Search Results (3,625)

Red algae (Rhodophyta) are an ancient lineage of photosynthetic eukaryotes that play important roles in marine ecosystems. However, genomic information for many species within the order Rhodymeniales remains limited, particularly for mitochondrial genomes. In this study, we sequenced, assembled, and analyzed the complete mitochondrial genome (mitogenome) of Rhodymenia intricata to investigate its genome organization, gene content, and phylogenetic position within Rhodymeniales. The mitogenome of R. intricata is a circular DNA molecule of 26,213 bp containing 49 genes, including 25 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes. The genome shows a strong A + T bias (70.9%) and positive AT and GC skews, typical of red algal mitogenomes. Comparative analysis with other Rhodymeniales mitogenomes revealed generally conserved gene content and organization, with several lineage-specific features such as the presence of the rpl20 gene, an additional open reading frame (orf148), and three rRNA genes (rnl, rns, and rns5). Codon usage analysis indicated a preference for leucine and isoleucine codons and dominant start and stop codons (ATG and TAA). Phylogenetic analysis based on a concatenated dataset of 23 mitochondrial PCGs strongly supported the monophyly of Rhodymeniales and confirmed the close relationship between R. intricata and R. pseudopalmata. Overall, this study presents the first complete mitogenome of R. intricata and expands mitogenomic resources for Rhodymeniales, providing new insights into mitogenome evolution and phylogenetic relationships in red algae. Full article

Rhizogenic Agrobacterium (Rhizobium) spp. are causative agents of hairy root disease (HRD), a major threat to hydroponic crop production worldwide. The use of specific bacteriophages is considered a prospective approach to control the development of HRD in greenhouses. A combination of diverse bacteriophages is a key step to overcome potential phage resistance in the pathogen. In this study, a novel lytic bacteriophage, named Miki, was identified and characterized for its antibacterial potential against a rhizogenic Agrobacterium sp. strain circulating in greenhouses in Central Russia. High-throughput sequencing revealed a 63,458 bp double-stranded DNA genome (G + C content 53%), with 117 predicted coding sequences, considering Miki as a lytic candidate phage for plant protection. Electron microscopy of phage Miki shows a morphology unusual for Agrobacterium phages, and phylogenetic analysis attributes it as a representative of a previously undescribed taxon at least at the genus level. The paper presents a detailed analysis of the genome and structural proteome of phage Miki, including in silico predictions and modeling of receptor-binding proteins, including central and proximal fibers resembling the adsorption apparatus of Escherichia phage T5. Full article

Carboxylesterases (CXEs) participate in diverse plant metabolic processes, including isoflavone biosynthesis. However, the soybean GmCXE subfamily remains poorly characterized, especially in relation to root isoflavone accumulation and the response to Fusarium oxysporum. Here, fifty-six putative GmCXE genes were identified in the soybean genome and classified into three major phylogenetic clades. Analyses of gene structure, conserved motifs, protein domains, and promoter cis-elements revealed conserved features as well as potential functional divergence among subfamily members. Collinearity and duplication analyses indicated that segmental duplication was the main driver of GmCXE subfamily expansion. Tissue-specific expression profiling and RT-qPCR validation selected five root-expressed genes as candidates associated with isoflavone accumulation. SNP variation analysis and allelic group analysis of 209 soybean accessions further prioritized GmCXE54 as a candidate gene for root isoflavone accumulation. Allelic groups defined by a putative promoter SNP, Chr.20-rs39215413, showed significant differences in root daidzein and total isoflavone contents, with accessions carrying the C allele exhibiting higher levels of both traits than those carrying the T allele. Functional analysis in soybean hairy roots showed that GmCXE54 overexpression increased daidzein and total isoflavone accumulation. At 3 h after F. oxysporum inoculation, GmCXE2, GmCXE39, and GmCXE54 were induced, with GmCXE54 showing the strongest response in the resistant accession ZD27. These findings clarify GmCXE subfamily evolution and identify GmCXE54 as a candidate gene associated with root isoflavone accumulation and early F. oxysporum response, offering new perspectives for improving soybean isoflavone-related traits and investigating root response mechanisms. Full article

