Search Results (747)

In this study, we investigated the long-term evolutionary dynamics of human norovirus GII.17[P17] using the RNA-dependent RNA polymerase (RdRp) region and the VP1 capsid gene, integrating phylogenetics, time-scaled inference, phylodynamics, and structure-based analyses. Maximum-likelihood phylogenies of both genomic regions consistently resolved four major clades (Clades 1–4). VP1 patristic-distance distributions indicated higher within-clade diversity in the phylogenetically basal Clades 1 and 3, whereas Clades 2 and 4 showed lower diversity, consistent with recent demographic expansion. Similarity-plot analysis identified pronounced variability in the VP1 P2 domain, while the S and P1 domains remained comparatively conserved, supporting P2 as the primary hotspot of diversification. Bayesian time-scaled analyses estimated the most recent common ancestor around 1993 (VP1) and 2000 (RdRp) and revealed two major lineages (Clade 1/2 and Clade 3/4), with the split between Clades 3 and 4 occurring around 2016–2017. Bayesian skyline plots showed a marked increase in effective population size after 2013, and substitution-rate estimates indicated faster evolution in VP1 than in RdRp, with higher VP1 rates in the Clade 3/4 lineage than in Clade 1/2. Capsid dimer modeling further mapped high-confidence conformational B-cell epitopes and positively selected residues predominantly to the distal surface of P2, with broadly conserved spatial patterns across clades. Compared with the Clade 1 reference (Kawasaki323), Clade 2 accumulated numerous P2 substitutions, whereas Clades 3 and 4 retained fewer changes and remained closer to Clade 1 at the amino-acid level. Together, these results suggest lineage turnover within GII.17[P17] driven by constrained diversification at the P2 surface, potentially contributing to the recent predominance of the Clade 3/4 lineage. Full article

Codon usage bias is important for regulating protein translation efficiency and accuracy. The HSP90 gene, a pivotal gene in plants, maintains homeostasis in plant protein stress responses and organelle immune defense functions. We systematically examine codon usage preferences in six forage grass species and the regulatory mechanisms of the HSP90 gene in governing codon preference. A set of metrics is evaluated, including effective codon number (ENC), codon adaptation index, and relative synonymous codon usage. Neutral evolutionary trajectories reveal usage preferences for six plant codons, with natural selection serving as the primary driving factor. The correlation between the ENC–GC3 curve (ENC relative to third-position GC content in synonymous codons) and codon bias index reveals these genes to exhibit moderate codon bias. The phenomenon of evolutionary constraints is exemplified by a propensity for C/G-terminating codons, concomitant with a suppression of NUA/NCG codons (NUA is an abbreviation for UA dinucleotide, and NCG is an abbreviation for CG dinucleotide). Phylogenomic reconstruction reveals a conserved diversification pathway, positioning P. giganteum A. Rich. at the basal node of the evolutionary framework. This study identified through systematic assessment that natural selection is the primary evolutionary force driving the biased use of codons in grass HSP90 genes. This finding provides actionable insights for enhancing abiotic stress tolerance in forage germplasm through precise codon engineering. Full article

Liverwort organellar genomes are generally highly conserved, but the subclass Pellidae (simple thalloids) shows unusual variation. This ancient yet unexplored lineage of simple thalloid liverworts provides an excellent model for investigating organellar genome evolution. In this study, we assembled four new plastid and four new mitochondrial Pellidae genomes using Oxford Nanopore sequencing, supplementing 86 plastomes and 82 mitogenomes from databases. We assessed nucleotide diversity and codon usage, and inferred phylogenies using IQ-TREE with fossil-calibrated dating. Plastomes ranged 120.6–126.5 kb, and mitogenomes 109–180 kb, with Apopellia endiviifolia featuring an exceptionally reduced mitogenome (~109 kb). Native RNA sequencing enabled a revised annotation of the mitochondrial atp1 gene in Apopellia, revealing two introns (previously thought absent) and reducing the intergenic region share to 36.26%, the lowest known among liverworts. Comparative analyses revealed contrasting evolutionary dynamics between organelles: Plastomes displayed higher nucleotide diversity and phylogenetically inconsistent codon usage patterns, likely influenced by compositional bias, whereas mitogenomes were more conserved and largely consistent with established phylogenetic relationships among the orders. Phylogenomic analyses yielded discordant topologies: Chloroplast data recovered Pellidae as a monophyletic clade, whereas mitochondrial data placed Pelliales (Pellia/Apopellia) as basal Jungermanniopsida, rendering Pellidae paraphyletic. Within Pellidae-relevant clades, several major divergences were dated to the Carboniferous–Permian, but with systematic chloroplast–mitochondrial offsets. These results highlight recurrent organellar incongruence and the dynamic evolutionary history of Pellidae organellar genomes. Full article

