Search Results (57)

The yellow flower lotus (Nelumbo lutea) is the sister species of the sacred lotus (N. nucifera). The evolution of gene expression patterns across multiple tissues during the species divergence of these two lotuses remains unexplored. The WUSCHEL-related homeobox (WOX) family, a plant-specific transcription factor family, plays a crucial role in tissue development and stress responses. In this study, utilizing a chromosome-level reference genome and a transcriptome database covering multiple tissues, we identified and categorized 11 NlWOX genes into three subfamilies. We identified seven syntenic gene pairs between NnWOXs and NlWOXs that originated from whole-genome duplications. Through conserved motif analysis, we found subfamily-specific motifs in the protein sequences of NnWOXs and NlWOXs. Variations in the three-dimensional conformations of homologous WOX genes indicate function divergences between the two lotus species. The gene expression matrix of NlWOX across tissues reveals expression divergences within N. lutea and between the two lotus species. By employing a weight gene co-expression network analysis pipeline, we developed eight NlWOX co-expression networks that differed from the co-expression networks of their syntenic genes. Overall, our findings suggest that genomic variations in the WOX orthologs contribute to the distinct expression patterns and regulatory networks observed during the evolution of these two lotuses. Full article

Plant-specific WUSCHEL (WUS)-related homeobox (WOX) family of transcription factors are involved in apical meristem maintenance, embryogenesis, lateral organ development, and hormone signaling. Among the members of this family, WOX1 is known to play essential roles in many species. However, the function of the peony ‘Feng Dan’ (Paeonia ostii L.) WOX1 (PoWOX1) remains unknown. The initial bioinformatic analysis revealed that PoWOX1 belongs to the modern clade of the WOX gene family and has a highly conserved homeodomain (HD), the WUS motif, the STF-box, and the MAEWEST/WOX4-box. Subsequent heterologous overexpression in Arabidopsis thaliana revealed that PoWOX1 promotes root growth, early shoot initiation, and flowering. The root vascular tissues, especially the arrangement and size of xylem cells, were different between the PoWOX1-overexpressing transgenics and the wild-type plants, and the pericycle cells adjacent to the xylem divided more easily in the transgenics than in the wild type. Furthermore, under in vitro conditions, the transgenic leaf explants exhibited more callus induction and differentiation than the wild-type leaf explants. Thus, the study’s findings provide novel insights into the role of PoWOX1 in promoting root development and callus tissue induction and differentiation, serving as a reference for developing an efficient regeneration system for the peony. Full article

(1) Background: WOX (WUSCHEL-related homologous box) is a plant-specific transcription factor involved in plant development and stress response. It has been reported to be involved in processes such as growth and development, stem cell division and differentiation, and organ development; (2) Methods: In this study, bioinformatics was used to identify and analyze the WOX gene family of Korean pine. The gene characteristics were identified and analyzed through yeast transcriptional activation assays as well as subcellular localization experiments; (3) Results: A total of 21 members of the WOX gene family of Korean pine were identified in this study. The phylogenetic tree divides the PkWOX genes into three sub-branches. 21 PkWOX genes are unevenly distributed on 7 of the 12 chromosomes. PkWOX16 was expressed in all tissues. PkWOX2, 3 had higher expression in the embryonic callus, non-embryonic callus, somatic embryo, and zygotic embryo. PkWOX2, 3 and 16 were located in the nucleus and in the cell membrane. The PkWOX2 and 3 proteins exhibited transcriptional self-activation activity, while PkWOX16 did not; (4) Conclusions: In this study, the members of the WOX transcription factor family in Korean pine were identified and systematically analyzed, laying a foundation for their subsequent functional research. Full article

The WOX (WUSCHEL-related homeobox) gene family plays pivotal roles in plant growth, development, and responses to biotic/abiotic stresses. Flax (Linum usitatissimum L.), a globally important oilseed and fiber crop, lacks a comprehensive characterization of its WOX family. Here, 18 LuWOX genes were systematically identified in the flax genome through bioinformatics analyses. Phylogenetic classification grouped these genes into three clades: Ancient, Intermediate, and WUS Clades, with members within the same clade exhibiting conserved exon–intron structures and motif compositions. Promoter analysis revealed abundant cis-acting elements associated with hormone responses (MeJA, abscisic acid) and abiotic stress adaptation (anaerobic induction, drought, low temperature). Segmental duplication events (nine gene pairs) contributed significantly to LuWOX family expansion. Protein–protein interaction networks implicated several LuWOX proteins in stress-responsive pathways. Expression profiling demonstrated that most LuWOX genes were highly expressed in 5-day-post-anthesis (DPA) flowers and embryonic tissues. qRT-PCR validation further uncovered distinct expression patterns of LuWOX genes under cold, drought, and salt stresses. This study established a foundational framework for leveraging LuWOX genes to enhance stress tolerance in flax breeding and functional genomics. Full article