The discrepancy between in situ microbial abundance and actual metabolic performance represents a critical challenge for interpreting microbial function from meta-omic data. Here, we integrated metagenomic and metatranscriptomic sequencing to investigate this decoupling between microbial abundance and cultivation-based physiological potential in Shanxi aged vinegar (SAV) solid-state fermentation. Lactobacillus acetotolerans dominated the community at both the genomic (40.89%) and transcriptomic (55.36%) levels, whereas Pediococcus acidilactici accounted for only 0.11%—a canonical rare-biosphere member. Source tracking via Sankey analysis showed that genes involved in acetate production were primarily attributed to Acetobacter pasteurianus, whereas genes involved in lactate production were predominantly associated with Lactobacillus spp. However, L. acetotolerans exhibited limited acid tolerance and lactic acid production, whereas the low-abundance P. acidilactici AAF1-5 displayed robust stress tolerance and superior lactic acid production under fermentation-relevant conditions—a striking contrast between microbial abundance and physiological performance. Metabolic interaction network analysis predicted that P. acidilactici may be co-inhibited by L. acetotolerans (I_xy = −2.737, resource competition) and A. pasteurianus (I_xy = −1.887, acid stress). To test whether ecological constraints, rather than intrinsic metabolic capacity, underlie this low abundance, we heterologously expressed the heat shock co-chaperone gene grpE from A. pasteurianus in P. acidilactici AAF1-5 as an experimental tool. The recombinant strain P. acidilactici-grpE exhibited significantly enhanced viability under acetic acid stress and, in simulated SAV fermentation, lactic acid content increased by 23.63% compared with the wild-type control. These results demonstrate that meta-omic abundance does not necessarily predict physiological performance and that low abundance may reflect ecological constraints rather than intrinsic functional deficiency. Our study provides an ecological framework for linking microbial abundance with physiological function beyond sequence-based abundance inference in complex fermentation microbiomes. Full article

Candidatus Hepatincolaceae is a poorly characterized family of obligate Alphaproteobacterial symbionts that are widely detected in ecdysozoans. They were previously assumed to play a nutrient-scavenging role in the gut lumen. In this study, two high-quality metagenome-assembled genomes (MAGs, 1.39 Mb and 1.48 Mb in size) were recovered from the gut of the snapping shrimp Alpheus brevicristatus via metagenomic sequencing. Phylogenetic and whole-genome similarity analyses confirm that these two MAGs represent two novel, undescribed genera within the family Ca. Hepatincolaceae. Metabolic reconstruction reveals that they not only retain the canonical nutrient-scavenging pathways conserved across all Hepatincolaceae members, but also encode previously undocumented functional modules for antioxidant defense, vitamin B₁ and B₂ biosynthesis, and short-chain fatty acid production. They maintain a high oxygen-affinity cytochrome bd terminal oxidase to thrive in the anoxic gut microenvironment. Consistent with their symbiotic lifestyle, their genomes exhibit typical signatures of reductive evolution, such as reduced genome size, low GC content, and gene loss in amino acid and nucleotide de novo biosynthesis pathways. This study presents the first reported high-quality genomes of marine Ca. Hepatincolaceae symbionts, which are predicted to possess multiple metabolic functions extending beyond nutritional mutualism. Full article

