The interaction between cadmium and water induces a nonlinear response in nitrogen cycling in paddy soils by restructuring microbial networks.

The GOLDEN2-LIKE (GLK) gene family, known for its role in chloroplast development, has recently been implicated in involvement of anthocyanin biosynthesis in kiwifruit (Actinidia spp.), but the underlying regulatory mechanism remains unclear. Here we report the characterization of a kiwifruit GLK homolog AcGLK2 in regulating anthocyanin accumulation. We found that expression of AcGLK2 is much higher exclusively in the red pigment-accumulated fruit tissue. Overexpression of AcGLK2 in Arabidopsis and kiwifruit significantly enhanced anthocyanin content, whereas its RNAi-mediated silencing compromised anthocyanin accumulation. RNA-Seq analysis revealed significant upregulation of many structural genes and transcription factors (TFs) associated with the flavonoid pathway in AcGLK2-overexpressing kiwifruit. ChIP-Seq analysis indicated that AcGLK2 directly binds to AcMYB5 and AcTRY. We showed AcMYB5, an R2R3-MYB TF, promotes anthocyanin accumulation by interacting with the bHLH protein AcbHLH42, while AcTRY, an R3-MYB protein, competitively inhibits the interaction between key MYBs and AcbHLH42, thereby repressing anthocyanin biosynthesis. Transgenic and molecular assays in tobacco, tomato, and kiwifruit demonstrated that AcGLK2 positively participates into regulation of anthocyanin accumulation through transcriptionally activating AcMYB5 expression and concomitantly suppressing AcTRY expression. This study reveals the dual regulatory mechanism of AcGLK2 in anthocyanin biosynthesis, broadening the understanding of GLK gene functions and providing a valuable genetic resource for molecular breeding of nutritional quality in kiwifruit and other crops.

Integrated metabolomic and transcriptomic analyses reveal that pectin metabolism mediates texture divergence in grape berries

In plant, lycopene β-cyclase is a crucial enzyme in carotenoid metabolic pathway, which can induce color alteration. Carrots (Daucus carota) possess two genes encoding lycopene β-cyclase, namely DcLcyB1 and DcLcyB2. Little is known regarding the functional disparities between these two proteins in regulating carrot carotenoid accumulation. We found that the expression level of DcLcyB2 was higher than that of DcLcyB1 in carrot roots. Enzyme reaction in E. coli demonstrated that both two DcLcyB proteins were capable of cycloconverting lycopene to β-carotene, but DcLcyB2 tended to have a higher preference for monocyclic carotene substrates, resulting in more α-carotene production. After the DcLcyBs were separately overexpressed in red carrots, the roots turned yellow, accompanied by the reduction of lycopene and β-carotene content and the entire carotenoid metabolism flowed downstream towards xanthophylls. The expression levels of DcCHXE, DcCYP97A3, DcCHXB1 and DcCHXB2 in the DcLcyB-OE lines raised sharply. After gene editing of DcLcyB1/2, the α-/β-carotene ratio changed conspicuously, particularly in the dclcyb2 mutants, where α-carotene content dropped sharply, while β-carotene remained high. The expression levels of most structural genes in carotenoid pathway responded dynamically. Our results enriched the understanding of functionally redundant but differentiated roles of two DcLcyB isoenzymes in carrot root coloring.

Systematic characterization of FBP gene family in Saccharum reveals ScFBP3 as a key regulator of sucrose-mediated plant branching.

Genome-wide analyses of SNF2 chromatin remodeling complexes reveal their involvement in regulating fruit ripening in "Fenjiao" banana (Musa ABB group, cv Pisang Awak).

Identification and functional analysis of GbMYB15 as a negative regulator in flavonoid biosynthesis of Ginkgo biloba.

Comprehensive evaluation of the novel purple-fleshed tomato germplasm black 'pearl' and analysis of anthocyanin synthesis mechanisms and components.

Pear PbrPRKs regulate pollen tube growth via modulation of apical actin and reactive oxygen species homeostasis.

Evolution of steroid receptor coactivator Taiman in arthropods.

