Search Results (2,547)

NAC (NAM, ATAF1/2 and CUC2) transcription factors constitute one of the largest plant-specific transcription factor families and play pivotal roles in plant growth, development, and responses to environmental stresses. Systematic characterization of NAC genes is essential for understanding regulatory networks underlying key agronomic and adaptive traits. As a conservation-priority woody species with distinctive biological and horticultural value, Sinojackia xylocarpa Hu lacks comprehensive knowledge of its NAC repertoire, and elucidating its NAC family will facilitate functional studies related to development and environmental adaptation. Based on whole-genome data of S. xylocarpa, we conducted a systematic survey and characterization of the NAC transcription factor family. In total, 115 SxyNAC genes encoding the conserved NAC domain were identified, and their loci were unevenly distributed across 12 chromosomes. Analyses of gene-duplication modes and collinearity indicated that whole-genome/segmental duplication events were the major driving force for the expansion of this family. Phylogenetic relationships, gene structures, and conserved motifs classified the SxyNAC members into 15 subfamilies, revealing a highly conserved N-terminal NAC domain and a markedly diversified C-terminal regulatory region with pronounced member- and lineage-specific differences. Promoter cis-element prediction showed extensive enrichment of light-responsive, phytohormone-responsive, and stress-related elements, suggesting that SxyNAC genes may participate in coordinated regulation of multiple environmental cues and endogenous hormone pathways. Transcriptome data from six fruit developmental stages, together with qRT-PCR validation of ten representative genes, demonstrated diverse temporal and tissue-specific expression patterns during fruit development and close associations with fruit growth regulation. Overall, our findings establish a framework for exploring the evolutionary trajectories and functional diversification of NAC genes in S. xylocarpa, and they offer a valuable resource for NAC-family research and conservation-focused functional genomics in other rare or threatened plant species. Full article

Background/Objectives: The impact of antimicrobial susceptibility testing methodology on the categorization and positioning of cefiderocol and aztreonam-avibactam against metallo-β-lactamase (MBL)-producing Gram-negative bacilli remains unclear. This study aimed to evaluate the in vitro activity of cefiderocol and aztreonam-avibactam against clinical MBL-producing isolates and to assess the agreement between different cefiderocol susceptibility testing methods. Methods: A total of 299 non-duplicate clinical MBL-producing Gram-negative isolates were collected from clinical samples between 2022 and 2025. Antimicrobial susceptibility testing was performed using broth microdilution, disc diffusion, and gradient strip diffusion according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Carbapenemase genes were identified by immunochromatography and multiplex PCR. Categorical agreement and error rates between cefiderocol testing methods were analyzed. Results:Klebsiella pneumoniae was the predominant species, mainly producing NDM alone or in combination with OXA-48-like carbapenemases. Aztreonam-avibactam demonstrated complete activity against all Enterobacterales isolates (262/262, 100%) and high activity against Pseudomonas spp. (33/37, 89%). Cefiderocol susceptibility among Enterobacterales varied markedly depending on the testing method. Disc diffusion yielded 14% susceptibility (37/262), which increased to 52% (136/262) after ATU resolution, whereas broth microdilution showed 85% susceptibility (224/262). This resulted in low categorical agreement (42%) and a high rate of major errors (58%), with no very major errors detected. Cefiderocol activity did not differ substantially across carbapenemase types and was highest against VIM-producing Pseudomonas spp. Conclusions: Aztreonam-avibactam showed consistent in vitro activity against MBL-producing Enterobacterales, whereas cefiderocol activity was strongly influenced by the susceptibility testing methodology. Disc diffusion substantially underestimated cefiderocol susceptibility compared with broth microdilution. These findings highlight the critical impact of testing methodology on cefiderocol categorization and support the therapeutic role of last-line agents in the management of MBL-producing Gram-negative infections, with direct implications for clinical microbiology laboratories and antimicrobial stewardship programs. Full article