Fruit ripening is accompanied by extensive reprogramming of secondary metabolism, which determines the antioxidant value of medicine-food homologous fruits. Ziziphus jujuba Mill. cv. ‘Junzao’ (Junzao) is a high-quality cultivar rich in bioactive compounds, yet its stage-dependent metabolite accumulation and the corresponding antioxidant capacity remain poorly resolved. In this study, widely targeted metabolomics was combined with the quantification of total phenolic (TPC), total flavonoid (TFC), and total triterpenoid (TTC) contents and with 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical (ABTS) radical-scavenging assays to profile Junzao fruits at five developmental stages. A total of 2388 secondary metabolites were identified, with flavonoids and terpenoids representing the major classes. TPC and TFC were highest at the immature YG (young-fruit) stage, whereas TTC peaked at the BS (white-ripe) stage; all three decreased during subsequent ripening, consistent with the stronger DPPH and ABTS radical-scavenging activities observed in early-stage fruits. Multivariate analyses revealed distinct metabolic profiles among developmental stages, and 2111 differentially accumulated metabolites (DAMs) were identified. K-means clustering resolved nine temporal accumulation patterns, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated dynamic regulation of flavonoid biosynthesis, phenylpropanoid metabolism, and triterpenoid-related pathways. Spearman correlation analyses further identified ten metabolites, comprising six flavonoids, three triterpenes, and one phenolic acid, that were strongly associated with antioxidant capacity (|r| ≥ 0.5, p < 0.05), highlighting their potential as biomarkers for quality evaluation. Overall, immature Junzao fruits exhibited superior antioxidant capacity, supporting their promise as functional-food ingredients and providing a basis for stage-specific harvesting and utilization. Full article

Background/Objectives: To describe the genetic resolution rate, molecular findings, and genotype–phenotype correlations of non-ABCA4 and non-BEST1 inherited macular dystrophies (IMDs) within an Irish inherited retinal disease (IRD) registry. Methods: Retrospective review of individuals with a clinical diagnosis of macular or cone dystrophy. Comprehensive phenotyping (dilated ocular biomicroscopy, multimodal retinal imaging, visual electrophysiology) and genetic testing (panel-based next-generation sequencing, single-gene testing, whole exome/genome sequencing, WES/WGS). Variants were interpreted using ACMG AMP criteria, and genotype-phenotype match was confirmed through multidisciplinary review. Results: 232 patients with macular/cone dystrophies were identified. ABCA4 and BEST1 accounted for most molecular diagnoses (47.4%). Removing ABCA4 and BEST1, 59.0% of IMDs were genetically unresolved, higher than the rate in general IRD cohorts. Deep phenotyping enabled diagnostic reclassification in 13/72 (18.1%), namely achromatopsia, congenital stationary night blindness, and oculocutaneous albinism. Further genetic testing resolved 35/72 (48.6%) of those unresolved on first-line testing, with PRPH2 being most prevalent (n = 12), followed by GUCY2D, CRB1, PROM1, and CRX. Characteristic phenotypic signatures—such as CRB1-associated retinal thickening and retinoschisis or PROM1-associated Stargardt-like changes—supported known genotype–phenotype correlations. Conclusions: Genetic resolution rates for rare IMDs remain lower than pan-retinal IRD phenotypes. Beyond ABCA4 and BEST1, IMDs exhibit substantial genetic and phenotypic heterogeneity (24 genotypes in this cohort), with low molecular diagnostic rates despite comprehensive sequencing approaches. Detailed multimodal phenotyping (i.e., structural, functional and extra-ocular) is essential to refine diagnosis, guide genetic testing and interpret candidate variants. Genetic testing is challenging when the retinal phenotype is advanced (i.e., atrophy) or lacks pathognomonic features. Meticulous phenotyping (functional, structural and systemic) and broader genomic strategies (e.g., WES/WGS) may further increase diagnostic yield, though gene panel content is constantly improving. Consistently improving molecular diagnostic rates will ensure equitable access to emerging gene-specific therapies. Full article

