Search Results (10,317)

The AP2/ERF superfamily is a key class of transcription factors involved in plant responses to various stresses. As an ancient species, the olive tree (Olea europaea L.) exhibits considerable stress tolerance and wide adaptability. In this study, we identified 348 AP2/ERF genes in the cultivated olive variety ‘Arbequina’ at the whole-genome level. According to protein sequence alignments and phylogenetic analyses via the Maximum Likelihood method, these genes were classified into four major families: AP2, ERF/DREB, RAV, and Soloist. The ERF/DREB family was further divided into DREB and ERF subfamilies, each encompassing six groups (A1–A6 and B1–B6), with the ERF subfamily being the largest. Members of each group exhibited relatively consistent gene structures and domain/motif compositions of their encoded proteins; however, the distribution of cis-elements and expression patterns varied. Each AP2/ERF gene contained 12 light-responsive, three MeJA-responsive, three ABA-responsive, two anaerobic induction, and one MYB binding site on average. With the threshold of p value < 0.5, control TPM > 0, and |log₂(fold change)| > 0, 50 candidate genes were simultaneously up-regulated (30) or down-regulated (20) under four stress treatments (acid–aluminum, cold, disease, and wound), among which nine showed potential protein–protein interactions. This study provides a comprehensive genomic characterization of the AP2/ERF family in olive and identifies key candidate stress-responsive genes, establishing a foundation for future functional studies on the molecular mechanisms of stress adaptation in the olive tree. Full article

RNA viruses exhibit high mutation rates and strong host adaptive capacity, posing major public health challenges. Although meta-transcriptomic studies have uncovered vast numbers of novel RNA viral sequences, identifying those with spillover risks remains difficult. Current virus host-prediction methods can only predict a narrow set of host labels at coarse taxonomic levels (e.g., kingdom or order), which hampers precise evaluation of cross-species transmission risk and may overlook potential zoonotic hosts. To overcome these limitations, we developed UniVH, a unified virus–host association prediction framework trained on an exceptionally broad spectrum of 90 viral families and 240 host families, enabling robust prediction even for phylogenetically distant or data-scarce hosts. UniVH achieved a host prediction accuracy of 71.2% for novel viruses discovered after 2020, representing a 15.3% improvement over conventional BLASTp-based homology approaches. Feature interpretation revealed that viral structural genes and host immune- and metabolism-related genes contributed most significantly to predictive performance. Model predictions indicated widespread host-range expansion, with 20 mammalian virus families doubling their documented mammalian host ranges and several showing marked increases in viruses with human-infection potential. This unified, interpretable framework represents an important methodological advance for future RNA virus spillover-risk evaluation and emerging virus prioritization. Full article

Restriction–modification (RM) systems contribute to genome plasticity in Mycoplasma hominis, a facultative pathogen with an extremely small but highly heterogeneous genome. The MhoVII RM system, which contains a fusion of two methyltransferases (MTases), M1 and M2, was recently identified within a family of Type II RM systems, but its specificity and biological function remained unknown. Phylogenetic analysis revealed that M1 and M2 belong to distinct MTase classes clustering within the YhdJ and MTaseD12 branches, respectively. In this study, the dissemination, expression and function of the MhoVII system was analyzed in detail using Oxford Nanopore-based methylation analysis, recombinant expression of the individual RM components in Escherichia coli, and methylation-sensitive restriction assays. It was thus possible to demonstrate that M1 and M2 methylate the complementary non-palindromic motifs GATG and CATC, and that the associated restriction endonuclease cleaves only DNA lacking 6mA methylation at these sites. The transcriptional analysis of mid-to-late logarithmic cultures indicated a polycistronic organization of the MhoVII genes, and GATG/CATC-driven methylation analysis revealed culture-dependent methylation differences, suggesting a post-transcriptional regulation, whereas in the infection of HeLa cells, MhoVII transcription was highest at the beginning and was then gradually downregulated in the later stages of infection. These findings establish MhoVII as a previously uncharacterized Type II RM system. Full article

