Search Results (16,601)

Soursop (Annona muricata L.) is a climacteric tropical fruit belonging to the Annonaceae family, widely cultivated in tropical and subtropical regions due to its economic importance, nutritional value, and abundance of bioactive compounds. Its pulp is highly appreciated for fresh consumption and food processing; however, its high respiration rate and ethylene production accelerate ripening, resulting in rapid quality deterioration and a short postharvest shelf life. During ripening, soursop fruit undergoes physiological, biochemical, and molecular changes associated with organic acid metabolism, in which citrate synthase (CS) and malate dehydrogenase (MDH) play key roles within the tricarboxylic acid cycle. However, the transcriptional dynamics of genes associated with the tricarboxylic acid cycle during postharvest storage of tropical fruits remains poorly characterized. This study aimed to identify in silico genes encoding CS and MDH and to evaluate changes in physicochemical traits, enzymatic activity, and the expression of selected CS and MDH genes during postharvest storage of soursop (A. muricata) GUANAY-1 fruit. Fruits were stored at 26 ± 1 °C and evaluated on days 1, 2, 3, 4, and 5. Titratable acidity, pH, total soluble solids, CS activity, MDH activity, and the expression of selected CS and MDH genes were analyzed. Physicochemical analysis showed that the major changes in acidity, TSS, and pH occurred on day 3. In silico analysis identified 16 CS genes and 47 MDH genes in soursop, whereas transcriptome analysis identified four CS genes and three MDH genes with differential expression, designated as CS1, CS2, CS3, CS4, MDH1, MDH2, and MDH3, respectively. The Neighbor-Joining analysis grouped the CS sequences into two clusters and the MDH sequences into three clusters. Differential expression analysis revealed that CS1, CS2, CS3, CS4, MDH1, MDH2, and MDH3 were upregulated on day 3 relative to day 0 of postharvest storage. Functional enrichment analysis indicated that these genes were mainly associated with cellular respiration and the tricarboxylic acid cycle. The highest CS activity was recorded on day 3, coinciding with the maximum expression of CS1, CS2, and CS4. In contrast, MDH activity peaked on day 2, whereas MDH1 and MDH2 reached their highest expression on day 3. Correlation analysis showed positive associations between CS2 and CS4 expression and both TSS and titratable acidity. Overall, these results demonstrate temporal changes in physicochemical traits, CS and MDH enzymatic activities, and the expression of selected CS and MDH genes during postharvest storage of GUANAY-1 soursop fruit. Full article

Background and Aim: Germline testing (GT) is increasingly relevant in pancreatic ductal adenocarcinoma (PDAC) because of therapeutic and familial implications. We evaluated real-world GT uptake, the diagnostic yield of pathogenic/likely pathogenic germline variants (P/LP), and their clinical implications. Methods: We retrospectively evaluated 674 consecutive patients with PDAC. GT was performed using targeted single-gene testing or multigene panels. Survival analyses among patients receiving platinum-based chemotherapy according to P/LP germline variant status in HRR-associated genes were exploratory. Results: Overall, 28.9% of patients underwent GT, increasing to 45.9% in 2021–2025 (p < 0.001). Results were available for 194 patients; 28 (14.4%) harbored P/LP variants, most commonly BRCA2 (4.6%) and ATM (3.1%). P/LP variants were identified in 6.8% of patients who did not meet classical referral criteria. Among the 28 carriers, 12 (42.9%) harbored BRCA1/2 or PALB2, variants with established therapeutic relevance, while eight (28.6%) carried ATM, FANCA, or FANCM, variants with potential therapeutic relevance. Of these 20 patients, 11 (55.0%) received matched therapy, and treatment was modified because of the germline result in six (30.0%). In exploratory analyses, among platinum-treated patients, carriers of P/LP germline variants in HRR-associated genes had longer PFS than non-carriers (23.9 vs. 4.8 months; log-rank p = 0.017), although only six HRR-associated variant carriers were included in this platinum-treated survival analysis. Conclusions: GT remained underused despite increasing implementation. Early systematic GT may identify clinically relevant variants missed by selective referral strategies and inform treatment, genetic counseling, and cascade testing. Survival findings require prospective validation. Full article

