Search Results (1,583)

Background/Objectives: Serratia liquefaciens is a bacterium commonly found in the rhizosphere and may possess PGPR capabilities. The present study aimed to elucidate the genomic, phylogenomic, and metabolic characteristics of S. liquefaciens strain UNJFSC002 to determine whether it is an effective PGPR. Methods: The genome of strain UNJFSC002 was obtained from NCBI and annotated using Prokka. Functional genome prediction, phylogenetic reconstruction, and comparative genomics were performed using bioinformatics tools. A GEM model was reconstructed to simulate metabolic fluxes associated with nitrogen fixation, phosphate solubilization, and phytohormone biosynthesis. Computational phenotyping and in silico functional validation were also performed. Results: The draft genome (5.19 Mb, GC 55.33%) contained 4792 protein-coding genes, 4 rRNAs, and 81 tRNAs, with 100% completeness. ANI and core genome phylogeny confirmed its taxonomic position within S. liquefaciens, with an identity higher than 98.8%. Pangenome analysis of 25 Serratia genomes revealed an open and highly dynamic pangenome (30,515 orthologous groups), indicating extensive genetic plasticity. Functional annotation identified key genes associated with nitrogen and phosphate acquisition, as well as the biosynthesis of IAA and GABA, findings that were supported by GEM simulations, reinforcing its potential as a biofertilizer. Conclusions: The genomic approach confirmed that strain UNJFSC002 harbors multiple active genes and metabolic pathways associated with plant growth promotion and environmental resilience. Full article

Background: Cultivated strawberry (Fragaria × ananassa) is one of the most valuable horticultural crops worldwide. Nevertheless, its productivity is increasingly constrained by high susceptibility to adverse environmental conditions, which are intensified by climate change. Drought represents a major limitation, often accompanied by water deficiency and elevated soil salinity. Plants counteract such abiotic stresses through complex molecular defense mechanisms involving transcription factors that regulate stress-responsive gene expression. Methods: In this study, we conducted a systematic bioinformatic analysis of the Tubby-like protein (TLP) transcription factor family in Fragaria × ananassa. RT-qPCR was used to analyze the expression patterns of FaTLP genes under different conditions to elucidate their potential roles in stress adaptation. Results: Eight FaTLP genes were identified in each of the four subgenomes, most of which retained the characteristic TUBBY and F-box domains. Gene expression profiling revealed that several FaTLP genes were differentially expressed in leaves under drought and salt stress, with FaTLP2 and FaTLP7 exhibiting strong induction. In addition, the expression of FaTLP2 and FaTLP7 under various oxidative and signaling-related treatments, as well as in different tissues of strawberry plants were analyzed. Promoter analysis identified multiple cis-regulatory elements associated with phytohormone signaling and abiotic stress responses, such as ABRE, MYB, and MYC motifs. Phylogenetic analysis showed that FaTLP2 and FaTLP7 share high sequence similarity with orthologous TLPs from other plant species known for enhanced stress tolerance, suggesting that these proteins may play conserved roles in the molecular mechanisms underlying drought and salinity resilience. Conclusions: This study provides valuable insights into the potential roles of FaTLPs in regulating environmental signal transduction and transcriptional control, contributing to abiotic stress tolerance in Fragaria × ananassa. Full article

The Crabtree and Warburg effects both involve elevated glycolytic flux and fermentation under aerobic conditions, yet their regulatory bases differ fundamentally. In the Crabtree effect, high-glucose concentrations suppress mitochondrial respiration, redirecting carbon flux toward fermentation. In contrast, the Warburg effect, characteristic of many cancer cells, features increased mitochondrial respiration to support biosynthetic and anaplerotic demands. We recently advanced an extended metabolic definition of the Warburg effect that incorporates enhanced amino acid catabolism and elevated lipid biosynthesis, reflecting broad mitochondrial engagement beyond oxidative phosphorylation. Revisiting the metabolic behavior of the snf1∆ strain of Saccharomyces cerevisiae, which lacks the Crabtree effect, reveals a phenotype analogous to this expanded Warburg effect framework. Under glucose-rich conditions that typically elicit the Crabtree effect, snf1∆ cells preserve high mitochondrial respiration while maintaining robust glycolysis and fermentation. These cells also display enhanced amino acid degradation that feeds the Krebs cycle and increased lipid synthesis, recapitulating hallmark features of the Warburg state. Notably, mutation of the AMPK gene, the human ortholog of SNF1, similarly drives Warburg-like reprogramming in mammalian models. Together, these data establish snf1∆ as a valuable eukaryotic model for dissecting the regulatory determinants of the Warburg effect. Full article