The plant-specific TCP transcription factor family plays crucial roles in morphogenesis and stress adaptation. While characterized in many species, this family remains unstudied in Punica granatum. We performed the first genome-wide analysis of the TCP family in pomegranate, identifying 24 PgTCP genes classified into the PCF, CIN, and CYC/TB1 subclades, supported by conserved gene structures and motifs. Evolutionary analysis indicated segmental duplication and purifying selection shaped this family. Expression profiling revealed distinct spatiotemporal patterns: PgTCP2/9/14/21 were highly expressed in flowers, with PgTCP21 also notably abundant in fruit tissues (seed coats and pericarp), suggesting roles in reproductive development. PgTCP19, an ortholog of the branching suppressor BRC1, showed dominant expression in dormant buds, implicating it in shoot architecture regulation. Furthermore, PgTCP5 and the miR319-targeted PgTCP22 were leaf-predominant, indicating a function in leaf development. Under abiotic stress, PgTCPs displayed dynamic, treatment-specific responses. A subset of genes was rapidly induced by cold, while PgTCP14 and PgTCP23 showed sustained upregulation during drought. Several light-responsive PgTCPs were suppressed under shading. This study provides a foundational resource, functionally classifies the PgTCP family, and identifies key candidates regulating organ development and stress resilience for future functional validation and molecular breeding in pomegranate. This work provides the first comprehensive overview of the TCP gene family in pomegranate and offers candidate genes for future functional studies related to development and stress responses. Full article

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our understanding of ABA-mediated stress adaptation in this economically important crop. Methods: A genome-wide analysis was performed to identify ClPYL genes in watermelon using a hidden Markov model search. Phylogenetic relationships were reconstructed using the maximum likelihood method. Segmental duplication events were analyzed using synteny analysis. Conserved motifs, gene structures, and promoter cis-acting elements were characterized using MEME and PlantCARE. Expression profiles under drought, salt, and cold stresses were examined by quantitative real-time PCR (qRT-PCR) with three biological replicates. Results: In this study, 15 ClPYL genes were identified in watermelon through genome-wide analysis. Phylogenetic reconstruction classified these genes into four subfamilies, with subfamily II being exclusively present in cucurbits—a lineage-specific feature not observed in Arabidopsis. Synteny analysis revealed eight segmental duplication events involving members of subfamilies I, III, and IV, while subfamily II members were not associated with these duplications. Members within the same subfamily share similar exon-intron structures and conserved motifs. Promoter analysis revealed that ClPYL genes are enriched with various cis-acting elements associated with hormone signaling and abiotic stress responses. Expression profiling demonstrated that ClPYL genes exhibit diverse and dynamic expression patterns under drought, high-salinity, and cold stresses. Notably, genes such as ClPYL5 under drought, ClPYL02 under salt, and ClPYL15 under cold stress displayed persistent stress-responsive expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the PYL family in watermelon and provide a set of candidate genes for functional studies aimed at dissecting ABA-mediated stress adaptation. This work establishes a genomic framework for developing stress-resilient watermelon varieties through molecular breeding. Full article

The widespread adoption of hybrid rice has played a pivotal role in ensuring food security in China. However, the heavy reliance on wild-abortive (WA) cytoplasmic male sterility (CMS) systems raises potential biosafety concerns. In this study, we screened a global collection of wild rice (Oryza rufipogon) accessions using orf182-specific molecular markers to characterize the geographic distribution patterns of this gene. Mitochondrial sequencing and assembly of 11 representative wild rice species harboring orf182 revealed 16 novel genes. A total of 469 mitochondrial genes were classified into 23 gene families, with nine families containing single-copy homologous genes, indicating significant gene duplication in mitochondria. We observed a strong positive correlation between mitochondrial genome size and the quantity and size of repetitive sequences. Collinearity analysis revealed extensive mitochondrial variation and large-scale inversions in Guangdong wild rice. Comparative genome analysis uncovered inversions, translocations, and several variations surrounding orf182, with a 71 bp repeat sequence mediating the formation of the orf182-nad6 chimeric gene. Gene copy number analysis (GCNV) revealed variable orf182 gene copy counts (1, 2, and 3) in wild rice species. Additionally, successful transformation of orf182 from various sources into sterile lines was achieved. These findings provide valuable resources for advancing hybrid rice development in China, thus contributing to enhanced food security. Full article