The dried roots and rhizomes of Salvia miltiorrhiza are widely used and economically important traditional Chinese medicinal materials. Land salinization affects the growth of S. miltiorrhiza, resulting in a decline in its quality and yield. WNK kinases belong to a unique family of serine/threonine kinases. They act as key regulators of plant growth, development and abiotic stress responses. However, this gene family has not been systematically characterized in Salvia miltiorrhiza. In this study, nine SmWNK genes were identified at the whole-genome level in S. miltiorrhiza. Phylogenetic analysis classified them into four structurally conserved subgroups. These genes are distributed across eight chromosomes and contain two pairs of intraspecific syntenic genes. Interspecific collinearity is far stronger between S. miltiorrhiza and dicots than between S. miltiorrhiza and monocots. Cis-element prediction indicated these cis-elements participate in light signaling, hormone responses, stress responses and developmental regulation. Quantitative real-time PCR revealed that eight SmWNK genes were significantly induced by salt stress, and SmWNK7 was selected as the key candidate for functional validation. Functional assays via heterologous overexpression in tobacco demonstrated that SmWNK7 overexpression promoted root elongation and enhanced salt tolerance. Compared with wild-type tobacco plants, SmWNK7-overexpressing transgenic tobacco lines had higher catalase (CAT) and peroxidase (POD) activities, lower malondialdehyde (MDA) content, and stronger root viability. These changes alleviated oxidative damage by enhancing the antioxidant defense system. Yeast two-hybrid screening yielded 40 SmWNK7-interacting annotated proteins, including 6 transcription factors and 1 protein kinase, which were enriched in 81 GO terms and 27 KEGG pathways. These findings confirm SmWNK7 positively regulates root growth and salt tolerance, laying a theoretical foundation for exploring SmWNK genes’ role in plant stress adaptation. Full article

Chrysanthemum morifolium is an important ornamental crop whose flowering is strictly regulated by photoperiod. However, the molecular mechanisms linking photoperiod signals to floral meristem identity and organ development in Asteraceae remain unclear. In this study, we identified and characterized CmAFL1, a FUL-like MADS-box gene specific to the Asteraceae family, in the short-day cultivar ‘Jinba’. CmAFL1 expression is upregulated under short-day conditions, primarily expressed in the shoot apical meristem during flower bud differentiation and predominantly in the receptacle during organ development. RNA interference-mediated silencing of CmAFL1 resulted in delayed flowering, arrested inflorescence development, malformed tubular florets, plant dwarfism, and excessive lateral branching, indicating its pleiotropic roles in flowering time, plant architecture, and floral organ patterning. At the molecular level, yeast one-hybrid assays revealed that the photoperiod pathway transcription factor CmCOL4 directly binds to the promoter region of CmAFL1. Furthermore, yeast one-hybrid and dual-luciferase assays confirmed that CmAFL1 directly interacts with and activates the promoter of the E-class floral organ identity gene CmSEP3. Together, our findings identify a novel transcriptional regulatory module CmCOL4-CmAFL1-CmSEP3 that potentially links photoperiod signaling to floral meristem identity and organ specification in Chrysanthemums. While further in planta validation is warranted, these findings provide novel insights into photoperiodic flowering regulation in Asteraceae and may serve as a theoretical foundation for molecular breeding strategies targeting flowering time manipulation in ornamental Chrysanthemums. Full article

Both genetics and the environment affect the phenotypes of polycystic kidney diseases (PKD), such as autosomal dominant (AD) PKD, autosomal recessive (AR) PKD and nephronophthisis (NPH). Variable phenotypes, pleiotropy, divergent severity and progression, even in family members who inherited the same disease-causing mutation(s), signal the involvement of networked genes and modifiers. Several PKD-linked genes function in development and renal tubule morphogenesis. Cystic renal tissues feature metabolic remodeling, functional reprogramming and dysregulation of several shared factors and pathways. ADPKD, ARPKD and NPH partially phenocopy each other. Understanding the developmental arc of cystic kidney disease and its complex phenotypes would improve diagnostics and help develop effective personalized treatments. However, this is challenging to study in vertebrate systems due to genetic redundancy, functional overlap, and a dearth of genetic tools. Underused in this context, Drosophila melanogaster offers high genomic and pathway conservation, a wealth of genetic tools, and rapid generation times, making it a reliable and sustainable model for mechanistic, genome-wide, and precision medicine studies. Here, we surveyed ADPKD, ARPKD, and NPH, compared renal and extrarenal phenotypes, and examined the network of shared and unique contributors, their healthy and diseased functions and conservation from the perspective of mechanistic whole-animal modeling. Full article

