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PubMed2025

Mpox: current knowledge and understanding-a scoping review.

Mpox in humans is a rash illness resulting from infection with monkeypox virus (MPXV). In 2022, a public health emergency of international concern (PHEIC) was declared with 115 countries reporting cases of Mpox. Most of these countries had not previously reported cases. This global outbreak was sustained primarily by human-to-human transmission within complex sexual networks. Whilst these cases were similar to previous clade II West African MPXV isolates, they were sufficiently genomically distinct to result in WHO recognizing two subclades within clade II: clade IIa and clade IIb. In 2024, a second PHEIC was declared, resulting from a marked increase in cases of clade I MPXV. In this scoping review, we compare the major clinical, epidemiological, and genomic features of the major mpox lineages and the implications for vaccination, transmission, infection control and treatment..

Humans↗

PubMed2026

Flavobacteria consume nitrous oxide produced by partial denitrifiers in coastal sediments.

Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed that diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling showed that both clade II nosZ flavobacterial isolates and whole sand communities exhibited a low apparent affinity for N2O under the tested experimental conditions, expanding the currently limited kinetic data available for N2O reducing microorganisms from coastal permeable sediments, including flavobacterial clade II N2O reducers. Collectively, these findings indicate that abundant N₂O reducing communities can substantially consume N2O within permeable sediments, thus limiting N2O accumulation despite active N2O production. Together with previous hydrodynamic models predicting low N2O release from permeable sediments, our results highlight the important role of specialized microbial communities in regulating N2O cycling under increasing nutrient pollution.

Nitrous Oxide↗

PubMed2025

Multi-Omics Analysis of Experimentally Evolved Candida auris Isolates Reveals Modulation of Sterols, Sphingolipids, and Oxidative Stress in Acquired Amphotericin B Resistance.

Clinical isolates of Candida auris show a high prevalence of resistance to Amphotericin B (AmB)-an uncommon trait in most Candida species. Alterations in ergosterol biosynthesis can contribute to acquired AmB resistance in C. auris laboratory strains but are rarely seen in clinical isolates. In this study, we experimentally evolved two drug-susceptible Clade II isolates of C. auris to develop AmB resistance. The evolved strains displayed a four to eight fold increase in MIC50 compared to the parental cells. We analyzed changes in their karyotype, genome, lipidome, and transcriptome associated with this acquired resistance. In one lineage, AOX2 was upregulated, and its deletion reversed the AmB resistance phenotype. The aox2Δ mutant also failed to evolve AmB resistance under experimental conditions. In the same lineage, restoring the UPC2 S332R and RTG3 S101T mutations to the wild-type allele restored AmB susceptibility. In another lineage, the ergosterol and sphingolipid pathways were observed to play a critical role, and upregulation of the ERG genes elevated the total sterol content, while significant downregulation of HSX11 (glucosylceramide synthase) resulted in lower levels of glucosylceramides. To our knowledge, this study is the first to show that AmB resistance in C. auris can be acquired through mechanisms both dependent on or independent of sterol content modulation, highlighting Aox2 and Upc2 as key regulators of amphotericin resistance.

Amphotericin B↗

PubMed2026

Detection and genomic characterization of a travel-associated ECSA lineage chikungunya virus infection in Mexico.