Efficient in vitro regeneration remains a major constraint in the genetic transformation, genome editing, and molecular breeding of wheat (Triticum aestivum L.), largely due to strong genotype-dependent recalcitrance and limited activation of developmental programs required for somatic embryogenesis. Plant regeneration relies on extensive transcriptional reprogramming and epigenetic remodeling orchestrated by morphogenic regulators that modulate meristem identity, as well as cellular pluri- and totipotency. In this review, we synthesize current molecular knowledge on key transcription factors (BBM, WUS/WUS2, GRF-GIF, WOX, LAX1, SERK, WIND1/ERF115) and signaling peptides (CLE/CLV-WUS module, phytosulfokine/PSK) that regulate embryogenic competence in monocot cereals, with emphasis on their orthologs and functional relevance in wheat. We highlight how controlled expression of these morphogenic genes, promoter engineering, and transient or excisable induction systems can significantly enhance regeneration capacity, reduce chimerism in CRISPR-Cas-edited plants, and facilitate genotype-independent transformation. We also discuss epigenetic and metabolic constraints underlying wheat recalcitrance and their potential modulation to improve culture responsiveness. By integrating evidence from wheat, rice, maize, and barley, we outline conserved gene-regulatory networks that reinitiate totipotency and propose strategies to accelerate doubled haploid production and speed-breeding pipelines. Collectively, morphogenic factors emerge as central molecular tools for overcoming regeneration bottlenecks and enabling next-generation wheat improvement. The objective of this review is to synthesize and critically evaluate current molecular knowledge on morphogenic regulators controlling in vitro regeneration in wheat (Triticum aestivum L.), with particular emphasis on their roles in genetic transformation and genome editing. Full article

Comparative transcriptomics offers a powerful approach to elucidate host–virus interactions across related pathogens, yet systematic evaluations across species-matched cellular systems remain limited. We performed a cross-species RNA sequencing analysis of respective species’ cells infected with three alphaherpesviruses—herpes simplex virus 1 (HSV-1), bovine alphaherpesvirus 1 (BHV-1), and equid alphaherpesvirus 1 (EHV-1)—to dissect conserved and virus-specific transcriptional responses. We show that certain orthologous genes and orthologous pathways are differentially regulated upon infection among the three species like pathways related to translation rRNA processing and TNF-alpha signalling. We find that the earliest sampled timepoint of infection, 2 h post infection (hpi), shows the most commonly enriched pathways among the three species compared to later timepoints. At 6 h and 9 h post infection, BHV-1- and EHV-1 infections have more in common with each other in terms of enriched pathways than with HSV-1 infections. Moreover, we provide a comprehensive analysis of temporal viral gene expression for all three herpesviruses. Together, these findings provide a comparative framework for understanding alphaherpevirus–host interactions and reveal both conserved core responses and species-specific transcriptional signatures. This work establishes a foundation for identifying broadly acting antiviral targets as well as virus-specific vulnerabilities that may inform host-directed therapies and cross-species disease management. Full article

Background/Objectives: Coupled with the already-problematic background rates of traditional cigarette consumption during pregnancy, the surging epidemic of electronic cigarette usage among pregnant women redoubles the importance of understanding the impacts of nicotine exposure during critical periods of development. To date, a burgeoning body of human epidemiological and animal model research indicates that not only the children but also the grandchildren of maternal smokers are at higher risk for neurodevelopmental disorders such as ADHD, autism, and schizophrenia and are predisposed to neurodevelopmental abnormalities which transcend these diagnoses. However, the roles of discrete cellular sub-populations in these and other intergenerational consequences of smoking during pregnancy remain indeterminate. Methods: Toward the resolution of this void in the literature, the present study characterized alterations in the gene expression profiles of dopamine receptor D1-expressing striatal cells from the first- and second-generation male progeny of female mice that were continuously exposed to nicotine beginning prior to conception, continuing throughout pregnancy, and concluding upon weaning of offspring. Results: Dopamine receptor D1-expressing striatal cells from our mouse models of the children and grandchildren of maternal smokers exhibit differential expression patterns for a multitude of genes that are (1) individually associated with neurodevelopmental disorders, (2) collectively overrepresented in gene set annotations related to brain, behavioral, neurobiological, and epigenomic phenotypes shared among neurodevelopmental disorders, and (3) orthologous to human genes that exhibit differential DNA methylation signatures in the newborns of maternal smokers. Conclusions: Together with our and others’ previous findings, the results of this study support the emerging theory that, by inducing extensive alterations in gene expression that in turn elicit cascading neurobiological changes which ultimately confer widespread neurobehavioral abnormalities, nicotine-induced epigenomic dysregulation may be a primary driver of neurodevelopmental deficits and disorders in the children and grandchildren of maternal smokers. Full article