Foodborne illnesses caused by Salmonella Typhimurium remain a major public health concern worldwide. Although ST19 has historically been a dominant lineage within this serotype, ST213 has become increasingly prevalent in Mexico. The biological factors underlying this epidemiological shift remain incompletely understood. In this study, we compared virulence-associated gene repertoires and stress-related phenotypes in representative S. Typhimurium ST19 and ST213 strains with distinct virulotypes (VTs). Comparative genomic analysis identified 119 virulence-associated genes distributed across 26 VTs, with most genes broadly conserved between genotypes. Representative strains were evaluated under simulated gastrointestinal tract (GIT) stress conditions, in post-stress recovery assays, and in a Caenorhabditis elegans infection model. Under the experimental conditions evaluated, the representative ST213 strains SAL109 (VT1), SAL115 (VT1), and SAL016 (VT12) tended to show higher persistence under host-associated stress conditions and greater intestinal colonization capacity in C. elegans than the ST19 strain SAL004 (VT23). However, strains sharing the same VT did not necessarily exhibit similar phenotypes, indicating that virulence-associated gene repertoires alone do not fully explain stress tolerance or host colonization behavior. Overall, these findings highlight phenotypic variability among strains with similar virulence gene content and support the importance of integrating genomic and phenotypic approaches to better understand the biology of emerging S. Typhimurium lineages. Full article

Pleurotus ostreatus is an important edible mushroom, and its growth and development are affected by genetic and epigenetic mechanisms. miRNAs play an important role in fungal epigenetic mechanisms. In previous studies, Po-3KAT was identified as a candidate target of Po-milR-1, and its product was a substrate for ergosterol synthesis. However, the potential relationship between Po-milR-1 and Po-3KAT has not been studied in P. ostreatus. Therefore, this study aims to explore the potential role of Po-milR-1 and Po-3KAT in P. ostreatus. By integrating the Po-milR-1 interference vector into the genome of P. ostreatus, it was found that the mycelial growth rate was accelerated and the fruiting body phenotype changed in the Po-STTM transformants. The expression analysis during development suggested an inverse expression pattern between Po-milR-1 and Po-3KAT. The analysis of qRT-PCR and HPLC showed that 2 mmol/L H₂O₂ promoted the expression of Po-3KAT, and the content of ergosterol increased to 1.17-fold, while 5 mmol/L H₂O₂ inhibited the expression of Po-3KAT, and the content of ergosterol decreased to 0.82-fold. In contrast to oxidative stress, 100 mmol/L and 250 mmol/L salt stress inhibited the expression of Po-3KAT, and the content of ergosterol decreased to 0.87-fold and 0.94-fold, respectively. These results suggest that Po-milR-1 and Po-3KAT may be involved in the regulation of growth, development, and stress responses in P. ostreatus, and may be associated with the change in ergosterol content. Full article

Xyloglucan endotransglucosylase/hydrolases (XTHs) are key cell-wall-remodeling enzymes that mediate xyloglucan modification, cell expansion, and organ elongation, yet the composition and variation in the XTH gene family across tea accessions remain unclear. In this study, we systematically identified and comparatively analyzed the XTH gene family across the genomes of nine tea accessions, yielding 477 putative XTH genes. Phylogenetic, conserved-motif, protein-domain, and conserved catalytic-motif analyses indicated that the major structural features of tea XTH proteins are broadly conserved, whereas orthogroup-based presence–absence variation (PAV) analysis revealed core, variable, and accession-specific components within the family. Using transcriptomic expression profiles across eight tissues, we selected eight CsXTH genes for internode expression analysis. Reverse transcription quantitative PCR (RT-qPCR) showed that all eight genes were expressed at significantly higher levels in the third internode (I3) than in the second internode (I2) in ‘Longjing 43’ (LJ43), and CsXTH27 retained the same internode-associated expression pattern in ‘Baihaozao’ (BHZ) and ‘Zhongcha 108’ (ZC108), supporting its selection for functional analysis. Transient overexpression of CsXTH27 significantly increased the lengths of I2, I3, and I4, as well as the total length of I1–I4, compared with the empty-vector control. This phenotype was accompanied by significantly increased XTH protein content in stems and an apparent tendency toward larger pith parenchyma cell profiles. Overall, these findings reveal both structural conservation and accession-level variation in the tea XTH gene family and provide preliminary functional evidence linking CsXTH27 to shoot internode elongation. Full article