BACKGROUND: In 2013, chikungunya virus (CHIKV), a re-emerging Aedes-borne virus, was introduced into the Americas. This led to synchronous epidemics across the region associated mainly with the Asian lineage, which eventually subsided. Resurgent outbreaks have been recorded since, principally in South America, largely driven by the East-Central-South-African (ECSA) lineage. In 2025, more than 300,000 CHIKV suspected cases were reported in Brazil and Cuba. CASE SUMMARY: In November 2025, a healthy adult male traveling from Cuba arrived in Merida, Mexico, and shortly after presented febrile symptoms consistent with an arboviral infection. CHIKV infection was diagnosed by RT-qPCR. Though the infection was mild, the patient developed a rash on the abdomen and neck that persisted for up to a month, with further inflammation of the joints of the left leg. Phylogenetic analysis of the viral genome indicated placement within the ECSA lineage, clustering with other contemporaneous virus genomes sampled from Brazil that belong to a recently described clade II within the country, in which viral genomes from Cuba also cluster. CONCLUSION: We identify a travel-associated ECSA lineage CHIKV case in Mexico. This viral lineage has not previously been detected in the country. This finding highlights the risk for subsequent local transmission and is consistent with reports of the presence of this lineage in Cuba. Ten years since the last CHIKV epidemic in Mexico, strengthened surveillance is required to anticipate potential local outbreaks within the region.

ECSA↗

PubMed2026

Near-Whole-Genome Sequencing of Peste Des Petits Ruminants Virus Lineage IV From the Savannah District, Northern Côte d'Ivoire in 2023.

Peste des petits ruminants (PPR) is a highly contagious viral disease affecting sheep and goats, causing substantial economic losses in endemic countries. In the Savannah district of Côte d'Ivoire, knowledge of the genetic diversity and molecular epidemiology of the PPR virus (PPRV) remains limited. This study investigated the genetic diversity and phylogenetic relationships of PPRV circulating in this region using whole-genome sequencing (WGS). A cross-sectional survey was conducted between September and December 2023. Nasal swabs collected from sheep and goats were screened for PPRV ribonucleic acid (RNA) using real-time reverse transcription polymerase chain reaction (RT-qPCR). Samples with low quantification cycle (Cq) values of less than 35 and successful multiplex PCR amplification profiles were selected for sequencing using the Oxford Nanopore MinION platform. Near-complete consensus genomes were generated through reference-based assembly and analysed alongside representative strains from all recognised PPRV lineages. Of the 355 samples analysed, 25 (7.0%) tested positive for PPRV RNA, with positive detections in all three surveyed regions (Poro, Tchologo and Bagoué). The four samples with the lowest Cq values, originating from all three administrative regions, were successfully sequenced, generating genomes that covered 82.0%-86.2% of the reference genome at a depth of ≥ 10 ×. The missing regions were mainly located at the 5' and 3' genomic termini, as well as in limited internal regions associated with amplicon dropout. Phylogenetic analysis revealed that all four sequences belonged to lineage IV and exhibited high nucleotide similarity (98.1%-99.9%). The Ivorian strains clustered with recent lineage IV viruses from West, North and Central Africa, whereas historical Ivorian lineages I and II formed distinct clades. These findings confirm the predominance of lineage IV in northern Côte d'Ivoire and provide baseline genomic data to support molecular epidemiological surveillance in the region.

PPRV↗

PubMed2026

Genome-wide characterization of MADS-box genes and their roles in axillary bud development in tobacco.

A total of 118 NtMADS-box genes were identified in tobacco, revealing their potential roles in axillary bud development. Preliminary overexpression analysis indicated that NtMADS91 promotes axillary bud development. MADS-box transcription factors are core regulators of plant development, but their functions in axillary bud development in Nicotiana tabacum L. have not been systematically elucidated. In this study, 118 NtMADS-box genes were identified from the tobacco genome. Phylogenetic analysis classified them into type I (comprising the Mα and Mγ subfamilies) and type II (comprising the MIKC* and MIKCC clades). Promoter analysis revealed that cis-acting elements were predominantly associated with light and hormone responses. RNA-seq analysis of axillary buds after topping identified 60 differentially expressed NtMADS-box genes, from which 12 candidate genes with significant expression changes were selected. Tissue-specific qRT-PCR revealed that seven of these genes were preferentially expressed in axillary buds, with members of the SOC1 and SVP subfamilies accounting for the majority. Exogenous application of abscisic acid and the strigolactone analog GR24 significantly suppressed the expression of most candidate genes, including NtMADS91. The preliminary overexpression analysis suggested that NtMADS91 may promote axillary bud growth, increasing both the number and length of axillary buds. This study lays a foundation for future dissection of the regulatory mechanisms of the NtMADS-box gene family in axillary bud development and provides promising candidate genes for research related to tobacco axillary bud development.