Codon usage bias (CUB) in mitochondrial genomes reflects evolutionary forces such as mutation, selection, and genetic drift, yet its dynamics in early-diverging fungal lineages like Conidiobolus (Zoopagomycota) remain unclear. This study systematically analyzed mitochondrial core protein-coding genes (PCGs) from eight Conidiobolus species to elucidate the drivers of CUB and phylogenomic patterns. Nucleotide composition revealed pronounced AT richness (73.32% ± 3.38%) and low GC3 (13.40% ± 5.11%), indicating a preference for A/T-ending codons. Neutrality and ENC-GC3s plots demonstrated that natural selection, rather than mutation pressure, predominantly shaped codon bias, supported by weak GC12-GC3 correlations (slopes: 0.037–0.335) and significant ENC deviations from mutation-driven expectations. PR2-bias analysis further highlighted a strong bias toward A over T and C over G. Correspondence analysis linked major codon usage variations to GC3s, CAI, and FOP indices. Phylogenetic reconstructions based on relative synonymous codon usage (RSCU) and concatenated mitochondrial sequences revealed discordant topologies, particularly in the placement of C. polytocus and C. polyspermus, suggesting divergent evolutionary trajectories. Optimal codon analysis identified species-specific preferences dominated by A/T termini. These findings underscore natural selection as the primary force driving AT-biased mitochondrial CUB in Conidiobolus, while phylogenomic discordance highlights complex evolutionary pressures in this ecologically diverse fungal genus. This study provides foundational insights into mitochondrial genome evolution and codon adaptation mechanisms in early-diverging fungi. Full article

Salmonella enterica serotype Mbandaka has emerged as a significant foodborne pathogen in poultry, posing increasing public health risks through its zoonotic transmission from poultry sources to humans, yet critical gaps remain in understanding its transmission inter-host transmission and antimicrobial resistance (AMR) mechanisms within the poultry industry. In this study, we addressed these knowledge gaps by conducting a comprehensive genomic analysis of 1813 S. Mbandaka genomes, including genotyping, phylogenetic reconstruction, and pangenome analysis. The results revealed that S. Mbandaka exhibits a global distribution pattern, with sequence type 413 (ST413) representing the dominant lineage. Phylogenetic analysis revealed frequent close genomic relatedness between human and poultry-derived strains (SNP ≤ 10), suggesting poultry as a potential major zoonotic reservoir for human S. Mbandaka infection. Furthermore, close genetic relationship was also detected among the human-derived strains, suggesting the potential community spread. In addition, genomic analysis indicated an increase over time in the number of antimicrobial resistance genes (ARGs) detected per genome, frequently associated with plasmids and insertion sequences (ISs). Notably, the ARGs significantly enriched in Chinese strains were primarily associated with the Col(pHAD28) plasmid. Comparative analysis demonstrated that the ARG profiles of S. Mbandaka were similar to those of other Salmonella serovars, suggesting the potential for cross-species transmission. In conclusion, these findings represent a large-scale retrospective genomic analysis of publicly available whole-genome sequences and elucidate the transmission dynamics and AMR mechanisms of S. Mbandaka in poultry, providing insights into its risks to poultry production and public health while guiding the development of targeted prevention strategies for the poultry sector. Full article

