jianjian Huang ,&nbsp;Jie Chen ,&nbsp;Hui Zhu ,&nbsp;Yuzhong Zheng ,&nbsp;Xueying Wen ,&nbsp;Suying Cai ,&nbsp;Yingchun Zhu ,&nbsp;Mo Ding ,&nbsp;Qinghan Wu ,&nbsp;Zikai Chen ,&nbsp;Fengnian Wu","doi":"10.1016/j.plgene.2025.100510","DOIUrl":"10.1016/j.plgene.2025.100510","url":null,"abstract":"<div><div><em>Baccaurea ramiflora</em> Lour. (Burmese grape), a wild fruit tree with edible, ornamental, and medicinal qualities. The mechanism behind the color accumulation in its fruit pulp, which can be either pink or milky-white, remains unclear. This study investigates the metabolome and transcriptome of two <em>B. ramiflora</em> pulp types—LR (milky-white at maturity) and BR (pink at maturity)—to elucidate their coloration processes. We identified 35 flavonoids, including nine involved in the anthocyanin synthesis pathway, confirming cyanidin as the pivotal pigment for the pink pulp coloration. An examination of the flavonoid and anthocyanin biosynthetic pathways in <em>B. ramiflora</em> pulp uncovered 39 differentially expressed genes associated with structural genes. The genes <em>F3′5′H</em> and <em>UFGT</em> exhibited high expression levels in the first two developmental stages of BR, significantly more than in LR, and were almost non-existent in later stages, signifying their crucial role in the differential color accumulation between BR and LR pulps. Additionally, the expression levels of <em>CHI</em> and <em>FLS</em>, early-stage structural genes in the anthocyanin synthesis pathway, correlated with the concentrations of naringenin and quercetin, indicating their importance in the anthocyanin biosynthesis pathway of <em>B. ramiflora</em> pulp. These discoveries provide new insights that could facilitate the breeding of <em>B. ramiflora</em> varieties with diverse pulp colors.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100510"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143800256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coetaneous activity of Sub1a and SK for maintenance of underwater growth in rice genotypes","authors":"Sandip Pal ,&nbsp;Dip Pal ,&nbsp;Rup Kumar Kar ,&nbsp;Debasish Panda ,&nbsp;Pradip Chandra Dey ,&nbsp;Narottam Dey","doi":"10.1016/j.plgene.2025.100502","DOIUrl":"10.1016/j.plgene.2025.100502","url":null,"abstract":"<div><div>Despite the availability of flood-tolerant genotypes with <em>Sub1a-</em>mediated elongation, <em>SK</em> has been depicted as the primary gene responsible for elongation under prolonged submergence. However, the combined role of both loci (<em>Sub1a</em> and <em>SK</em>) are prerequisites for the survival of rice plants under flash floods followed by stagnant floods that are yet to be revealed. The combinatorial action of <em>Sub1a</em> and <em>SK</em> in a selected group of lowland rice with the simultaneous presence of both loci were studied for their physio-biochemical performance under induced flash flood followed by water stagnation for 21 days. Among the lines, var. Ganga Sali showed elongation and Kalapatia showed quiescence growth with varied degrees of aerenchyma formation. Further, it was endorsed that var. Ganga Sali showed the highest enzymatic activity of ADH and minimal for PDC under submerged conditions. RT PCR-based expression analysis of <em>Sub1a, SK1, SK2, adh1, pdc1, and susy1</em> genetic loci under differential submergence showed a mixed response to the depth and duration of the induced flood, among which <em>Sub1a</em> and <em>SK2</em> showed distinct differences between normal and test plant tissue. From expression analysis, the differential activity of <em>Sub1a</em> and <em>SK2</em> was recorded, which showed that during the onset of flood, <em>Sub1a</em> starts to express in both the var. Ganga Sali and var. Kalapatia, but as the flood prevails for a longer period, the expression of <em>Sub1a</em> is masked by both <em>SK1</em> and <em>SK2</em>. Overall, the study demonstrates the combinatorial role of both the genes in two studied rice lines under different flood regimes and their effect on phenotype. The present work may be the first report on the combinatorial expression of <em>Sub1a</em> and <em>SK</em> under differentially induced submergence on a mixed rice population.