Nicotiana↗

PubMed2026

Genome-wide identification and characterization of 1-amino-cyclopropane-1- carboxylate synthase (ACS) gene family in Carica papaya and expression insights in response to hormone stress.

ACC-synthase (1-aminocyclopropane-1-carboxylate synthase), also known as the ACS gene, plays a pivotal role in ethylene production, which is of great importance in the fruit ripening process for producing saleable yield (marketable fruit). The ACS gene family presumably controls stress responses, plant growth and development, and particularly fruit ripening. Computational biology was used as an essential tool to identify seven ACS genes in Carica papaya (red hermaphrodite) using an RNA-seq database (NCBI GEO). Further, the phylogenetic relationships of ACS genes determined gene family resemblance in the genomes of Hordeum vulgare, Musa acuminata, C. papaya, and Arabidopsis thaliana; therefore, the identified gene families were further classified into four distinct clades (Type-I, Type-II, Type-III, and Type-IV) in alignment with the well-established Arabidopsis classification. Moreover, encompassing gene structure, domain motifs, cis-element phylogenetic profiling, synteny, and transcriptomic profiling unveiled latent structural and functional attributes within CpACS genes. Through segmental duplication of CpACS, insights into evolutionary duplication events were predicted. The paralogous behavior of ACS genes in C. papaya and a comprehensive transcriptomic analysis demonstrated both up- and down-regulation patterns in response to ethylene treatment at different time points during the fruit ripening process, using the papaya manual handbook V2 (2021). Gene expression showed upregulation of two essential CpACS genes, CpACS5 and CpACS6. RT-qPCR validates the expression of these important genes during fruit ripening. However, one gene, CpACS7, is expressed in the later stages of fruit development. Our results demonstrated novel avenues for understanding the expression pathways of the ACS gene family in red hermaphrodite papaya, and most of these genes were linked to regulating various abiotic stresses, plant growth, and fruit development.

Carica↗

PubMed2026

ECLIPSE: exploring the dark proteome of ESKAPE pathogens through the sequence similarity network of the Protein Universe Atlas.

MOTIVATION: The accelerating crisis of antimicrobial resistance among the critical so-called ESKAPE pathogens demands the urgent identification of novel molecular targets. However, a substantial fraction of ESKAPE proteomes remains functionally uncharacterized, with many genes annotated as encoding hypothetical proteins. These protein sequences often lack significant similarity to known protein families when conventional homology-based annotation methods are used and thus remain "dark". This limits our ability to explore their roles in pathogenicity, and it is thus crucial to bridge this substantial gap in pathogen biology by developing new strategies to illuminate these "dark" regions of the ESKAPE pan-proteome. RESULTS: We introduce ECLIPSE (ESKAPE Connectome Linkage and Inference for Proteome Sequence Exploration), a network-based computational framework that systematically identifies and prioritizes functionally dark protein families in ESKAPE pan-proteomes. ECLIPSE embeds target ESKAPE pathogen proteomes within the global sequence similarity network of the Protein Universe Atlas. It detects connected components composed entirely of unannotated proteins, called the "dark proteome." As a case study, we applied ECLIPSE to a pan-proteome of 3 460 657 protein sequences from 635 strains of Pseudomonas aeruginosa (PA). ECLIPSE identified 120 985 proteins (4%) residing in completely dark connected components. Furthermore, we have performed a taxonomic diversity analysis using normalized Shannon indices to characterize each dark component by its enrichment in ESKAPE pathogens. The analysis utilized the evenness (E) value (see Methods 2.1), which distinguishes Pseudomonas-specific (target-specific) from ESKAPE-enriched dark components. We then developed the Dark Proteome Prioritization Score (DPPS), a composite multidimensional scoring framework (see Methods 2.5). It ranks these dark components by biological relevance across four orthogonal axes: (i) functional darkness, (ii) P. aeruginosa proportion in the Atlas, (iii) AMR-clade taxonomic restriction, and (iv) conservation across the 635 P. aeruginosa strains. This framework outputs a robust four-tier scoring system; the prioritized Tier I components were validated by weight sensitivity analysis and remained stable across 500 Monte Carlo weight perturbations. Structural characterization of one of the top-ranked ESKAPE-enriched dark components revealed that it belongs to the beta-barrel fold DUF1302 (PF06980) family, for which no experimentally solved three-dimensional structure exists in the PDB. The genomic context analysis indicates that it is co-localized with a LuxR-type transcriptional regulator. Collectively, ECLIPSE identifies evolutionarily conserved, structurally defined, and functionally dark proteins enriched across ESKAPE pathogens; these dark proteins can further be utilized as alternative antimicrobial targets for experimental characterization. AVAILABILITY AND IMPLEMENTATION: The source code and dataset are available for free at: Github: https://github.com/surabhilata/ECLIPSE.git, Zenodo: DOI: 10.5281/zenodo.21064323.