Toll-like receptors (TLRs) are essential pattern recognition receptors of the innate immune system and play critical roles in pathogen invasion in teleosts. In this study, we identified and characterized full-length open reading frames of three TLRs belonging to the TLR11 subfamily from Schizothorax prenanti, termed spTLR19 (2868 bp), spTLR20 (2835 bp), and spTLR21 (2946 bp), encoding 955, 944, and 981 amino acids, respectively. All three proteins exhibited the conserved domain architecture typical of TLRs, comprising a leucine-rich repeat (LRR) domain, a transmembrane region, and a Toll/IL-1 receptor (TIR) domain. Phylogenetic and homology analyses revealed that spTLR19 and spTLR20 clustered most closely with their homologues from Cyprinus carpio, while spTLR21 showed the highest similarity to Onychostoma macrolepis TLR21. Expression profiling showed that these TLRs were ubiquitously expressed across examined tissues, with relatively higher expression in immune-related tissues such as spleen and gills. Furthermore, challenge with Streptococcus agalactiae and Aeromonas veronii significantly up-regulated the expression of spTLR19, spTLR20, and spTLR21 in spleen, liver, and gills, suggesting their involvement in antibacterial immune responses. These findings enhance the functional understanding of the teleost TLR11 subfamily and provide a foundation for elucidating disease resistance and immune regulation in S. prenanti. Full article

The grapevine (Vitis vinifera L.) is one of the most important horticultural crops, with thousands of varieties cultivated worldwide. In this study, we analyzed chloroplast SNV markers using a whole-genome shotgun sequencing approach to investigate the genetic diversity and phylogeny of 409 cultivated V. vinifera accessions originating from nine countries across Southeast and Central Europe, as well as a heterogeneous set of additional accessions maintained by INRAE. Shotgun sequencing allowed high coverage, enabling the detection of 93 SNVs across 24 chloroplast genes, including 11 non-synonymous variants. The ycf1 gene showed the highest variability, consistent with its role in species differentiation. Haplotype analysis revealed 102 distinct haplotypes, with clear geographic structuring: ATT predominated in the eastern Mediterranean, ATA in western Europe, and GTA mainly in a heterogeneous group of varieties from a French collection. To validate the shotgun approach, seven SNV markers were analyzed using target capture sequencing, confirming the accuracy of detected variants with only minimal discrepancies, which is mostly attributable to homopolymeric regions and low-frequency alleles. Phylogenetic analyses using both trees and networks delineated three major haplotype clusters, reflecting human-mediated dispersal of grapevine cultivars through historical viticultural practices. This study represents the largest chloroplast genome analysis of cultivated V. vinifera to date, providing a large cpDNA resource for assessing chloroplast diversity and maternal haplotype structure in cultivated grapevine. The results highlight the power of combining high-throughput sequencing and chloroplast genomics for population-level studies in perennial crops. Full article

Background: Intensive poultry production systems can act as reservoirs for antibiotic-resistant and multidrug-resistant (MDR) Escherichia coli, posing a public health risk through food and environmental transmission. Methods: This study investigated the genomic characteristics of antibiotic-resistant E. coli isolated from an intensive poultry production system in the uMgungundlovu District, KwaZulu-Natal, South Africa. Chicken litter, wastewater, and floor swab samples were collected over three consecutive production cycles. Putative E. coli isolates were detected using the Colilert-18 system, cultured on eosin methylene blue agar, and genomically confirmed by quantitative PCR (q-PCR) targeting the uidA gene. Whole genome sequencing was performed using the Illumina MiSeq platform, followed by bioinformatic analyses to assess resistance genes, mobile genetic elements, and phylogenetic relationships. Results: Of 150 presumptive E. coli, 70 were genomically confirmed as E. coli and resistant to at least one antibiotic, with 74% exhibiting multidrug resistance. Resistance was highest to tetracycline (100%), ampicillin (94%), and trimethoprim–sulfamethoxazole (76%), while ciprofloxacin resistance was rare (3%). Genomic analysis identified multiple antibiotic resistance genes conferring resistance to fluoroquinolones, β-lactams, aminoglycosides, amphenicols, fosfomycin, and sulfonamides, as well as the disinfectant resistance gene qacI. These genes were frequently associated with mobile genetic elements, including plasmids, integrons, transposons, and insertion sequences. Predominant sequence types included ST155, ST48, ST1286, and ST602, with phylogenetic relatedness to poultry-associated isolates from Cameroon, Ghana, Nigeria, and Tanzania, as well as environmental E. coli strains previously identified in South Africa and Ghana. Conclusions: The detection of diverse, mobile MDR E. coli lineages in poultry environments clearly signals a substantial risk for resistance gene dissemination into the food chain and surrounding ecosystems. Immediate attention and intervention are warranted to mitigate public health threats. Full article