Background: Genome-scale metabolic models (GEMs) are foundational tools for systems biology, enabling quantitative interrogation of human metabolism across physiological and pathological states. However, many legacy reconstructions exhibit heterogeneous identifier usage, incomplete pathway integration, and limited thermodynamic refinement, constraining reproducibility, interoperability, and translational applicability. Methods: We present EHMN 2026, an update of the Edinburgh Human Metabolic Network. The reconstruction was refined through systematic identifier reconciliation using MetaNetX and ChEBI mappings, duplicate reaction consolidation, thermodynamic directionality assessment, and structured pathway annotation via Reactome. The final model was encoded in Systems Biology Markup Language (SBML) Level 3 Version 2 with the Flux Balance Constraints (FBC2) package, ensuring explicit gene–protein–reaction (GPR) representation and compatibility with modern constraint-based modelling toolchains. Results: EHMN 2026 comprises 11 compartments, 14,321 metabolites (species), and 22,642 reactions, supported by 3996 gene products. Of all reactions, 9638 (42.6%) contain GPR associations, linking metabolic transformations to 2887 unique Ensembl gene identifiers (ENSG). Pathway integration yielded 2194 unique Reactome identifiers, providing structured pathway-level organisation of metabolic functions. Thermodynamic refinement reduced infeasible energy-generating cycles and improved reaction directionality coherence while preserving global network connectivity. The reconstruction is fully SBML-compliant and portable across major modelling platforms. Compared with Recon3D and Human1, EHMN 2026 uniquely combines native Reactome reaction-level annotation, systematic MetaNetX identifier harmonisation, documented thermodynamic cycle elimination (37 cycles, 0 remaining), and an 11-compartment architecture supporting organelle-specific modelling—features designed for QSP and multi-layer integration applications. Conclusions: EHMN 2026 delivers a rigorously harmonised, thermodynamically refined, and pathway-annotated human metabolic reconstruction with enhanced annotation depth and standards-based interoperability. By combining genome-scale coverage with structured gene and pathway integration, the model establishes a robust computational backbone for reproducible metabolic analysis and provides a scalable foundation for future multi-layer systems pharmacology and integrative modelling frameworks. Full article

Background: The WRKY transcription factor family represents one of the most crucial transcription factor families in plants, regulating diverse physiological processes. The heartwood of Dalbergia odorifera is a prized material for both high-quality rosewood and traditional medicinal applications, exhibiting exceptional economic value. However, the roles of WRKY transcription factors in the growth and development of D. odorifera, particularly their correlation with heartwood formation, remain unexplored. Methods: WRKY transcription factors were identified through bioinformatics analysis using the published genome data of D. odorifera. Phylogenetic comparative analysis was performed based on the Arabidopsis classification system. Collinearity analysis was conducted to investigate the evolutionary dynamics and expansion mechanisms of the WRKY gene family, and differential expression analysis was performed across tissues. Results: A total of 94 WRKY genes were unevenly distributed across 10 chromosomes and systematically designated as DodWRKY1 to DodWRKY94 according to their chromosomal positions. The WRKY family was classified into three major clades (Groups I, II, and III), with Group II further subdivided into five subgroups (IIa–IIe). Purifying selection served as the primary force shaping the WRKY family, with whole-genome or segmental duplication acting as the dominant expansion mechanism; these duplication events contributed to functional divergence, whereas genes within the same subgroup retained conserved structural features and motif compositions. DodWRKY14 (subgroup IIb) and DodWRKY58/68 (subgroup IIc) were highly expressed in the transition zone, suggesting a potential involvement in heartwood formation. Conclusions: This study provides a comprehensive characterization of the DodWRKY family and identifies candidate genes associated with heartwood formation, thereby establishing a foundation for further investigation into the molecular mechanisms underlying heartwood development. Full article

The yellowfin seabream (Acanthopagrus latus) is an important aquaculture species, yet endocrine gene regulation during practical fasting and feeding schedules remains poorly understood. Here, we identified and characterized two duplicated proglucagon genes (Gcga and Gcgb) and examined tissue distribution of expression and transcriptional responses to feeding-related challenges. Sequence and phylogenetic analyses confirmed that Gcga and Gcgb cluster with teleost proglucagon paralogs and contain conserved peptide domains. Both genes were broadly expressed, with the strongest relative qRT-PCR signal detected in brain and fin, while other tissues (including intestine, gill, stomach, and liver) showed comparatively low but detectable expression. Because the liver is a central metabolic organ and displayed reproducible feeding-dependent regulation, we further quantified hepatic transcription under two paradigms. In a short-term starvation–refeeding trial, hepatic Gcga was significantly suppressed during fasting and rebounded after refeeding, whereas Gcgb showed a distinct, weaker response. In an acute peri-feeding assay, hepatic Gcga and Gcgb displayed rapid but differential regulation around meal time, and Gcgb expression differed between feeding and non-feeding groups. Together, these results support transcriptional divergence between the two proglucagon paralogs in nutritional regulation within a liver-focused metabolic-response model. Our findings provide baseline molecular information for A. latus and offer endocrine insights relevant to evaluating feeding strategies in aquaculture. Full article