Background: In plants, members of the MADS-box gene family encode transcription factors that regulate a wide range of developmental processes, including cell differentiation, organ identity, floral induction, and responses to environmental stimuli. Moreover, MADS-box genes play central roles in the well-known ABCDE model of floral development. Teak (Tectona grandis), a woody species belonging to the Lamiaceae family, is recognized for its medicinal and agricultural significance. The recent availability of a chromosome-level genome assembly for T. grandis has enabled the genome-wide identification of 87 MADS-box genes, which are distributed across 18 pseudo-chromosomes. Methods: The amino acid sequences of these genes were compared with orthologous proteins from Arabidopsis thaliana, Sesamum indicum, and Amborella trichopoda to infer the phylogenetic relationships. The structures of key floral quartets in the MADS-box proteins were predicted, and the stability of these predicted tetramers were analyzed via molecular dynamics simulations. Results: The phylogenetic analysis classified the genes into 33 Type I and 54 Type II MADS-box members, forming four major clades (MIKC^C, MIKC*, Mα, and Mγ), while the Mβ-type clade was absent. A conserved motif analysis revealed that the Type II genes exhibited greater motif diversity than the Type I, suggesting that T. grandis Type II MADS-box genes possess more complex structures and potentially broader functions. The transcriptomic data from different tissues showed that the MIKC-type genes were particularly active during flower development. Although stable over the simulation time, the T. grandis AP3 ortholog had shorter I and K domains and had an odd mode of protein–protein interaction. Conclusion: Overall, the presented genome-wide analysis provides a comprehensive base for understanding the evolutionary diversification of the MADS-box gene family in T. grandis and identifies candidate genes for future structural and functional characterization. Full article

Leishmania guyanensis is one of 15 American human-pathogenic species, frequently linked to therapeutic failure due to its marked genetic plasticity and adaptability under drug pressure. To broaden the genomic understanding of this species, its biological traits, and potential therapeutic alternatives, we sequenced the L. guyanensis strain MHOM/BR/75/M4147. Raw reads underwent quality-filtering and assembly. Taxonomic classification utilized BLASTn and Kraken2, confirming that 99.95% of contigs matched Leishmania. The assembled genome size was 31 Mb, with an N50 of 4743 bp and 40.85× coverage. Variant calling subsequently identified 36,665 SNPs, 8210 indels, and chromosomal aneuploidies. Genomic annotation identified 3119 proteins with known molecular functions in L. guyanensis, alongside 6371 orthologous genes shared with L. major and L. panamensis. The search for pharmacological relevance yielded ten candidate genes, including one calpain and nine GSK3 family members. Phylogenetic reconstruction using the polA1 gene consistently grouped L. guyanensis, demonstrating strong discriminatory capacity, with L. martiniquensis emerging as the most divergent species. Overall, these findings expand the available genomic framework for L. guyanensis and support advances in species-specific diagnostic approaches. Full article

Seed germination is a critical developmental stage exhibiting high vulnerability to salt stress. The role of MYB transcription factors (TFs) in mediating this process in Cannabis sativa L. remains largely unexplored. In this study, we performed a genome-wide analysis and identified 115 CsMYB genes, which were phylogenetically classified into 12 distinct subgroups. In silico promoter analysis revealed a significant enrichment of abscisic acid (ABA)- and methyl jasmonate (MeJA)-responsive cis-elements, suggesting their potential linkage to phytohormone signaling pathways under stress conditions. To investigate their expression during salt stress, we profiled a subset of candidate CsMYB genes during seed germination under 150 mM NaCl treatment based on RNA-seq screening at 24 h post-imbibition (hpi) under salt stress. These candidates exhibited distinct temporal expression profiles: CsMYB33 and CsMYB44 were transiently induced at the early stage (12 h post-imbibition), while CsMYB14, CsMYB78, and CsMYB79 showed sustained upregulation from 24 h to 5 days. In contrast, CsMYB58 and CsMYB110 were downregulated. Synteny analysis indicated a closer evolutionary relationship between CsMYBs and their Arabidopsis thaliana orthologs compared to those in monocots. Protein–protein interaction predictions, based on orthology, further implicated these CsMYBs within putative ABA signaling and reactive oxygen species (ROS) homeostasis networks. Collectively, our findings provide a systematic genomic identification and genomic characterization of the CsMYB family and propose a model for the potential multi-phase involvement of selected CsMYBs in the salt stress response during seed germination. This work establishes a foundational resource and identifies key candidate genes for future functional validation aimed at enhancing salt tolerance in C. sativa. Full article