The global rise of multidrug resistance (MDR) across bacterial pathogens poses a severe threat to public health, with the food chain serving as a critical reservoir and transmission route for resistant clones. This study investigated the genomic epidemiology of Staphylococcus aureus in retail pork from Beijing, China, and Copenhagen, Denmark, with a focus on MDR patterns and associated genetic elements. Among 134 isolates, the livestock-associated clonal complex CC398 was the dominant lineage (24.63%) and exhibited a high burden of MDR (48.48%), carrying resistance genes to β-lactams (blaZ and mecA), tetracyclines (tetM and tetK), and aminoglycosides. Notably, MRSA isolates displayed a significantly higher MDR prevalence (73.53%) compared to MSSA isolates (18.00%), underscoring methicillin resistance as a key marker for broader resistance phenotypes. Phylogenetic analysis revealed the segregation of CC398 into distinct sub-lineages, with the livestock-associated branch consistently linked to a characteristic tetracycline–β-lactam MDR profile. Furthermore, high frequencies of mobile genetic elements, such as the rep16 plasmid, were associated with MDR dissemination in CC398. These findings highlight retail meat as an important reservoir for MDR S. aureus and illustrate how livestock-adapted clones contribute to the environmental burden of antimicrobial resistance. This study underscores the need for integrated One Health surveillance that connects veterinary, food safety, and human health sectors to monitor and contain the spread of MDR bacteria across ecological niches. Full article

Deep-sea octopuses of the genus Graneledone currently include ten recognized species, yet their phylogenetic relationships remain insufficiently resolved. Here, we provide molecular phylogenetic analyses for eight species based on three mitochondrial markers (16S, COIII, COI) and formally describe a new species from the southeastern Pacific off south-central Chile. Four specimens previously reported lacked evidence necessary for taxonomic validation; in this study, we examine eight additional individuals collected between 436 and 1482 m depth, generating new mitochondrial sequences and proposing an updated phylogenetic hypothesis for the genus. Species delimitation analyses strongly support the recognition of a new species. The newly described octopus is medium-sized, lacks an ink sac, and bears a single series of suckers on arms of similar length. Key diagnostic traits include 43–45 suckers on the hectocotylized (right third) arm, six to seven gill lamellae per demibranch, a VV-shaped funnel organ, and five to seven transverse folds on the ligula. Among all examined characters, the number of opposite suckers provides the most robust morphological distinction from congeners distributed across the Pacific, Atlantic, and Antarctic oceans. Our results highlight the value of integrative taxonomy in resolving species boundaries within Graneledone and reveal previously undocumented diversity in the deep Southeastern Pacific. Continued sampling and molecular analyses will be essential for identifying additional cryptic lineages and refining evolutionary hypotheses for this poorly explored deep-sea octopod lineage. Full article

Chikungunya virus (CHIKV) poses an increasing global public health threat, as evidenced by the significant 2025 Foshan outbreak in China. Rapid, whole-genome sequencing (WGS) is critical for outbreak response but is challenged by primer mismatches across diverse lineages and a lack of direct sequencing platform comparisons. To address this, we developed a novel lineage-inclusive primer set and performed parallel WGS on 24 clinical samples from the outbreak using both Illumina (NGS) and Oxford Nanopore Technologies (TGS) platforms. Our lineage-inclusive primer set successfully amplified full-length CHIKV genomes across all samples. Comparisons revealed that Illumina NGS provided higher raw read accuracy, while Nanopore TGS achieved more complete coverage of terminal UTRs with a faster turnaround time. Crucially, after polishing, variant calls between the two platforms were 100% concordant. Phylogenetic analysis was consistent with a single introduction event, with all outbreak isolates forming a monophyletic clade within the ECSA lineage most closely related to contemporaneous strains from Réunion Island. This study validates a lineage-inclusive amplicon-based sequencing strategy and demonstrates that NGS and TGS offer complementary advantages. When integrated, they provide a robust framework for real-time genomic surveillance, enhancing preparedness and guiding public health interventions against CHIKV. Full article