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100502"},"PeriodicalIF":2.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143760245","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":"Genetic Diversity and Population Structure of Sorghum mutant genotypes revealed through genetic Characterization","authors":"Abera Takele ,&nbsp;Tesfaye Disasa ,&nbsp;Tileye Feyissa ,&nbsp;Alemu Lencho ,&nbsp;Chemeda Birhanu","doi":"10.1016/j.plgene.2025.100501","DOIUrl":"10.1016/j.plgene.2025.100501","url":null,"abstract":"<div><div>Sorghum (<em>Sorghum bicolor</em> (L.) Moench) is a climate-resilient cereal vital for food security, especially in arid and semi-arid regions. Understanding the molecular characterization of sorghum mutant genotypes is crucial for crop improvement, yet their genetic diversity and population structure remain poorly understood. This study assessed 190 randomly selected mutant genotypes from 2000 M₂ lines generated via Ethyl Methanesulfonate (EMS) treatment, alongside two parental lines, using 10 Simple Sequence Repeat (SSR) markers. Key diversity metrics, including polymorphic information content (PIC), genetic diversity (GD), and allelic richness (Ar), were analyzed. The SSR analysis revealed significant polymorphism, with mean values of 0.84 (PIC), 0.83 (GD), and 6.41 (Ar), indicating substantial genetic variation. Analysis of Molecular Variance (AMOVA) showed that 97 % of genetic variation occurred among individuals, with only 2 % and 1 % attributed to population and within-individual variations, respectively. The high within-population variation suggests extensive genetic diversity due to mutagenesis and selection. Despite this, moderate population divergence was observed, indicating genetic relatedness among groups. Cluster analysis identified two distinct genetic groups, with most clusters containing mutants from both parental lines, reflecting shared ancestry. Several mutants with high genetic diversity were identified as promising candidates for multi-location agronomic trials, particularly for drought resilience and yield stability. These findings highlight the potential of these genotypes for breeding programs aimed at enhancing sorghum resilience and productivity.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100501"},"PeriodicalIF":2.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143704785","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":"Identification and comparative analysis of flowering genes in the Sugar pathway from five Gossypium species","authors":"Lei-Ming Liu ,&nbsp;Chuan-Bo Jiang ,&nbsp;Yi-Lin Yang ,&nbsp;Tian-Run Mei ,&nbsp;Ruo-Fei Liu ,&nbsp;Hai-Liang Liu ,&nbsp;Xian-Zhong Huang","doi":"10.1016/j.plgene.2025.100500","DOIUrl":"10.1016/j.plgene.2025.100500","url":null,"abstract":"<div><div>Flowering is a critical plant growth stage coordinated by internal and external factors. Changes to endogenous sugar levels can promote or inhibit flowering, but research on the regulation of flowering-related genes associated with the sugar pathway in cotton is limited. Here, a genome-wide study identified 165 flowering and sugar pathway-related genes in five cotton species: <em>Gossypium herbaceum</em>, <em>G. arboreum</em>, <em>G. hirsutum</em>, <em>G. barbadense</em>, and <em>G. raimondii</em>. The genes were phylogenetically classified into nine subfamilies and showed a high degree of conservation. Notably, no homologs of <em>INDETERMINATE DOMAIN 8</em> (<em>IDD8</em>), <em>SUCROSE-PROTON SYMPORTER 9</em> (<em>SUC9</em>), or <em>AGP GALACTOSYLTRANSFERASE 2</em> (<em>GALT2</em>) were identified. A synteny analysis provided evidence of varying degrees of gene expansion, and a selection pressure analysis indicated that the genes had undergone purifying selection, with <em>Ka</em>/<em>Ks</em> ratios of &lt;1. The similarity among the genes identified in <em>G. herbaceum</em>, <em>G. arboreum</em>, and <em>G. raimondii</em> was higher than between these