Klebsiella pneumoniae (KP) is a critical-priority organism due to prevalent last-line antibiotic resistance. Alternative treatments, including vaccines and monoclonal antibodies (mAb), depend on antigen (Ag) expression at infection sites for immunotherapeutic activity. However, the relationship between genome-encoded Ag presence and Ag expression is often overlooked. Here, we use the KP type 3 fimbrial (T3F) subunit MrkA as a prototype to build a generalisable framework to assess Ag expression and its correlation with in vivo immunotherapeutic efficacy. We perform genomic analysis of 1649 KP genomes for T3F genes, including structural and regulatory components. We generate isogenic mutants with absent, normal or overexpressed MrkA and profile MrkA expression at single-cell level from murine pneumonia and bacteraemia models. We compare anti-MrkA mAb efficacy in vivo against strains with normal and enhanced MrkA expression. T3F structural and regulatory genes are highly conserved, however, regulatory gene disruption (mrkH) is more common than structural gene disruption and, in both cases, MrkA Ag is not expressed. In vivo Ag profiling revealed site-specific differences in MrkA expression, with ∼20% of KP cells expressing MrkA in the lung versus ∼5% in the bloodstream. Anti-MrkA mAb activity was dependent on MrkA abundance, with significantly enhanced efficacy following infection with MrkA-overexpressing KP. Regulatory genes are as important to characterise as structural gene presence when evaluating antigen candidates in clinical isolates, and Ag expression can vary by anatomical context. For MrkA, Ag abundance determines anti-MrkA mAb activity, suggesting infections with high MrkA expression will respond better to therapy.

Glutathione S-transferases (GSTs) play crucial roles in plant stress responses, particularly in salt stress acclimation, by participating in reactive oxygen species scavenging, detoxification, and regulation of hormone signaling. Avicennia marina, a pioneer mangrove species, exhibits long-term adaptation to extreme habitats such as high salinity, yet its GST gene family has not been systematically characterized. This study provides the first genome-wide characterization and identification of the GST gene family in A. marina, identifying 25 AmGST genes classified into five subfamilies: GSTU, GSTF, GSTT, EF1G and TCHQD. Evolutionary analysis indicated that AmGSTs have undergone strong purifying selection. Gene structure and conserved motif analyses revealed subfamily-specific sequence patterns. Promoter analysis identified numerous cis-acting elements associated with stress responses and hormone regulation. Homology modeling and molecular docking predicted that three representative AmGST proteins, AmEF1G02, AmGSTF03 and AmGSTU08, can bind to glutathione (GSH) and indole-3-acetic acid (IAA) through multiple hydrogen bonds, suggesting their potential role in antioxidant defense and hormone modulation. Quantitative real-time PCR analysis showed distinct expression patterns of different AmGSTs under salt treatment and exogenous auxin treatment. Notably, AmGSTF03 was consistently upregulated by salt and further enhanced by IAA, while the auxin-specific responsiveness of AmEF1G02 (strongly induced by IAA regardless of salinity) suggests its role as a potential crosstalk node between auxin signaling and detoxification pathways. AmGSTU08 exhibited early transient upregulation under salt and auxin, supporting its involvement in rapid stress responses. This study establishes that the A. marina GST family has been shaped by strong purifying selection and subfamily-specific structural divergence, highlighting the evolutionary conservation and functional diversity of AmGSTs. The potential dual binding ability of some protein members represented by AmEF1G02, AmGSTF03, and AmGSTU08 to GSH and IAA, as well as their different expression patterns, suggests that AmGSTs may serve as a molecular bridge connecting auxin signaling and antioxidant defense. These findings systematically reveal the composition, evolutionary features, and potential functions of the A. marina GST family in salinity stress and hormone regulation, providing new insights into the molecular mechanisms of salt tolerance in mangroves and candidate gene resources for improving crop salt tolerance.