The Keap1-Nrf2 signaling pathway is a central regulator of transcriptional responses to oxidative stress and is strongly linked to diverse pathologies, particularly cancer. In the cytoplasm, Keap1 (Kelch-like ECH-associated protein 1) promotes proteasomal degradation of Nrf2 (NF-E2–related factor 2). Oxidative stimuli disrupt the Keap1-Nrf2 interaction, facilitating Nrf2 nuclear accumulation and activation of antioxidant and detoxifying genes. Recent evidence suggests that Keap1 family proteins also enter the nucleus, bind chromatin, and regulate transcription, but the underlying mechanisms remain less understood. Here, we show that the Drosophila Keap1 ortholog, dKeap1, accumulates in the nucleus and gradually assembles stable nuclear foci in cells following oxidative treatment. FRAP analyses revealed reduced mobility of dKeap1 within these foci. Both the N-terminal (NTD) and C-terminal (CTD) domains of dKeap1 were required for foci formation. Two intrinsically disordered regions (IDRs) were identified within the CTD, and CTD-YFP fusion proteins readily formed condensates in vitro. Conversely, deletion of the Kelch domain resulted in robust cytoplasmic foci even under basal conditions, and in vitro assays also indicated that the Kelch domain suppresses dKeap1 condensate formation. Together, these findings reveal a novel molecular mechanism for the nuclear function of dKeap1, providing new insight into the broader roles of Keap1 factors in oxidative response, development, and disease. Full article

Candidozyma auris (formerly Candida auris) is an emerging multidrug-resistant fungal pathogen with confirmed cases in over 30 countries. Although whole-genome sequencing (WGS) analysis defined distinct clades during characterization of underlying genetic mechanism behind multidrug resistance, Clade II remains under-evaluated. In this study, a three-level comparative genomic strategy (Global, Clade, Phenotype) was employed by integration of unbiased genome-wide comparative SNP screening (GATK v4.1.9.0), targeted BLAST profiling (BLAST+ v2.17.0), and in silico protein analysis (ColabFold v1.5.5; DynaMut2 v2.0) for systematic evaluation of mechanisms of antifungal resistance in thirty-nine Clade II C. auris clinical isolates and fourteen reference strains. Global and clade-level analyses confirmed that all the clinical isolates belong to Clade II, according to phylogenetic clustering and mating type locus (MTL) conservation. At the phenotype level, a distinct subclade of fluconazole-resistant mutants was identified to have a heterogenous network of mutations in seven key enzymes associated with cell membrane dynamics and the metabolic stress response. Among these, four core mutations (TAC1B, CAN2, NIC96, PMA1) were confirmed as functional drivers based on strict criteria during multitier in silico protein analysis: cross-species conservation, surface exposure, active site proximity, thermodynamic stability, and protein interface interaction. On the other hand, three high-level fluconazole-resistant clinical isolates (≥128 μg/mL) that lacked these functional drivers were subjected to comprehensive subtractive genomic profiling analysis. The absence of coding mutations in validated resistance drivers, yeast orthologs, and convergent variants suggests that there is an alternative novel non-coding or regulatory mechanism behind fluconazole resistance. These findings highlight Clade II’s evolutionary divergence into two distinct trajectories towards the development of a high level of fluconazole resistance: canonical protein alteration versus regulatory modulation. Full article

Laodelphax striatellus is one of the most destructive rice pests. However, the functions of TARs in rice pests remain largely unknown. Here, we cloned LsTAR1 from L. striatellus. LsTAR1 shares considerable sequence identity with its orthologous receptors, and clusters closely with its corresponding receptor groups. LsTAR1 was most highly expressed in the egg stage and brain of L. striatellus. Knockdown of LsTAR1 by RNA interference (RNAi) prolonged the preoviposition and oviposition period, and reduced the fecundity. Furthermore, LsTAR1 knockdown significantly decreased the mRNA levels of vitellogenin (LsVg) in the fat body and ovary, and increased the transcript levels of Vg receptor (LsVgR) in the ovary, as well as altered the expression levels of genes related to juvenile hormone (JH) and 20-hydroxyecdysone (20E) pathway. Additionally, LsTAR1 knockdown markedly reduced the honeydew excretion of the adults and affected the expression of neuropeptide signaling genes involved in insect feeding. Notably, disruption of LsTAR1 signaling via RNAi or an antagonist reduced the survival rates of L. striatellus. This study uncovers the crucial roles of LsTAR1 in reproduction, feeding, and survival in L. striatellus, and highlights its potential as a promising target for developing novel pest management strategies. Full article