The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025^T, isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025^T within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, “P. massiliensis”, P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5–89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C_15:0, iso-C_17:0 3-OH, and C_15:0. Conditioned medium from ASD2025^T antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025^T (=VKM B-3926^T = JCM 37967^T) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed. Full article

Puccinia striiformis f. sp. elymi (Pse) is a specialized forma specialis of stripe rust infecting Elymus dahuricus, yet its mitochondrial evolution remains poorly understood. In this study, we assembled the complete mitogenome of Pse using PacBio HiFi sequencing, yielding a circular mitogenome of 72,952 bp. This reveals a striking asymmetric evolutionary pattern with a 28.34% genomic contraction compared to the wheat stripe rust P. striiformis f. sp. tritici (Pst-CYR32). Our analysis demonstrates that this streamlining is strictly driven by a massive and systematic loss of mitochondrial introns. The Pse mitogenome exhibits negative GC-skew (−0.0184) consistent with strand-asymmetric mutational pressure, while maintaining a strictly conserved and syntenic complement of all 14 core protein-coding genes (PCGs), alongside 24 tRNAs and 2 rRNAs. Phylogenomic analysis positions Pse as sister to the Pst clade with strong support (100% bootstrap). A 748-bp SNP cluster within nad4 (14.2% sequence divergence versus 3.1% genome-wide average) provides a candidate molecular marker for lineage differentiation, pending population-level validation. This study establishes a genomic foundation for investigating mitochondrial reductive evolution in host-specialized rust lineages, highlighting the dynamic role of introns in driving organellar genome size variation. Full article

Juncus (Juncaceae) comprises over 300 species with high morphological plasticity, and its systematics remain incompletely resolved due to limited genomic resources. Here, we generated complete plastid genomes for two Korean Juncus species (J. decipiens and J. gracillimus) and incorporated plastid coding genes from an additional species to reconstruct phylogenetic relationships and examine plastome evolution within Juncaceae. Comparative analyses revealed substantial plastome size variation across Juncus and Luzula, largely driven by changes in inverted repeat (IR) length, with Luzula plastomes showing pronounced IR expansion. Within Juncus, extensive structural rearrangements were detected, including multiple inversion events, and closely related taxa shared conserved inversion patterns. Phylogenomic analyses recovered well-supported clades that were associated with structural traits such as extreme small single-copy (SSC) contraction and consistent loss of the plastid ndh, some rps and rpl gene families, indicating clade-specific plastome evolution in Juncaceae. To support applied molecular identification, we identified J. decipiens-specific plastid diagnostic SNPs (matK, rpl2) and validated allele-specific PCR markers using individuals from different species within the Juncus genus. In parallel, transcriptome sequencing of J. decipiens generated 133,559 transcripts and 66,324 unigenes, enabling discovery of high-confidence nuclear exonic SNP loci by mapping reads to a J. effusus nuclear genome. Collectively, our results provide new insights into plastome structural evolution and gene loss in Juncus and deliver validated plastid and nuclear markers for authentication and future conservation or utilisation studies on J. decipiens. Full article

Anthurium (Araceae) is one of the most species-rich Neotropical genera, yet its infrageneric classification remains unresolved. This study tests the monophyly of the morphologically defined Anthurium sect. Pachyneurium diagnosed by rosulate habit, involute prefoliation, and absence of a collective vein with a focus on Brazilian species. Using target capture sequencing (Angiosperms353 probe set), we generated a phylogenomic dataset for 35 Anthurium species (18 from sect. Pachyneurium) and conducted maximum likelihood and coalescent-based analyses. Our results demonstrate that sect. Pachyneurium is not monophyletic as traditionally circumscribed. Brazilian species previously assigned to the section are recovered in three geographically structured and strongly supported lineages: Amazonian, Atlantic Forest, and Caatinga/Cerrado. The Atlantic Forest lineage is unexpectedly resolved as sister to A. coriaceum (sect. Urospadix), revealing an evolutionary relationship not predicted by morphology. Divergence-time estimates place the origin of crown Anthurium in the Paleocene (~62 Ma), with diversification of the Brazilian lineages occurring during the Miocene (20–3 Ma), coinciding with major geoclimatic events in South America. Our findings indicate that key diagnostic morphological characters are homoplastic and provide a phylogenomic framework for revising the infrageneric classification of Anthurium. By identifying evolutionarily distinct lineages, this study also contributes to prioritizing conservation efforts in threatened Neotropical biomes. Full article