GATA transcription factors (TFs) are zinc finger proteins that regulate diverse developmental and stress-responsive processes in plants. Despite the growing economic importance of Cannabis sativa L. (hemp) as a source of fiber, seed oil, and bioactive compounds, the GATA TF gene family has not been systematically characterized in this species. This study aimed to perform a comprehensive genome-wide identification and characterization of GATA TF genes in C. sativa L. and to investigate their expression responses during early seed germination under abiotic stress conditions. A total of 17 GATA TF genes (CsGATAs) were identified in the C. sativa L. genome and phylogenetically classified into three clusters: Cluster I (12 members), Cluster II (one member), and Cluster III (four members). Evidence of localized gene family expansion was observed, with tandem duplication events identified in CsGATA2, CsGATA5, CsGATA6, CsGATA10, CsGATA11, and CsGATA14, distributed across Clusters I and III. Gene structure analysis revealed significant variation, with exon numbers ranging from 2 to 10. Promoter analysis of the 2000 base pairs (bp) upstream regions showed enrichment of stress and hormone-responsive cis-acting elements, with abscisic acid (ABA) responsive elements present in 12 of the 17 promoters. Transcriptomic profiling during early germination under cold stress (4°C), salt stress (200mM NaCl), and combined cold and salt stress revealed distinct expression patterns. CsGATA3 was consistently downregulated across all three stress conditions (log2FC of -1.14 under salt stress, -1.08 under cold stress, and -1.23 under combined stress). In contrast, CsGATA9 and CsGATA14 responded specifically to combined stress, with CsGATA9 downregulated (log2FC of -1.62) and CsGATA14 upregulated (log2FC of + 1.62). qRT-PCR analysis of five differentially expressed CsGATA genes confirmed the RNA-seq expression trends, showing strong concordance between the two platforms (Pearson r = 0.83, p < 0.001). This study provides the first genome-wide characterization of the GATA TF family in C. sativa L. and reveals gene family expansion driven by tandem duplication. The identification of stress-responsive members, particularly CsGATA3 as a broadly downregulated gene across all stress conditions and CsGATA14 as specifically induced under combined stress, highlights candidate transcriptional modulators of abiotic stress adaptation during hemp seed germination. These findings lay a foundation for functional studies and molecular breeding strategies aimed at improving stress tolerance in hemp.

Partial gene duplications (PGDups) are a significant contributor to genetic disease. The precise genomic location and structure of PGDups are often unresolved using conventional methods, so prenatal diagnosis for PGDups is challenging, especially without ultrasound abnormalities. We retrospectively applied structural variation sequencing (SVseq) to 26 amniotic fluid samples with PGDups initially identified by chromosomal microarray or sequencing. SVseq utilized mate-pair library construction and high-throughput sequencing to map PGDup structures. Pathogenicity was classified using ACMG guidelines, followed by postnatal phenotypic follow-up. SVseq deciphered the PGDup structure for all twenty-six cases. Twenty-two (84.62%) were tandem duplications (TDs), three (11.54%) chromosomal complex rearrangements (CCRs), and one (3.85%) had no duplication. Among twenty-two TDs, thirteen were extragenic (TDEG), preserving gene integrity, and were classified as benign or variants of uncertain significance (VUS). Nine were intragenic (TDIG), disrupting gene structure, and were rated pathogenic or likely pathogenic (P/LP) or VUS. Postnatal follow-up revealed obvious abnormal phenotypes in only two TDIG cases (one inherited and one de novo). SVseq effectively resolves PGDup location and structure, allowing confident pathogenicity assessment and clear genotype-phenotype correlation. SVseq is a robust method for prenatal PGDup evaluation that could be adopted in diagnostic protocols to improve clinical outcomes.

Polygala tenuifolia Willd. (P. tenuifolia) is one of the source plants of the traditional Chinese medicine 'Yuanzhi' and is widely used in clinical practice. As a meso-xerophytic medicinal plant with strong environmental adaptability, it is listed as a nationally protected wild medicinal species in China. However, the molecular mechanisms underlying its drought tolerance remain unclear. Therefore, a genome-wide identification of the ERF subfamily inP. tenuifoliawas conducted to provide candidate genes for drought adaptation research and functional validation. Ethylene-responsive factors (ERFs) play important roles in plant responses to drought stress. In this study, 78 PtERF genes were systematically identified for the first time in P. tenuifolia. Phylogenetic analysis classified these genes into five subgroups (B1-B5), with members within the same subgroup exhibiting similar gene structures and conserved motifs. Collinearity analysis revealed that segmental duplication was the primary driving forceunderlying PtERF family evolution. Cis-acting element analysis revealed that PtERF promoter regions were enriched with drought-responsive cis-elements, including abscisic acid and methyl jasmonate (MeJA)-responsive elements. Transcriptome analysis combined with RT-qPCR verification identified five core drought-responsive genes, among which PtERF33 expression exhibited the highest level of upregulation. Further investigation showed that PtERF33 produced two alternatively spliced transcripts: the full-length PtERF33.1 transcript and the intron-retained PtERF33.2 transcript. These two transcripts exhibited opposite expression patterns under drought stress, suggesting that they may regulate drought responses through functional antagonism. These findings provide a systematic basis for identifying drought-resistant ERF genes in P. tenuifolia and establish a foundation for clarifying the role of alternative splicing in drought adaptation in this species.

SAUR21-like genes in broccoli and Arabidopsis: Comparative expression and functional characterization.