Terpenes are major determinants of tea aroma, and terpene synthases (TPSs) catalyze key steps in terpenoid biosynthesis. To capture gene-family variation beyond a single reference, we performed a pan-genome–based analysis of TPS genes across nine Camellia genomes (three wild tea relatives and six cultivated Camellia sinensis accessions) and integrated pan-transcriptome profiling across eight tissues. We identified 381 TPS genes; wild species contained more TPSs than cultivated accessions (mean 58.3 vs. 34.3), suggesting a putative contraction. Phylogenetic analysis with Arabidopsis TPSs classified Camellia TPSs into five subfamilies, dominated by TPS-b (149) and TPS-a (140), whereas TPS-c was rare (8). Gene-structure and physicochemical analyses revealed marked subfamily divergence, with TPS-c showing highly conserved coding-region length. Orthology clustering assigned 355 TPSs to 19 orthogroups, including five core groups (190 genes, 53.5%) and 14 dispensable groups (165 genes, 46.5%); core/non-core status was significantly associated with subfamily composition. Tandem and proximal duplication contributed most to TPS expansion (29.4% and 29.1%), and all orthogroups exhibited copy-number variation, with pronounced lineage-specific expansions. Ka/Ks analyses indicated pervasive purifying selection (median 0.516) but heterogeneous constraints among subfamilies. Finally, cultivated tea showed higher TPS expression in most tissues, especially mature leaf and stem, and TPS-g displayed the broadest and strongest expression. Together, these results provide a pan-genome resource for Camellia TPSs and highlight how domestication, duplication, and CNV shape terpene-related genetic diversity. Full article

Panax notoginseng, a high-value medicinal crop, suffers substantial yield losses due to Fusarium oxysporum-mediated root rot, for which no molecularly defined control targets are currently available. Histone acetyltransferases (HATs) serve as crucial epigenetic regulators of fungal development and stress responses; however, their functional roles in F. oxysporum remain largely unexplored. In this study, we systematically identified six FoHAT genes via genome-wide analysis and classified them into evolutionarily conserved subfamilies through phylogenetic comparison with orthologs from Saccharomyces cerevisiae, Homo sapiens, and Arabidopsis thaliana. Structural analyses revealed distinct motif compositions and domain architectures among FoHAT members, while promoter cis-element profiling suggested potential subfunctionalization via stress-responsive regulatory mechanisms. Functional investigations demonstrated that major notoginsenosides present in P. notoginseng root exudates—R₁, Rg₁, Rg₂, Re, and Rd—dynamically influenced both spore germination and FoHAT expression profiles. Intriguingly, each notoginsenoside exerted concentration-dependent non-linear effects on spore germination, either inhibiting or promoting the process. Concurrently, notoginsenoside exposure triggered compensatory transcriptional responses, most notably a rebound in Fo-Hat1_N expression from 9% to 112% under Rd treatment. This work establishes an initial epigenetic framework for combating Fusarium root rot in medicinal plants and offers a foundation for developing HAT-targeted small-molecule inhibitors. Full article

Macrobrachium nipponense is an important commercial freshwater prawn species in China. Since larger individuals command higher market value, there is a pressing need to identify growth-related genes and single-nucleotide polymorphisms (SNPs) to facilitate genetic improvement in this species. Previous studies have suggested a potentially regulatory role of an actin-like protein (ACTL) in the growth of M. nipponense. Therefore, the present study aimed to functionally characterize the role of ACTL in growth and identify growth-associated SNPs within this gene. The open reading frame of Mn-ACTL is 1131 bp, encoding a protein with 377 amino acids. Blastx and phylogenetic analyses indicated that Mn-ACTL shares a close evolutionary relationship with orthologs from Macrobrachium rosenbergii and Palaemon carinicauda. The highest expression level of Mn-ACTL in muscle tissue detected by qPCR suggested its potential involvement in growth regulation. RNA interference experiments showed that prawns injected with dsGFP exhibited larger body sizes than those injected with dsACTL, indicating that knockdown of Mn-ACTL expression inhibits growth performance in M. nipponense. Furthermore, muscle tissue from the dsACTL-injected group displayed looser myofibril packing, visibly eroded areas, and increased sarcomere spacing. Collectively, these results demonstrated that ACTL positively regulates growth in M. nipponense. Additionally, the T allele at locus S28_17149891 and the G allele at locus S28_17145758 were significantly associated with growth traits (p < 0.05). In conclusion, this study confirmed the positive regulatory role of ACTL in growth and identified growth-associated SNPs in M. nipponense, providing valuable insights for breeding new varieties with enhanced growth performance in this species. Full article