Rotavirus A (RVA) is a leading cause of severe diarrhoea in children, and interspecies transmission significantly drives the genomic diversity of human RVAs. Cats represent a key host species, requiring in-depth analysis regarding RVA transmission to humans. This review evaluated the literature on the complex genotype constellations of feline RVAs in relation to relevant canine and human RVAs to define the role of feline RVAs in the evolutionary history of human strains. The review traces the methodological shift from genogrouping by RNA-RNA hybridisation to the current genotype constellation system enabled by whole-genome sequencing. While early methods identified a shared genomic closeness between human AU-1 and feline FRV-1, whole-genome sequencing indicated that several human RVA strains, including AU-1, HCR3A, and Ro1845, likely resulted from direct transmission of feline/canine strains, due to shared genotype constellations and high sequence identity with animal strains like feline FRV-1, Cat97 and canine CU-1. Evidence of reassortment—such as the emergence of G1P[9] and G9P[9] strains after the feline-derived G3P[9] crossed into the human population—suggests these feline-like strains have successfully overcome the host-species barrier and are capable of onward human-to-human transmission, not just dead-end spillover events. However, definitive confirmation of sustained transmission or contemporary spillover requires stringent phylogenetic criteria: multiple human strains with >99% identical sequences in a monophyletic lineage for sustained transmission, or an identical human–feline pair across all genome segments for contemporary spillover. Confirming the status of the AU-1-like constellation as a third, low-frequency human RVA type requires future studies applying these strict criteria. Full article

Recent advances in high-throughput sequencing technologies have significantly enhanced the accuracy of phylogenetic inference, enabling comprehensive genome-wide analyses. Fusarium fungi, which include numerous agriculturally and medically important species, are typically classified at the species complex (SC) level. Clarifying the evolutionary relationships and distinctiveness of these SCs is therefore essential for accurate identification and understanding of their biology. Recent large-scale phylogenetic studies based on genomic data have provided a more resolved understanding of the evolutionary relationships among Fusarium SCs, supporting the view that most represent evolutionarily coherent and stable lineages. However, the phylogenetic position of Fusarium commune has not been explicitly examined, despite incongruence between phylogenies inferred from nucleotide and amino acid sequence data. This study aimed to clarify the phylogenetic placement of F. commune at the SC level by re-examining its position using a genome dataset independent of those employed in previous studies. Our results are largely consistent with previously reported genome-scale phylogenetic analyses of the genus Fusarium and support the stability of most SCs. However, F. commune was not clearly included in any of the currently recognized SCs and instead formed an independent lineage. These findings provide insights into the evolutionary history of Fusarium SCs and contribute to a better understanding of the taxonomic position of F. commune. Full article

Barnyard grass, a widespread and persistent weed in rice paddies, belongs to the same family as rice and may act as a bridge host for the rice blast fungus. This study utilized comparative genomics to analyze six Pyricularia oryzae strains isolated from barnyard grass (Baicao series) and rice (GDYJ7 and ZJX18), integrating pathogenicity assays, whole-genome sequencing, and functional annotation. Pathogenicity tests demonstrated host specificity, as Baicao series strains caused typical lesion symptoms on barnyard grass but not on rice leaves, while GDYJ7 and ZJX18 caused lesions mainly on rice. Genomic analyses indicated that Baicao series strains possessed larger genomes (41.04 Mb to 41.16 Mb) with a higher content of repetitive sequences (6.68% to 7.09%) compared to rice strains GDYJ7 and ZJX18 (38.69 Mb and 39.05 Mb; 3.66% and 3.71% repeats). Phylogenetic analysis confirmed that Baicao series strains represent a grass-infecting pathotype of P. oryzae species, as they were grouped with the established grass-isolated P. oryzae strains, while GDYJ7 and ZJX18 were grouped with rice-isolated P. oryzae strains. However, Baicao series, GDYJ7 and ZJX18 are all relatively distant from P. grisea species. PCR amplification revealed that Baicao series strains harbored significantly fewer avirulence genes (Avr-Pib, Avr-Pizt, PWL3) than GDYJ7 and ZJX18 (Avr-Pib, Avr-Pizt, Avr-Pi9, Avr-Pik, PWL2), with Baicao9 retaining only Avr-Pib. In summary, our results suggested that the genomic sequences of the barnyard grass-isolated strains serve as a valuable resource for the study of P. oryzae strains with differential host preference and provide novel insights into the evolution of pathogen genomes during host adaptation. Full article