NIN-like protein (NLP) transcription factors are key regulators of plant nitrate signaling and stress responses. Although extensively studied in Arabidopsis thaliana and various crops, it has rarely been reported in woody plants, particularly in drought-tolerant tree species. In this study, 10 PeNLP genes were identified in the drought-tolerant tree Populus euphratica Oliv. through comparative genomics. These genes were unevenly distributed across seven chromosomes, and the gene-family expansion was mainly driven by whole-genome duplication (WGD). Analysis of conserved domains showed that PeNLPs contained 4–10 characteristic motifs, and most members possessed the typical RWP-RK and PB1-related domains. Collinearity analysis identified 18 NLP orthologous gene pairs between P. euphratica and its relatives (Populus pruinosa and Salix sinopurpurea), which exceeded the 15 pairs detected between P. euphratica and A. thaliana, indicating that the NLP family is more conserved within the Salicaceae. Phylogenetic analysis divided PeNLPs into three subfamilies, and their promoter regions harbored diverse cis-acting elements associated with hormone signaling, environmental stress, growth, and light response. Transcriptome and qRT-PCR analyses further demonstrated that PeNLPs were generally downregulated under drought stress. Overall, this study systematically characterized the evolution, structure, and drought responsiveness of the PeNLPs, providing a theoretical basis and genetic resources for improving nitrogen use efficiency and drought resistance in trees. Full article

Drought stress is a major abiotic factor limiting maize yield and stability. Although Jumonji C (JMJ) histone demethylases are known to regulate plant growth, development, and stress responses, their systematic characterization in maize has remained limited. Here, 27 ZmJMJ genes were identified in the maize genome through BLAST and conserved-domain analyses and classified into five subfamilies: JMJD6, KDM3/JHDM2, KDM4/JHDM3, KDM5/JARID1, and JmjC domain-only. Members within the same subfamily showed similar physicochemical properties, domain composition, and motif distribution, whereas clear divergence was observed among subfamilies. Chromosomal mapping revealed that ZmJMJ genes were unevenly distributed across nine chromosomes, with two interchromosomal homologous gene pairs, suggesting roles for segmental and/or whole-genome duplication in family expansion. Promoter analysis indicated widespread enrichment of elements related to light responsiveness, growth and development, and hormone and stress responses. Expression profiling showed that most ZmJMJ genes were highly expressed in leaves, while several displayed tissue specificity. Under drought stress, ZmJMJ17a, ZmJMJ17b, ZmJMJ28, and ZmJMJ32 were significantly induced, highlighting them as promising candidates for functional studies and molecular breeding for drought tolerance in maize. This study provides a foundation for elucidating the evolution and functions of the ZmJMJ family and identifies candidate genes for drought-related functional validation and molecular breeding. Full article

Salt stress inhibits plant growth, requiring salt-tolerant genes for the development of resilient plants. A key tolerance mechanism is potassium/sodium homeostasis, governed by Shaker K⁺ channels. Given that Shaker K⁺ channels from salt-sensitive species have been extensively studied while their counterparts in salt-tolerant plants remain largely unexplored, this study investigates the evolution and function of these channels in salt-tolerant bermudagrass to address this knowledge gap. Genomic analysis identified 25 Shaker K⁺ channel genes, an expanded family relative to other species. Phylogenetics placed them into five groups (I–V), with groups I, II, III, and V expanded via segmental duplication. Salt stress response screening revealed that only CdKAT1.1 was rapidly upregulated. Functional assays in yeast demonstrated that both CdKAT1.1 and its closest homolog CdKAT1.2 improve potassium uptake and salt tolerance, but the enhancement from CdKAT1.1 was significantly greater. This work elucidates the expansion and functional divergence of Shaker K⁺ channels in bermudagrass. CdKAT1.1 emerges as a superior regulator of potassium efficiency and salt tolerance, making it a prime candidate for molecular breeding to improve plant resilience in saline-alkaline soils. Full article

Sigma factors (SIGs) are nuclear-encoded regulators of chloroplast gene transcription. We conducted a genome-wide analysis in Brassica napus, identifying 23 SIG genes that were phylogenetically classified into six distinct subfamilies. Characterization of gene structure, conserved motifs, and chromosomal locations indicated family expansion primarily through segmental duplication under purifying selection. Promoter analysis identified cold-responsive elements enriched in BnSIG5A. Expression profiling showed that BnSIG5 subfamily members, particularly BnSIG5A, are strongly induced by cold stress. Analysis of Arabidopsis SIG5 mutants confirmed previously reported roles of AtSIG5 in cold tolerance. Heterologous expression in yeast, and the strong cold induction of BnSIG5A together with its chloroplast localization, suggest that BnSIG5A may play a conserved role, providing a foundation for future functional studies in B. napus. This work establishes a genomic framework for the SIG family in rapeseed and identifies BnSIG5A as a high-priority candidate for further investigation. Subcellular localization confirmed chloroplast targeting of BnSIG5A. Heterologous expression in yeast and analysis of Arabidopsis SIG5 mutants suggest conserved functions in cold tolerance, providing a foundation for future functional studies in B. napus. This work establishes a genomic framework for understanding SIG-mediated stress responses in rapeseed and identifies BnSIG5A as a promising candidate for further investigation. Full article