Chimonanthus praecox, also known as wintersweet, is a traditional ornamental plant in China. It blooms during the cold winter months and emits a long-lasting fragrance. The WUSCHEL-related homeobox (WOX) transcription factor family is a plant-specific family of homeodomain (HD) transcription factors that plays diverse roles in plant development. We identified 13 WOX family genes (CpWOX1–CpWOX12 and CpWUS) and systematically analysed their physicochemical properties, evolutionary relationships, conserved domains, and expression regulation characteristics. The subcellular localization prediction indicates that all CpWOX proteins are localized in the nucleus and contain a conserved homeobox domain, with the WUS clade specifically containing a WUS-box motif. Phylogenetic analysis revealed that these genes are divided into three evolutionary branches: the WUS, ancient, and intermediate clades. Promoter analysis suggests that CpWOX genes may be involved in hormone responses, abiotic stress, developmental regulation, and encodes a nuclear-localised protein with self-activating activity. It is highly expressed in the stamen and root and is induced by low and high temperatures, salt stress, and methyl jasmonate. This study revealed the evolutionary characteristics of the WOX family genes in wintersweet and the function of CpWUS in regulating flowering time and root development, providing a theoretical basis for understanding the developmental regulatory mechanisms in wintersweet. Full article

The WUSCHEL-related homeobox (WOX) belongs to a plant-specific transcription factor gene family that plays crucial roles in plant growth and development. Barley ranks as the fourth global cereal crop and is recognized as a model crop for the study of cereal genetics. However, genome-wide characterization, functional validation, and stress-related studies of the WOX gene family in barley remain limited, hindering efforts to leverage their potential for improving salt tolerance and regeneration efficiency in breeding programs. In this study, we identified 12 HvWOX genes assigned from chromosome 1 to chromosome 5. Phylogenetic analysis revealed that these HvWOX genes can be classified into three clades (WUS, ancient, and intermediate). Gene structure analysis revealed that the exon numbers of HvWOX genes varied in the WUS and intermediate clades but were highly conserved in the ancient clade. Tissue-specific analysis revealed that the most common HvWOX genes were highly expressed in reproductive tissues such as anthers or ovaries. Cis-element analysis suggested that there were multiple stress- and hormone-responsive elements in the HvWOX gene promoters. In addition, overexpression of HvWOX8 in Arabidopsis significantly enhanced root elongation under salt stress (50–100 mM NaCl), suggesting its direct role in salt tolerance. Transcriptomic analysis further revealed that HvWOX8 modulates hormone signaling and electron transfer pathways during ATP synthesis under stress conditions. In conclusion, our results provided a comprehensive understanding of the gene characteristics, expression patterns, and potential roles of barley WOX genes. Full article

WUSCHEL-related homeobox (WOX) genes play significant roles in plant development and stress responses. Difficulties in somatic embryogenesis are a significant constraint on the uniform seedling production and genetic modification of Coffea arabica, hindering efforts to improve coffee production in Yunnan, China. This study comprehensively analyzed WOX genes in three Coffea species. A total of 23 CaWOXs, 12 CcWOXs, and 10 CeWOXs were identified. Transcriptomic profile analysis indicated that about half of the CaWOX genes were actively expressed during somatic embryogenesis. The most represented CaWOXs were CaWOX2a, CaWOX2b, CaWOX8a, and CaWOX8b, which are suggested to promote the induction and development of the embryogenic callus, whereas CaWOX13a and CaWOX13b are suggested to negatively impact these processes. Co-expression analysis revealed that somatic embryogenesis-related CaWOXs were co-expressed with genes involved in embryo development, post-embryonic development, DNA repair, DNA metabolism, phenylpropanoid metabolism, secondary metabolite biosynthesis, and several epigenetic pathways. In addition, qRT-PCR showed that four WOX genes responded to cold stress. Overall, this study offers valuable insights into the functions of CaWOX genes during somatic embryogenesis and under cold stress. The results suggest that certain WOX genes play distinct regulatory roles during somatic embryogenesis, meriting further functional investigation. Moreover, the cold-responsive genes identified here are promising candidates for further molecular analysis to assess their potential to enhance cold tolerance. Full article