Background/Objectives: β-Glucosidases from lactic acid bacteria are valuable biocatalysts for carbohydrate conversion, flavour enhancement, and bioactive glycoside biotransformation. Although GH3 family enzymes have been characterized from several Lactobacillus species, no systematic study exists for Lentilactobacillus buchneri—a GRAS strain with plant-polysaccharide-degrading potential. This work aimed to clone, heterologously express, and comprehensively characterize a novel GH3 β-glucosidase (LbBgl3) from L. buchneri, with a particular focus on its catalytic properties, substrate profile, stability, and the unexpected EDTA-mediated thermostabilization mechanism. Methods: A novel β-glucosidase gene (LbBgl3) from L. buchneri was successfully expressed in Escherichia coli. Results: Biochemical characterization revealed that LbBgl3 is a cold-adapted, moderately acidophilic enzyme, exhibiting optimal activity at 37 °C and pH 5.0, with a maximum specific activity of 799.67 U·mg⁻¹. Under optimal conditions, the enzyme displayed kinetic parameters toward pNPG with a K_m of 1.697 mM, V_max of 442.5 μmol·mg⁻¹·min⁻¹, k_cat of 634.32 s⁻¹, and k_cat/K_m of 373.79 mM⁻¹·s⁻¹. LbBgl3 exhibited high salt tolerance, with activity peaking at ~140% at 0.5 M NaCl and retaining ~68% at 2.0 M NaCl, while showing sensitivity to glucose inhibition. Notably, EDTA significantly enhanced both the activity and stability of LbBgl3. At 50 mM, the relative activity increased to 161%, and stability at 25 °C was prolonged. Molecular docking simulations suggested that EDTA binds near the substrate-binding pocket, forming hydrogen bonds with Ala57, Gln766, Ser768, and Lys770, thereby stabilizing the local conformation and enhancing thermal resistance. Conclusions: This study presents the first characterization of a GH3 β-glucosidase from L. buchneri and reveals a non-classical stabilizing effect of EDTA, offering valuable insights for enzyme engineering and biocatalytic applications. Full article

Wheat is a globally important staple crop, whose growth and yield formation rely on the precise regulation of phytohormone signaling. The PR10/Bet v 1 (Pathogenesis-related protein 10/Betula verrucosa 1) family consists of conserved small-molecule ligand-binding proteins that participate in phytohormone signaling and plant development; however, systematic investigations of this family in wheat remain limited. Here, we performed a genome-wide identification of 75 PR10/Bet v 1 members in wheat, which were phylogenetically classified into three subfamilies: 21 known members belonging to the PYL (Pyrabactin resistance 1-like) subfamily, and 54 members assigned to two previously uncharacterized subfamilies. Bioinformatic analyses revealed that whole-genome/segmental duplication has driven the expansion of this gene family, which has evolved under strong purifying selection. Expression profiling and promoter analysis revealed differential expression patterns, along with abundant cis-acting elements responsive to multiple hormones. Quantitative RT-PCR (qRT-PCR) of 12 representative genes revealed marked transcriptional changes in several members within 1 h of treatment with BR (Brassinosteroid), ABA (Abscisic acid), CK (Cytokinin), or SA (Salicylic acid) suggesting that these genes may be directly involved in hormone-regulated processes. This study provides a fundamental framework for exploring the regulatory functions of the wheat PR10/Bet v 1 family, and valuable hormone-responsive candidate genes for the genetic improvement of wheat agronomic traits. Full article

Somatic embryogenesis (SE) is an indispensable biotechnological platform for plant regeneration, micropropagation and genetic modification. Members of WUSCHEL-related homeobox (WOX) transcription factor family are key regulators in SE, yet their roles in Catalpa bungei remain largely unexplored. C. bungei is a high-quality ornamental tree species endemic to China with prominent horticultural ornamental value. Here, we present the first genome-wide identification and expression profiling of the CbWOX gene family during SE in C. bungei. Fourteen CbWOX genes were identified and phylogenetically classified into three major clades. These genes are distributed across the 11 chromosomes of C. bungei, and their promoter regions are enriched with cis-regulatory elements associated with phytohormone response, stress adaptation, and growth/development. Integrated transcriptome and quantitative real-time PCR (qPCR) data indicated that CbWOX2, CbWOX5, CbWOX8, and CbWOX9 were highly expressed in embryogenic callus (EC), while CbWOX1.1 and CbWOX13 were predominantly expressed in non-embryogenic callus (NEC). Notably, only eight of the fourteen CbWOX genes were significantly expressed during SE, with distinct expression profiles across developmental stages. CbWOX4.1 and CbWOX4.2 were specifically associated with yellow-green hypocotyl callus development, while CbWOX2 and CbWOX8 were highly expressed at the EC stage. During later SE stages, CbWOX1.2, CbWUS, CbWOX5, and CbWOX13 showed significant expression at the globular embryo (GE) stage, while CbWOX1.3 was specifically upregulated at the cotyledon embryo (CE) stage. Our study provides a comprehensive genomic and transcriptomic foundation for the CbWOX family in C. bungei and reveals candidate genes with stage-specific expression during SE. These findings lay a solid basis for subsequent functional research to boost SE efficiency and advance the large-scale propagation of this precious ornamental tree. Full article