The rising global food demand requires boosting agricultural productivity without compromising environmental sustainability, especially in the face of intensive agrochemical use and soil degradation. Based on this, strain TRQ67 was isolated from wheat rhizosphere soil in the Yaqui Valley, Mexico, and characterized morphologically, biochemically, and genomically. Strain TRQ67 possesses a genome of 4.04 Mbp across 37 contigs with a G + C content of 46.3%, comprising 4127 coding DNA sequences (CDSs), and was identified as Bacillus velezensis through Overall Genome Relatedness Indices (OGRIs), including Average Nucleotide Identity (OrthoANI = 99.12%) and Genome-to-Genome Distance Calculator (Formula 2: 92.6%). The genome revealed key functional genes associated with auxin biosynthesis (trpABCDEF and yhcX), iron acquisition (dhbABF), nutrient solubilization (gabD, acnAB and pyc), stress response (clpCEPX and pspA), antifungal metabolite synthesis (srfAABCD, fenABCD and bmyABC), chemotaxis and motility (cheABCD, motAB, flgBCDEF, swrC), bacterial fitness (acoABR, acuABC and budABC), exopolysaccharide production (epsDEFHI), sporulation (spo0ABEF) and bioremediation. Predicted gene functions were supported by in vitro phenotypic assays; strain TRQ67 was able to solubilize phosphate (Solubilization Index of 4.1 ± 0.46), biosynthesize siderophores (Production Index of 1.70 ± 0.16), and produce indoles (6.52 ± 0.63 µg mL⁻¹). Furthermore, this strain demonstrated antagonistic activity against phytopathogenic fungi Fusarium languescens and Bipolaris sorokiniana, resulting in reductions in fungal growth area of 87.33% and 89.28%, respectively. These antagonistic effects are consistent with the presence of Biosynthetic Gene Clusters (BGCs) encoding lipopeptides (surfactin and fengycin), polyketides (difficidin, bacillaene and macrolactin H), dipeptides (bacilysin) and siderophores (bacillibactin), as identified through antiSMASH analysis. Finally, the strain significantly improved root (27.63%) and shoot (5.82%) biomass in wheat plants under controlled conditions. These results highlight Bacillus velezensis TRQ67 as a promising microbial inoculant with plant growth promotion capabilities and potential antifungal activity against phytopathogenic fungi, as evidenced by strong in vitro antagonistic activity, supporting its further evaluation for sustainable agricultural practices. Full article

Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded our ability to identify and interpret SVs across plant species. In this review, we summarize recent progress in understanding the formation mechanisms, classification, and functional consequences of plant SVs. We discuss major sources of SV generation, including transposable element activity, non-allelic homologous recombination (NAHR), horizontal gene transfer (HGT), and genome restructuring following polyploidization. We further highlight how LRS and graph-based pan-genomes overcome limitations of traditional linear reference genomes and enable more comprehensive characterization of genetic diversity. Beyond variant discovery, we emphasize the importance of integrating genomic, transcriptomic, epigenomic, proteomic, metabolomic, and spatial omics datasets to decipher how SVs influence gene regulation and complex agronomic traits. We also discuss current challenges, including repetitive genomes, polyploidy, computational complexity, and translation of SV knowledge into practical breeding applications. Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement. Full article