The adaptation of plants to land requires sophisticated biological processes and signaling. Transcription factors (TFs) regulate several cellular and metabolic activities, as well as signaling pathways in plants during stress and growth and development. The WUSCHEL-RELATED HOMEOBOX (WOX) genes are TFs that are part of the homeodomain (HD) family, which is important for the maintenance of apical meristem, stem cell niche, and other cellular processes. The WOX gene family is divided into three clades: ancient, intermediate, and modern (WUS) based on historical evolution linkage. The number of WOX genes in the plant body increases as plants grow more complex and varies in different species. Numerous research studies have discovered that the WOX gene family play a role in the whole plant’s growth and development, such as in the stem, embryo, root, flower, and leaf. This review comprehensively analyzes roles of the WOX gene family across various plant species, highlighting the evolutionary significance and potential biotechnological applications in stress resistance and crop improvement. Full article

Plant height and leaf morphology are considered complex agronomy traits; both are significantly related to nutrient utilization, lodging resistance, and photosynthetic efficiency, which ultimately affect biomass and yield. However, the molecular mechanism of leaf morphogenesis is still unclear. WOX is a group of plant-specific transcription factor families that regulate growth and development, cell division, and differentiation in plants. In the present study, we identified and characterized the m-876 mutant in barley (Hordeum vulgare L.), which exhibited an extreme reduction in leaf width and plant height. Using a map-based cloning strategy, the m-876 mutant was narrowed down to an 11.4 Mb genomic interval on the long arm of chromosome 5. By analyzing the gene annotation information and nucleotide sequences, we found that HvWOX3A (HORVU.MOREX.r3.5HG0467090) had a G-to-A substitution at the second exon in the m-876 mutant, resulting in a change of the coding amino acid from Tryptophan to a premature stop codon at the 200th amino acid position. Remarkably, the mutation of the HvWOX3A gene leads to changes in gene expression in the m-876 mutant. Collectively, our results indicate that the loss function of the HORVU.MOREX.r3.5HG0467090 gene might be responsible for the phenotypic variation in barley mutants. Full article

Salt stress represses the growth and development of plants that mainly depend on the continual propagation and differentiation of stem cells. WUSCHEL (WUS)/WUSCHEL-RELATED HOMEOBOX (WOX) family proteins determine stem cell fate in plants under ever-changing environments. It is not yet known how plant stem cell homeostasis is regulated under salt stress. Methionine synthase catalyzes the formation of methionine by methylating homocysteine in the one-carbon metabolism pathway. In this work, we investigated the role of Arabidopsis METHIONINE SYNTHASE 2 (AtMS2) in stem cell homeostasis under salt stress. The results showed that AtMS2 represses the stem cell maintenance of Arabidopsis in response to salt stress. Under normal growth conditions, AtMS2 is mainly localized in the cytoplasm. However, under salt stress, it exhibits significant accumulation in the nucleus. AtMS2 interacts with the WUS/WOX protein, and, together, they repress WUS/WOX expression by binding to its promoter. The mutation in AtMS2 resulted in enhanced salt tolerance. Therefore, AtMS2 might act as a key negative regulator to repress the stem cell maintenance and growth of Arabidopsis under salt stress. Full article

Tree peony (Paeonia suffruticosa Andr.) is a woody plant with high ornamental, medicinal, and oil values. However, its low rooting rate and poor rooting quality are bottleneck issues in the micropropagation of P. ostii. The WUSCHEL-related homeobox (WOX) family plays a crucial role in root development. In this study, based on the screening of the genome and root transcriptome database, we identified ten WOX members in P. ostii. Phylogenetic analysis revealed that the ten PoWOX proteins clustered into three major clades, the WUS, intermediate, and ancient clade, respectively. The conserved motifs and tertiary structures of PoWOX proteins located in the same clade exhibited higher similarity. The analysis of cis-regulatory elements in the promoter indicated that PoWOX genes are involved in plant growth and development, phytohormones, and stress responses. The expression analysis revealed that PoWOX genes are expressed in distinct tissues. PoWOX4, PoWOX5, PoWOX11, and PoWOX13b are preferentially expressed in roots at the early stage of root primordium formation, suggesting their role in the initiation and development of roots. These results will provide a comprehensive reference for the evolution and potential function of the WOX family and offer guidance for further study on the root development of tree peony. Full article