Nucleotide-binding site leucine-rich repeat (NLR, historically termed NBS-LRR) proteins are among the most rapidly evolving components of plant innate immunity, yet comparative analyses of NLR subfamily diversification between wild and cultivated accessions of tomato (Solanum lycopersicum) have remained limited. Here, we compared the NLR gene family across three representative tomato accessions—the wild species S. chilense and the cultivated tomatoes S. lycopersicum Heinz1706 (large-fruited) and S. lycopersicum LA1464 (cherry tomato)—by integrating genome-wide identification, phylogenetic reconstruction, motif analysis, orthologous clustering, selection-pressure assessment, and expression profiling. We identified 220, 223, and 245 candidate NLR genes in S. chilense, Heinz1706, and LA1464, respectively, and classified them into TIR-type (TNL) and coiled-coil-type (CNL) subfamilies at a consistent ratio of approximately 1:5 across all three accessions. Motif analysis revealed pronounced structural divergence between TNL and CNL proteins, most notably in the region corresponding to the second conserved motif of the NB-ARC domain. Orthologous clustering identified 67 gene clusters shared among the three accessions; within these, TNL genes showed greater sequence divergence (higher Ka and Ks values) than CNL genes but significantly lower Ka/Ks ratios (ω), indicating stronger purifying selection despite their greater raw divergence. Expression profiling further showed that CNL genes were more broadly expressed across tissues and were induced by multiple pathogen-associated molecular patterns, whereas TNL gene expression was more spatially restricted and preferentially induced by effector-related treatments. These results indicate that the TNL and CNL subfamilies of the tomato NLR repertoire have followed distinct evolutionary trajectories and regulatory strategies. As these conclusions are based on comparative genomic and transcriptomic evidence from three accessions rather than on functional validation, they should be regarded as hypotheses; nonetheless, they offer candidate genomic resources and a comparative framework that may inform future disease-resistance breeding in tomato. Full article

Animal activity plays an important role in regulating soil methane (CH₄) and nitrous oxide (N₂O) emissions. As a global invasive gastropod, golden apple snail (GAS, Pomacea canaliculata) has established great populations in wetlands, which has disturbed the soil ecological process. However, the impact of GAS activities on greenhouse gas (GHG) emissions is still unclear. A 25-day mesocosm experiment was conducted to examine CH₄ and N₂O fluxes, soil properties, microbial community, and GHG-related functional genes under low-density (GASL), high-density (GASH) and control (CK, without snail) treatments. Results showed that GASL significantly increased soil porosity and total nitrogen content by 18.6% and 7.6% on the 25th day. GASH significantly increased soil urease and sucrase activities by 18.1% and 30.0%. GASH significantly decreased the CH₄ emission flux by 18.7% and increased the N₂O emission flux by 33.1% on the 25th day. The 25-day cumulative CH₄ and N₂O emissions from female and male snail accounted for 0.002% and 2.3% of the total CH₄ and N₂O emissions in the GASH treatment, respectively. Moreover, GAS altered the soil microbial community composition. GASL significantly decreased the relative abundance of the phylum Chloroflexota by 11.3%, and increased the relative abundance of the family Nitrospiraceae by 24.5%. Compared with CK, GASH reduced the abundance of functional genes of mcrA, AOA-amoA, and nosZ by 16.9%, 19.7%, and 21.1%, respectively, while increasing the abundance of pmoA, AOB-amoA, and nirS by 18.4%, 65.3%, and 54.2%, respectively. These findings indicate that GAS disturbs soil physiochemical and microbial properties, and the conclusions are limited to a short-term mesocosm experiment. Full article

Double-flowered cultivars are generally considered more attractive than single-flowered varieties in ornamental plants. The AP2/ERF transcription factors superfamily plays pivotal roles in plant development, including floral organ formation. Here, a total of 248 AP2/ERF genes were identified in the genome of L. speciosa, and these genes were unevenly distributed on the 24 chromosomes. Phylogenetic analysis classified LsAP2/ERF genes into five distinct groups; the ERF subfamily was the largest, whereas the AP2 subfamily was associated with floral development. Gene duplication events contributed to the expansion of LsAP2/ERF family members, with segmental duplication identified as the primary contributor. Promoter cis-element analysis revealed an abundance of light-responsive and hormone-responsive elements. Spatiotemporal expression profiling showed that core AP2 subfamily members (LsAP2/ERF4/9/10/13/219) exhibited distinct expression patterns during flower bud development. Moreover, heterologous overexpression of LsAP2/ERF10 in tobacco resulted in transgenic lines with altered petal morphology, supporting its potential functional involvement in floral development. This study provides comprehensive characterization of the AP2/ERF family in L. speciosa, laying the foundation for elucidating its molecular mechanisms in floral morphogenesis. Full article