Corydalis impatiens (Papaveraceae) is a traditional Tibetan medicinal plant (“Pa Xia Ga”) whose mitochondrial genome evolution remains unexplored, particularly in the context of high-altitude adaptation. This study presents the first complete mitochondrial genome sequence of an alpine Corydalis species to establish a comparative framework with the lowland congener C. pauciovulata for investigating environment-associated mitochondrial evolution. Using Illumina sequencing and reference-guided assembly, we characterized a 688,959 bp circular genome containing 74 genes, with GC content variations reflecting functional compartmentalization—elevated in structural RNA genes (tRNAs: 51.24%; rRNAs: 52.79%) versus protein-coding genes (44.19%). We identified 719 RNA editing sites concentrated in NADH dehydrogenase genes, suggesting post-transcriptional optimization of respiratory complex I under hypoxic conditions. The genome harbors 50 dispersed repeats (7.50%) and 67 SSRs with A-rich predominance, providing species-specific markers for authenticating “Pa Xia Ga” in Tibetan medicine quality control. Phylogenomic analysis confirms close affinity with C. pauciovulata while resolving intrageneral relationships within Ranunculales. These findings establish a dual-reference system for distinguishing conserved genus-level features from altitude-associated adaptations, enabling future comparative mitogenomics across the 465-species genus and supporting DNA-based medicinal plant identification. Full article

A new shallow-water gorgonian coral species in the family Acanthogorgiidae, Paraplexaura binyuani sp. nov., is described from a specimen collected at Huaguang Atoll in the South China Sea at a depth of 22 m. The new species is distinguished from its congeners by abundant polyp sclerites, predominantly flattened rods, and by the coenenchyme bearing numerous large spindles reaching up to 0.6 mm in length, which are approximately two to three times longer than those reported for most described species of Paraplexaura. Phylogenomic analyses based on ultraconserved elements (UCEs) recover Paraplexaura as monophyletic and place P. binyuani sp. nov. as sister to P. cryptotheca, consistent with its morphological distinctiveness and supporting its recognition as a separate species. Full article

Muscomorpha is one of the most diverse groups in Brachycera, yet its higher-level phylogenetic relationships remain controversial, primarily concerning the monophyly and placement of Syrphoidea, the position of Platypezoidea, internal relationships in Calyptratae and Acalyptratae, and the non-monophyly of Eristalinae in Syrphidae. This study utilized 81 Muscomorpha species, including 22 newly sequenced Syrphidae species, and reconstructed their phylogeny with multiple datasets and models. The results confirmed monophyly of most superfamilies except Syrphoidea, with Platypezoidea as sister to the remaining Muscomorpha. Oestroidea was sister to Muscoidea. Within Syrphidae, Syrphinae monophyly and Syrphini relationships were strongly supported, while Eristalinae was non-monophyletic. Milesiini, Eristalini, Volucellini, Brachyopini, and Rhingiini were monophyletic. Divergence time estimation using MCMCTree indicated that Muscomorpha originated in the Middle Jurassic at approximately 171.66 Mya, with Syrphoidea diverging in the Late Jurassic at 151.05 Mya, Acalyptratae in the Early Cretaceous at 117.50 Mya, Calyptratae in the Late Cretaceous at 84.66 Mya, and Syrphidae at 103.44 Mya. These findings provide a robust phylogenomic framework for Muscomorpha evolution. Full article