Pearl millet is a vital dryland, nutrient-rich C4 crop with significant potential to reduce hidden hunger among vulnerable groups. However, its wider commercialization is limited by the short shelf life of its flour. Several endogenous compounds, particularly antioxidant flavonoids, are associated with reduced rancidity. Among these, C-glycosyl flavonoids are considered important contributors to the enhanced shelf life of flour. C-glycosyltransferases (CGTs) encode proteins containing the UDP-glycosyl transferase domain and are predicted to play a regulatory role in flavonoid glycosylation. However, a detailed study on the quality of pearl millet flour is lacking. In this study, 32 PgCGT genes were identified and mapped to all the chromosomes except chromosome 3. Most of the CGT genes (18) are predicted to be located in chloroplasts. Gene structure analysis showed that most (25) genes had only one exon. Motif analysis identified conserved motifs within the CGT gene family in pearl millet. Comparative synteny analysis across cereal genomes suggested that purifying selection likely shaped the evolution of this gene family, with 15, 18, 20, and 15 conserved orthologs identified in rice, sorghum, foxtail millet, and maize, respectively. Promoter analysis identified cis-regulatory elements predicted to be associated with seed-specific regulation and endosperm-specific expression. The low-rancid genotype DS-SP-15 showed significantly higher flavonoid content at day 0 (131.44mg QE/100g) and day 10 (141.88mg QE/100g) than the high-rancid genotype DS-SP-9, which recorded 107.04mg QE/100g and 117.17mg QE/100g at the respective time points. The observed gene expression differences in contrasting inbred lines at various times suggest a potential role in flour shelf life in pearl millet. This study provides a comprehensive characterization of the PgCGT gene family and highlights possible functional divergence among its members. These results provide a solid foundation for future functional validation and targeted genome editing to improve grain quality and extend the shelf life of pearl millet flour.

Circulating C1QC in cancer: analytical platforms, evidence gaps, and prospects for clinical chemistry translation.

The Gretchen Hagen 3 (GH3) family plays an essential role in plant growth, development and resistance to environmental stress. Although, the members in GH3 family have been reported in some monocots, their exploration in Phyllostachys edulis needs to be further explored. In the present study, we identified totally 23 GH3 genes from P. edulis at the genomic level, which were categorized into two subfamilies (I and II) based on phylogenetic analysis. Subsequent analyses concentrated on the molecular features of these genes, including their gene structure, conserved motifs, cis-acting elements in promoters, and syntenic regions in the genome. Furthermore, qRT-PCR results indicated that most PeGH3 genes were extensively expressed across all the tested tissues. Meanwhile, some of them were also responsive to abiotic stresses such as salt and drought, as well as hormone treatments including naphthalene acetic acid (NAA) and salicylic acid (SA) based on RNA-seq data analysis. According to the tissue-specific and stress-responsive expression results, PeGH3-4, PeGH3-8, PeGH3-14, and PeGH3-18 were likely to play significant roles in plant growth and in response to abiotic stress. Subcellular localization analysis demonstrated that these four PeGH3 proteins were predominantly localized in the cytoplasm and nucleus. To further clarify their function in stress tolerance, PeGH3-4, PeGH3-8, PeGH3-14, and PeGH3-18 were expressed in yeast, which proved their ability to enhance yeast tolerance to salt and drought stresses. This research enhances the understanding of PeGH3 genes and provides genetic resources for breeding bamboo plants with improved resistance to stress, especially to salt and drought.

Since feline panleukopenia virus (FPV) is considered the most likely ancestor of canine parvovirus (CPV), comprehensive comparisons of nucleotide organization in corresponding viral genes between CPV and FPV may provide novel insights into the evolutionary dynamics underlying the divergence of these two viruses. Here, we characterize the evolutionary patterns of CPV and FPV genes across multiple levels of nucleotide organization. Both viruses exhibited highly conserved nucleotide usage at nonsynonymous sites, with Ka/Ks patterns consistent with strong purifying selection, whereas synonymous sites showed greater variability. CpG dinucleotides were markedly underrepresented across all four viral genes, suggesting host-associated selective pressure and/or intrinsic nucleotide compositional constraints. Extensive nonrandom biases in synonymous codon usage, codon neighboring nucleotide context, and codon pair usage further revealed fine-scale genomic optimization shaped by natural selection and nucleotide compositional constraints. Structural protein genes (VP1 and VP2) displayed stronger codon usage bias and higher tRNA adaptation than nonstructural genes. Moreover, CPV genes showed greater translational adaptation to feline hosts than to canine hosts. These findings highlight how closely related parvoviruses exploit flexible nucleotide organization to facilitate host adaptation while maintaining essential protein functions.