The SWEET (Sugars Will Eventually be Exported Transporter) family, a class of sugar transporters identified in recent years, plays important roles in plant growth and development. Increasing evidence suggests that SWEET genes are also involved in plant responses to abiotic stresses, including salt stress. However, the genome-wide composition and salt-responsive functions of SWEET genes in Elymus nutans Griseb. have not been systematically characterized to date. This study presents the first genome-wide identification of the SWEET gene family in E. nutans and functional characterization of EnSWEET15 in salt stress response, providing candidate genes and a theoretical basis for improving salt tolerance in this species. A total of 12 EnSWEET genes were identified from the E. nutans genome and were unevenly distributed across eight chromosomes. Phylogenetic analysis classified them into four subfamilies, and promoter analysis revealed abundant cis-elements related to hormone signaling and stress responses, suggesting roles in abiotic stress adaptation. Expression analysis showed that EnSWEET15 was significantly upregulated in both roots and leaves under salt stress. The full-length EnSWEET15 coding sequence (930 bp ORF) was cloned and functionally characterized. Heterologous overexpression in Arabidopsis thaliana indicated that EnSWEET15 enhances salt tolerance. Transgenic lines showed reduced reactive oxygen species (ROS) accumulation and increased activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), compared with wild-type plants under salt stress. Overall, this study identifies EnSWEET15 as a positive regulator of salt tolerance via modulating ROS homeostasis, providing novel insights into SWEET-mediated salt stress response in perennial forages and valuable genetic resources for salt-tolerant breeding of E. nutans. Full article

The Stress-Repressive Zinc Finger (SRZ) family is a class of zinc finger proteins in plants that has been closely associated with plant growth, development, and stress responses. In this study, we conducted a genome-wide identification of the SRZ family members and identified 14 and 10 members in rice and Arabidopsis, respectively. We further characterized their phylogenetic relationships, gene structures, conserved motifs, promoter cis-elements, synteny, and spatiotemporal expression patterns. To investigate the functional role of this family in rice, we generated targeted mutants of OsSRZ1 using the CRISPR/Cas9 system. Phenotypic analysis revealed that srz1 knockout mutants exhibited significantly reduced plant height. Notably, the homozygous mutant srz1 completely failed in panicle exsertion from the flag leaf sheath, resulting in complete enclosure, whereas the heterozygous mutant srz1(h) exhibited only partial panicle exsertion. Further cytological observations revealed abnormal floral organ development and premature anther senescence in srz1, accompanied by a significant reduction in seed setting rate—srz1(h) set significantly fewer seeds, whereas srz1 exhibited complete sterility with a seed setting rate of 0%. Collectively, these findings suggest that members of the SRZ family may play important roles in rice growth and development. Our results demonstrate that OsSRZ1 is a critical regulator of plant height and panicle exsertion by regulating internode elongation, and that its disruption leads to premature anther programmed cell death (PCD) and consequent seed setting failure. Full article

Background: CLTC-related neurodevelopmental disorder is a rare condition primarily characterized by global developmental delay (GDD) and intellectual disability (ID). To date, approximately 41 cases involving CLTC gene alterations have been reported. We present the first individual with a complete deletion of the CLTC gene. Methods: The proband is a male from a non-consanguineous family, presenting with congenital nystagmus, hypotonia, GDD, and autism spectrum disorder (ASD). Chromosomal microarray analysis and trio exome sequencing were performed. A systematic review of previously reported CLTC variant cases was conducted to delineate the phenotypic spectrum. Results: A de novo 363-kb heterozygous deletion at 17q23.1 spanning the entire CLTC gene was identified. The systematic review confirmed GDD/ID as core features and revealed various ocular abnormalities in a subset of cases. These findings indicate that the clinical phenotype extends beyond neurodevelopment, with multi-system involvement. Conclusions: The phenotypic heterogeneity of CLTC-related disorders underscores the need for comprehensive physical examination to identify extra-neurological manifestations. Accurate diagnosis relies on integrating detailed clinical phenotyping with comprehensive genomic testing. Early, precise diagnosis facilitates multidisciplinary management, informed genetic counseling, and the establishment of long-term surveillance protocols. Full article