Numerous members of the WOX gene family play pivotal roles during the processes of growth and development in many plants, as has been demonstrated. Cymbidium goeringii, Cymbidium ensifolium, and Cymbidium sinense are ornamental plants with a fascinating floral morphology that are economically important in China. However, there is limited knowledge about the members of the WOX gene family and their functions in these three Cymbidium species. Hence, the WOX genes in three Cymbidium species were identified on the ground of the genomes data of C. goeringii, C. ensifolium, and C. sinense in this study. These identified WOX genes were further studied for their physicochemical properties, evolutionary relationship, gene structure, protein structure, and cis-acting elements of promoters, as well as the expression pattern of the WOX genes in different tissues of C. goeringii. The findings revealed that eight WOX genes in C. goeringii, twelve WOX genes in C. ensifolium, and nine WOX genes were identified. These WOX genes were further subdivided into WUS, ancient, and intermediate clades. The length of the coding region ranged from 149 to 335 aa, and it was predicted that all WOX genes would be located on the cell nucleus. The promoter cis-acting elements primarily comprised stress response, phytohormone response, plant growth and development, and transcription factor elements. Furthermore, both the transcriptomic data and RT-qPCR analysis showed that most WOX genes may be involved in multiple developmental stages of C. goeringii. To sum up, these results may serve as a theoretical foundation for further study of the function analysis of WOX genes in orchids. Full article

The WUSCHEL-related homeobox (WOX) transcription factor plays a vital role in stem cell maintenance and organ morphogenesis, which are essential processes for plant growth and development. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are valued for their ornamental and medicinal properties. However, the specific functions of the WOX gene family in Dendrobium species are not well understood. In our study, a total of 30 WOX genes were present in the genomes of the three Dendrobium species (nine DchWOXs, 11 DhuWOXs, and ten DnoWOXs). These 30 WOXs were clustered into ancient clades, intermediate clades, and WUS/modern clades. All 30 WOXs contained a conserved homeodomain, and the conserved motifs and gene structures were similar among WOXs belonging to the same branch. D. chrysotoxum and D. huoshanense had one pair of fragment duplication genes and one pair of tandem duplication genes, respectively; D. nobile had two pairs of fragment duplication genes. The cis-acting regulatory elements (CREs) in the WOX promoter region were mainly enriched in the light response, stress response, and plant growth and development regulation. The expression pattern and RT-qPCR analysis revealed that the WOXs were involved in regulating the floral organ development of D. chrysotoxum. Among them, the high expression of DchWOX3 suggests that it might be involved in controlling lip development, whereas DchWOX5 might be involved in controlling ovary development. In conclusion, this work lays the groundwork for an in-depth investigation into the functions of WOX genes and their regulatory role in Dendrobium species’ floral organ development. Full article

WUSCHEL-related homeobox (WOX) transcription factors are unique to plants and play pivotal roles in plant development and stress responses. In this investigation, we acquired protein sequences of foxtail millet WOX gene family members through homologous sequence alignment and a hidden Markov model (HMM) search. Utilizing conserved domain prediction, we identified 13 foxtail millet WOX genes, which were classified into ancient, intermediate, and modern clades. Multiple sequence alignment results revealed that all WOX proteins possess a homeodomain (HD). The SiWOX genes, clustered together in the phylogenetic tree, exhibited analogous protein spatial structures, gene structures, and conserved motifs. The foxtail millet WOX genes are distributed across 7 chromosomes, featuring 3 pairs of tandem repeats: SiWOX1 and SiWOX13, SiWOX4 and SiWOX5, and SiWOX11 and SiWOX12. Collinearity analysis demonstrated that WOX genes in foxtail millet exhibit the highest collinearity with green foxtail, followed by maize. The SiWOX genes primarily harbor two categories of cis-acting regulatory elements: Stress response and plant hormone response. Notably, prominent hormones triggering responses include methyl jasmonate, abscisic acid, gibberellin, auxin, and salicylic acid. Analysis of SiWOX expression patterns and hormone responses unveiled potential functional diversity among different SiWOX genes in foxtail millet. These findings lay a solid foundation for further elucidating the functions and evolution of SiWOX genes. Full article

The WUSCHEL-related homeobox (WOX) gene family has a critical effect on plant development and abiotic stress. However, there have been no genome-wide studies on WOX genes within sweet cherry (Prunus avium L.). In the present work, eight PavWOX genes were discovered within sweet cherry at the genome-wide level, and they were mapped to six chromosomes. Based on phylogenetic relationships, these genes were classified into three groups, with genes in one group having similar gene structures and conserved motifs. Meanwhile, the PavWOX genes possessed cis-acting elements and functions associated with hormone responses, stress responses, and development. As revealed by expression patterns, certain PavWOX genes are specifically expressed within tissues, suggesting that they may have unique functions. Additionally, the gene family expression patterns under drought stress were analyzed. PavWOX4, PavWOX5, PavWOX13A, and PavWOX13B had increased expressions upon drought stress. In addition, the transcription factor of PavWOX4 and PavWOX13A was localized in the nucleus, confirming the estimated results. Our findings lay the foundation for determining the expression patterns and functions of the PavWOX gene family within sweet cherry and shed more light on the underlying regulatory mechanisms. Full article