Different crops have varying effects on soil factors, and their associated microbial community compositions also differ. Currently, there is limited comparative research on crops with distant phylogenetic relationships, such as those between gramineous and leguminous species. In this study, a pot experiment combined with high-throughput sequencing was conducted to enable a detailed comparison of microbial communities and soil factors across four crops: wheat, soybean, and two maize varieties. Compared to leguminous crops, differences between gramineous crops may be relatively smaller. The results showed that among the gramineous and leguminous crops, soybean had the lowest effect on soil electrical conductivity (EC) and available phosphorus (AP) (121.68 ± 2.70, 34.74 ± 1.02). The dominant fungi and bacteria phyla were Ascomycota and Proteobacteria; both were most abundant in the ZD958 variety, at 75.12% and 30.47%, respectively. The fungal diversity of ZD958 was most similar to that of W998, whereas the bacterial diversity of XY335 more closely resembled that of SB13. EC and AP were the key factors influencing fungal community composition, while alkali-hydrolyzable nitrogen (AN) was the key factor affecting bacterial community composition. These findings provide a basis for further in-depth research. Full article

Pseudolysimachion pyrethrinum var. gasanensis (Gasan spike speedwell) is a valuable Korean endemic variety with significant horticultural potential. Despite its morphological distinctiveness, its taxonomic status and evolutionary position have remained a subject of debate. In this study, we assembled and characterized the first complete chloroplast (cp) genome of P. pyrethrinum var. gasanensis using high-throughput sequencing. The complete plastome is 152,251 bp in length, exhibiting a typical quadripartite structure with a large single-copy (LSC) region (83,191 bp), a small single-copy (SSC) region (17,690 bp), and two inverted repeats (IRs) (25,685 bp each). The genome contains 133 genes, including 88 protein-coding, 37 tRNA, and 8 rRNA genes. Genomic analysis identified 42 simple sequence repeat (SSR) units across 38 distinct loci, predominantly mononucleotide A/T motifs, which serve as potential molecular markers for variety-level identification. Selective pressure analysis revealed that the majority of protein-coding genes are under strong purifying selection (Ka/Ks < 1.0), emphasizing the evolutionary stability of the plastome. Comparative analysis of IR boundaries using IRscope revealed a high degree of structural conservation among Pseudolysimachion species, with minor variations at the junction sites. Phylogenetic analysis based on 18 complete plastomes strongly supported the monophyly of the genus Pseudolysimachion (Bootstrap = 100%) and placed P. pyrethrinum var. gasanensis as a sister to the European P. spicatum. These genomic resources provide a foundational tool for the molecular breeding, systematic conservation, and sustainable utilization of this endemic variety, while offering clarity to its taxonomic classification within the tribe Veroniceae. Full article

Despite the central role of the gustatory nervous system in regulating feeding behavior in the larvae of the major agricultural pest Helicoverpa armigera, the systemic molecular basis of this process is largely unknown. To investigate the molecular basis, we performed RNA-seq on dissected brains and gnathal ganglion (GNG) from fifth-instar larvae, revealing 944 differentially expressed genes (DEGs) that are potentially involved in feeding behaviors. Bioinformatic analyses revealed significant enrichment of these DEGs in pathways including “taste transduction”, “neuroactive ligand–receptor interaction”, and “feeding behavior”. Furthermore, 41 candidate genes closely associated with feeding behaviors were screened, including neuropeptides, neuropeptide receptors, gustatory receptors, and feeding-mediated proteins. Phylogenetic analyses demonstrated that these key genes are evolutionarily conserved. Quantitative real-time PCR (qPCR) results confirmed that most of these candidate genes were significantly upregulated during the fifth instar stage, and their expression was further enhanced under starvation conditions (p < 0.05). Our study presents the first systemic feeding-mediated transcriptomic profile in the insect central nervous system and identifies key feeding-mediated genes in H. armigera larvae. These findings advance our understanding of the molecular basis of feeding in Lepidopteran pests and offer potential target genes for developing gustatory-based pest control strategies. Full article