species and the allopolyploid cotton species, indicating the earlier divergence of these genes. A network analysis of protein interaction revealed <em>G. hirsutum</em> proteins to be associated primarily with sugar synthesis, transport, and metabolism. Yeast two-hybrid assays demonstrated that GhTPS1–1 and GhHXK1–1 can interact with GhPGI1–1. RNA-sequencing data for 46 genes from eight tissue-types in <em>G. hirsutum</em> revealed that most were highly expressed in stems and flowers. This study provides a comprehensive phylogenetic and network analysis of flowering-related genes in the sugar pathway across five <em>Gossypium</em> species, laying a foundation for future in-depth research on the functional mechanisms of these genes.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100500"},"PeriodicalIF":2.2,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143644510","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 cloning and characterization of CtCuZnSOD gene from Cyamopsis tetragonoloba under drought stress","authors":"Mamtesh Kumari ,&nbsp;Rashmi Gangwar ,&nbsp;Harry Kaur ,&nbsp;Ramasare Prasad","doi":"10.1016/j.plgene.2025.100499","DOIUrl":"10.1016/j.plgene.2025.100499","url":null,"abstract":"<div><div>CuZnSOD plays a crucial role in mitigating drought-induced oxidative stress by serving as the primary defense against reactive oxygen species (ROS). This study identifies and characterizes CuZnSOD in <em>Cyamopsis tetragonoloba</em>, revealing tissue-specific expression of the <em>CtCuZnSOD</em> gene. Its significant upregulation under drought stress, particularly in leaf tissues, underscores its essential role in the plant's adaptive defense mechanism. A key achievement of this research was the successful cloning of the full-length CtCuZnSOD gene, which consists of a 453 bp open reading frame (ORF) encoding a 150 amino acid protein. The expression of the recombinant protein in <em>E. coli</em> led to the purification of a protein with a molecular weight of 15.22 kDa. Remarkably, the enzyme displayed thermostability, retaining over 20 % of its activity at 80 °C, and functioned effectively across a wide pH range, with optimal activity at pH 5.0. Its inhibition by potassium cyanide and hydrogen peroxide confirmed its classification as CuZnSOD. The enzyme demonstrated remarkable stability, retaining activity even in the presence of strong denaturants such as urea, SDS, DTT, and β-mercaptoethanol. This robustness, confirmed by in silico analysis, underscores its significance for diverse applications. This study underscores the pivotal role of CuZnSOD in bolstering plant resilience against environmental stressors, particularly drought conditions. Additionally, the CtCuZnSOD enzyme's stability and resilience under harsh conditions render it a highly valuable candidate for applications in both agricultural biotechnology and enzyme technology, where the presence of stable enzymes is critical for effectiveness.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100499"},"PeriodicalIF":2.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143593136","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":"Differential expression of genes related to tillering in lowland rice varieties cultivated under upland condition","authors":"Muazr Amer Hamzah ,&nbsp;Parameswari Namasivayam ,&nbsp;Nur Fatihah Mohd Yusoff ,&nbsp;Chai-Ling Ho","doi":"10.1016/j.plgene.2025.100498","DOIUrl":"10.1016/j.plgene.2025.100498","url":null,"abstract":"<div><div>Rice tillering is a key determinant of yield and is influenced by genetic, hormonal, and environmental factors. Building upon previous findings that upland conditions reduced tiller production in lowland rice varieties, this study investigated the differential expression of tillering-related genes in two lowland rice varieties, Kadaria and MR269, cultivated under upland and lowland conditions. The transcript abundance of genes involved in tillering, phytohormone biosynthesis, and stress response at the basal part of the rice plant was analyzed using the NanoString nCounter® system. The down-regulation