Hepatitis B virus (HBV) genotype F is one of the most genetically divergent and evolutionarily ancient HBV lineages and predominantly circulates in indigenous and admixed populations of the Americas. Here, we performed a comprehensive evolutionary and inferred functional characterization of the HBV genotype F via the largest curated dataset of complete genomes. Phylogenomic reconstruction, recombination screening, and phylogenetic network analyses were integrated with codon-based selective pressure inference, surface protein posttranslational modification profiling, mutational analysis of antigenic regions, and reverse transcriptase (RT) drug resistance assessment. The HBV-F subgenotype exhibited a well-resolved phylogenetic structure and limited intragenotypic recombination, while intergenotypic recombination contributed substantially to reticulate evolutionary signals. Selective pressure analyses revealed strong purifying selection in replication-associated domains of the polymerase, in contrast to episodic adaptive evolution in surface-exposed and regulatory proteins, particularly the X protein. N-glycosylation sites in large surface proteins are highly conserved. Some mutations in the major hydrophilic region (MHR) were significantly detected, whereas RT drug resistance mutations were rare and followed canonical lamivudine-associated pathways. Collectively, these findings highlight the balance between deep evolutionary conservation and localized adaptive flexibility in shaping the HBV genotype F and provide a genotype-specific framework for interpreting viral fitness, immune interactions, and antiviral resistance. Full article

Background/Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) is a major causative pathogen in Republic of Korea. While numerous variants exist, the long-term evolutionary history of indigenous lineages remains unclear. Therefore, this study aimed to reconstruct the high-resolution population structure of Korean MRSA. Methods: A total of 191 MRSA clinical isolates collected between 1999 and 2025 were obtained from four Korean biobanks. Whole-genome sequencing was conducted and international MRSA genomes from the National Center for Bioinformatics were used as a control group. A genome-wide association study, including single-nucleotide polymorphism (SNP)-based phylogenomic analysis, principal component analysis (PCA), and ADMIXTURE, was performed for distribution analysis. A time-scale epidemiological analysis was conducted using SNP-based phylogenetic data. Additional profiling was performed via core genome multilocus sequence typing (cgMLST) for comparison with the SNP-based phylogenomic results. Finally, antimicrobial resistance and virulence factor genes were annotated using the ResFinder and VirulenceFinder databases. Results: Phylogenetic analysis identified five major clades: 1 (ST5), 2 (ST6), 3 (ST72), 4 (ST1/ST188), and 5 (ST8/ST239/ST254). Time-scaled analysis estimated that these major clades began to diverge in the early 20th century (e.g., Clade 1 around 1918). Notably, Korean ST5 isolates formed a sublineage distinct from North American strains, characterized by unique AMR profiles and divergence in the 1960s. ST72 formed an independent clade that was phylogenetically closer to clade 4 (ST1/ST188) than to the canonical CC8 group (clade 5). Furthermore, the ST1 isolates showed a temporal split into an older lineage and a recent sublineage, with expanded AMR pro-files. Conclusions: By integrating time-scale phylogenetics with cgMLST, we elucidated the evolutionary history and transmission dynamics of Korean MRSA. Full article

MADS-box transcription factors are key regulators of plant development and environmental responses. Here, we performed an integrated phylogenomic and expression analysis of the MADS-box gene family in Capsicum annuum, identifying 97 members that fall into 52 Type I and 45 Type II genes. Comparative phylogeny, exon–intron organization, conserved motifs, and chromosomal mapping allowed classification into 15 subfamilies. Gene duplication analysis revealed that segmental duplication has been a major driver of family expansion. Expression profiling across multiple tissues, together with promoter cis-element prediction and stress-responsive transcriptome data, demonstrated that Type II genes exhibit broad and dynamic expression patterns, particularly under ABA treatment and temperature stress. A key finding of this study is the complete absence of the Mβ lineage, a Type I subfamily typically associated with gametophyte and endosperm development in other angiosperms. No Mβ-like sequences were detected in the pepper genome, and Type I genes overall showed extremely low expression, suggesting that the Mβ lineage has undergone lineage-specific evolutionary loss and that its functions may be compensated by other Type I members or by expanded Type II regulatory modules. Together, this study provides the first evidence for the evolutionary disappearance of the Mβ subfamily in Capsicum and offers a comprehensive resource for dissecting the developmental and stress-responsive roles of MADS-box genes in pepper. Full article