WRKY is a crucial transcription factor involved in plant growth, development, and responses to abiotic stress. In the present study, a total of 182 AaWRKY transcription factor members were identified across the Artemisia argyi genome and found to be distributed across 17 chromosomes. Evolutionary analysis revealed that segmental duplication served as the primary driver for family expansion, with the evolutionary trajectory shaped by strong purifying selection (Ka/Ks < 1.0). Phylogenetic classification categorized these members into seven highly conserved subgroups, while physicochemical analysis indicated that most AaWRKYs are unstable, hydrophilic proteins, consistent with the rapid turnover required for transcriptional switches. Transcriptomic profiling unveiled significant tissue-specific expression patterns, with over 50% of the members predominantly enriched in roots and specific genes, such as AaWRKY11, implicated in the regulation of leaf senescence. Protein–protein interaction (PPI) network analysis identified AaWRKY110 as a central regulatory hub linking the MAPK signaling pathway with the isoflavonoid biosynthetic machinery. Furthermore, comparative transcriptomic analysis between aphid-resistant (Ai20K) and susceptible (Ai72G) cultivars demonstrated that resistance is conferred by a priming mechanism involving high basal expression of key candidates, including AaWRKY82, 108, 128, and 71. In contrast, the susceptible genotype exhibited a delayed and ineffective hypersensitive-like response. Collectively, these findings elucidate the evolutionary dynamics of the AaWRKY family and provide critical genetic targets for the concurrent improvement of medicinal metabolite accumulation and biotic stress resilience in Artemisia argyi via molecular breeding. Full article

Cinnamoyl-CoA reductase (CCR) is the first rate-limiting enzyme in the lignin biosynthetic pathway in higher plants. It catalyzes the conversion of cinnamoyl-CoA into the corresponding cinnamaldehydes. Tea plant (Camellia sinensis) is a perennial woody species. Systematic identification and functional characterization of the CCR gene family in tea plants is still limited. In this study, 202 CCR genes were identified from six tea plant cultivars, and a significant expansion of the CCR gene family was observed during the domestication process from wild to cultivated tea plants. A total of 50 CsCCR genes were identified in the tea cultivar ‘Shuchazao’, and they were distributed across 13 chromosomes. Multiple sequence alignment revealed that the key catalytic motifs NWYCYGK and H-X-X-K were fully conserved in CsCCR1, CsCCR2, and CsCCR3. Phylogenetic analysis showed that CsCCR1/2/3 clustered with AtCCR1/2 and PtrCCR2, which were known to be involved in lignin biosynthesis. Transcriptome data analysis showed that CsCCR3 exhibited significantly higher transcript abundance in stems than in young, mature, and old leaves. CsCCRL9, CsCCRL33, CsCCRL34, and CsCCRL36 also showed relatively high expression levels in stem. RT-qPCR further confirmed the high expression of CsCCR3 and CsCCRL33 in stems. Furthermore, comparison of CCR members derived from tandem and segmental duplication in the tea cultivar ‘Shuchazao’ showed clear differences in Ka/Ks ratios, expression correlations, and the distribution of stress-responsive cis-acting elements. This study provides new insights into the expansion and duplication-related functional divergence of the CCR gene family in tea plant and identifies key candidate genes potentially involved in lignin biosynthesis and stress responses. Full article

Expansins are essential regulators of plant cell wall loosening, yet their roles in eggplant (Solanum melongena L.) remain poorly understood. This study performed a genome-wide analysis and identified 26 SmEXP genes, categorized into five evolutionary groups. All SmEXP proteins harbor characteristic DPBB_1 and Expansin_C domains. These genes are unevenly distributed across 10 chromosomes out of the 12 eggplant chromosomes, with Chromosome 8 identified as a major distribution hotspot. Synteny and selection pressure analyses suggest that segmental duplications and strong purifying selection have driven the family’s evolution. Promoter analysis revealed various cis-acting elements associated with light, phytohormones, and abiotic stress. Transcriptomic profiling showed that 14 SmEXP genes were significantly upregulated during the rapid fruit expansion phase (14 DAP), indicating their crucial role in fruit morphogenesis. Furthermore, some specific members (SmEXP1, 4, 10, and 13) exhibited distinct upregulation under heat stress (38 °C and 43 °C), suggesting involvement in thermotolerance. These findings identify key expansin genes controlling eggplant development and stress response, providing targets for genetic improvement. Full article