of <em>PIN Protein 9</em> (<em>OsPIN9</em>) and up-regulation of <em>Dwarf 14</em> (<em>D14</em>) in both lowland rice varieties may lead to auxin accumulation and enhanced strigolactone signaling in rice plants cultivated under upland conditions, hence causing them to produce fewer tillers. In addition, the up-regulation of <em>Cytochrome P450 735A4</em> (<em>CYP735A4</em>), a gene involved in cytokinin biosynthesis, was also observed in rice plants cultivated under upland conditions. The differential expression of <em>LAX Panicle 2</em> (<em>LAX2</em>), <em>PIN Protein 1b</em> (<em>OsPIN1b</em>), <em>PIN Protein 2</em> (<em>OsPIN2</em>), and <em>Pyrabactin Resistance 1 Like</em>/<em>Regulatory Components of ABA Receptor 10</em> (<em>OsPYL</em>/<em>RCAR10</em>) was unique to specific rice varieties, suggesting varietal differences in tillering responses to a possible water stress imposed by the upland conditions. These findings contribute to the understanding of potential molecular pathways influencing tiller production in lowland rice varieties cultivated under water-limited upland conditions.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100498"},"PeriodicalIF":2.2,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143577784","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":"Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of U's genomes","authors":"Prabhakaran Soundararajan ,&nbsp;AT Vivek ,&nbsp;Gokul Babu Suresh ,&nbsp;Bhavya Shukla ,&nbsp;Kanchan B.M. Singh ,&nbsp;Shailesh Kumar ,&nbsp;Abinaya Manivannan","doi":"10.1016/j.plgene.2025.100497","DOIUrl":"10.1016/j.plgene.2025.100497","url":null,"abstract":"<div><div>WUSCHEL-related homeobox (WOX) is an evolutionarily important gene family involved in key developmental processes such as embryo patterning, stem cell regulation, apical meristem maintenance, etc. <em>Brassica</em> contains several widely diversified and economically important vegetables grown worldwide. In this study, a pangenome-wide identification and characterization of the WOX gene family among all the species of <em>Brassica</em> Triangle of U's have been performed. WOX gene family was identified from the genomes of 31 <em>Brassica</em> species/morphotypes. About 26–28, 28, and 26–31 copies of <em>WOX</em> genes are present in diploid progenitors such as <em>B. rapa</em> (AA), <em>B. nigra</em>(BB), and <em>B. oleracea</em> (CC), respectively. In allotetraploid species, the number of <em>WOX</em> genes exceeds more than 50 copies. However, their number varies between morphotypes at the pangenome level. Motif and gene structure analysis showed distinct and conserved patterns between homoeologous genes. Non-synonymous (Ka)/Synonymous (Ks) ratio indicated that more number of modern/WUS clade orthologs underwent positive selection followed by those of the intermediate clade. Interacting networks between the <em>WOX</em> and miRNA showed that the CC genome has more complex network pattern compared to the AA genome. Although the <em>WOX</em>-miRNA interactions observed in both AABB and AACC genomes were distinct, they exhibited similarity in overlapping connections. Transcriptome data, analyzed from unfertilized ovule to seven developmental stages of embryos and their seed coat, sourced from public databases across six genomes, illustrated that <em>WOX</em> genes are expressed in a spatio-temporal manner throughout these developmental stages. Furthermore, qPCR analysis of <em>WOX</em> genes at two stages, such as 2–3 days old (leaf and root primordia) and 3 weeks old seedlings (leaf and root) in <em>B. juncea</em> and <em>B. oleracea</em> provides details of stage- and tissues-specific expression patterns between AB and C genomes. Overall, the present study sheds light on evolution and characterization of the WOX gene family in <em>Brassica</em> at the pangenome level for further functional validation.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100497"},"PeriodicalIF":2.2,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143687095","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}