Background/Objectives: The emergence of plasmid-mediated mcr genes has enabled horizontal dissemination of resistance to colistin, a last-resort antibiotic against multidrug-resistant Enterobacterales. In Tunisia, genomic data on mcr-positive Escherichia coli are still limited. This study reports the genomic characterization of human clinical mcr-positive E. coli isolates from the Military Hospital of Tunis. Methods: Between August 2023 and March 2025, seven E. coli isolates with low-level colistin-resistance (MIC = 4–8 µg/mL) were collected from six patients. They were characterized by antibiotic susceptibility testing and WGS to determine resistome, MLST, genetic relatedness, and plasmid content. Results: The E. coli isolates belonged to diverse sequence types (STs), except for two isolates collected from the same patient 2.5 months apart, which were highly related. Overall, this pattern is consistent with a polyclonal spread. The mcr-1.1 gene was located on IncI2 (n = 5) or IncX4 (n = 2) plasmids, which exhibited high similarity both among themselves and in comparison with plasmids previously reported in human and livestock isolates. Most isolates were multidrug-resistant, harboring acquired resistance genes to multiple antibiotic classes, and chromosomal mutations conferring fluoroquinolone resistance. Three isolates additionally carried chromosomal insertions of the bla_CTX-M-55 gene. Resistance to cefiderocol was observed in one isolate and was associated with CirA and Fiu truncation. Conclusions: These findings highlight ongoing dissemination of mcr-1.1-positive E. coli isolates in Tunisia, primarily driven by plasmid transfer. Continuous genomic surveillance and One Health-oriented antibiotic stewardship are essential to limit the spread of colistin-resistance and the emergence of resistance to newer agents such as cefiderocol. Full article

Sugarcane (Saccharum spp. hybrid) is the most important sugar crop. However, its genetic improvement is severely constrained by genotype-dependent regeneration recalcitrance and lengthy tissue culture cycles. Here, we established a simple, efficient, and genotype-flexible in planta transformation system using two-leaf-stage plantlets. By systematic optimization of three key parameters: Agrobacterium cell density (OD₆₀₀ = 0.5), dark incubation duration (2 weeks), and infection frequency (two rounds), we achieved a maximum transformation efficiency of 51.2%. The protocol was successfully applied to eight diverse sugarcane varieties, with transformation efficiencies ranging from 33.3% to 51.2%, demonstrating broad genotype applicability. Using this optimized system, we introduced Sh4CL13 into sugarcane. Transgenic lines exhibited a 3.25-fold increase in Sh4CL13 transcript levels and a 13.7-fold elevation in chlorogenic acid (CGA) content compared to controls. Feeding bioassays with Mythimna separata larvae revealed that transgenic lines significantly prolonged larval developmental duration, reduced pupal weight, and decreased adult emergence rates. This in planta transformation system bypasses tissue culture, offers a practical platform for functional genomics and molecular breeding in sugarcane and potentially other monocot crops. Full article

Sorghum is a strategic food-security and livestock-feed crop in Africa, and molecular characterization of its germplasm underpins genetic diversity assessment and hybrid parent selection. This study evaluated 106 sorghum accessions (23 A-lines, 28 B-lines, 32 R-lines, and 23 hybrids) from ICRISAT and Seed Co gene banks using 79 single nucleotide polymorphism (SNP)-based Kompetitive Allele-Specific PCR (KASP) markers. Genetic diversity, population structure, cluster analysis, and analysis of molecular variance (AMOVA) were assessed to support heterotic grouping. Gene diversity ranged from 0.23 in R-lines to 0.32 in hybrids, and polymorphic information content from 0.19 to 0.26, indicating moderate marker discriminatory power. Population structure analysis identified an optimum of K = 3: Cluster 1 comprised paired A- and B-lines forming a putative maintainer pool, Cluster 2 was dominated by R-lines forming a divergent restorer pool, and Cluster 3 formed a second seed-parent subgroup. AMOVA confirmed highly significant differentiation (ΦST = 0.55; p < 0.001), with molecular variance partitioned among the three clusters (44.0%), among individuals within clusters (45.2%), and among breeding-line types (10.8%). These findings provide a genomic framework for assigning sorghum accessions to putative heterotic groups and accelerating hybrid parent selection for climate-resilient sorghum production. Full article