Proteome↗

PubMed1992

Mitochondrial DNA phylogeny of the Old-World monkey tribe Papionini.

The evolution of the Old World monkey tribe Papionini, composed of macaques, baboons, mandrills, drills, and mangabeys, was examined using mitochondrial DNA (mtDNA) sequence data on the cytochrome oxidase subunit II gene. When analyzed cladistically, these data support a baboon clade of savannah (Papio) plus gelada (Theropithecus) baboons, as well as a clade containing drill (Mandrillus) plus mangabey (Cerocebus) genera. This result stands in opposition to most morphological phylogenies, which break up the baboon clade by placing Papio and Mandrillus as sister taxa and Theropithecus as a more distantly related lineage. Analyses of COII gene sequences also suggest that the papionin ancestral stock divided into two lineages, one leading to macaques and the other to the purely African genera. From a molecular evolutionary perspective, the papionin COII gene sequences reveal a pattern of amino acid replacements concentrated in the regions spanning the mitochondrial membrane.

Amino Acid Sequence↗

PubMed1991

Molecular phylogeny of the superorder Archonta.

The superorder Archonta has been hypothesized to include primates, tree shrews, bats, and flying lemurs as descendants of a common ancestor. More recently, a diphyletic origin for bats has been proposed. To evaluate these hypotheses, the nucleotide sequence of the mitochondrial cytochrome oxidase subunit II gene was determined from a bushbaby (Galago senegalensis), flying lemur (Cynocephalus variegatus), tree shrew (Tupaia glis), spear-nosed bat (Phyllostomus hastatus), rousette bat (Rousettus leschenaulti), and nine-banded armadillo (Dasypus novemcinctus) and was compared with published sequences of a human, cow, and mouse. Phylogenetic analyses of the sequences give evidence that primates, tree shrews, and flying lemurs have a recent common ancestor but that bats are genealogically distant. The monophyletic origin of bats is supported. Contrary to interpretations based on morphological data, tree shrews are shown to be no more closely affiliated with primates than are flying lemurs. Analyses of the cytochrome oxidase subunit II gene give marginally more support to a Dermoptera-Scandentia clade than to a Dermoptera-Primates clade.

Animals↗

PubMed2026

Identification and functional characterization of a novel antiviral chicken interferon-υ.

Interferons are critical mediators of antiviral immunity in vertebrates. While type IV interferon (IFN-υ) has been identified in fish and amphibians, its existence and function in chickens remained unknown. Through systematic genomic screening, we identified and cloned a novel chicken interferon gene, designated ChIFN-υ. Phylogenetic analysis placed ChIFN-υ within a distinct clade alongside zebrafish and clawed frog IFN-υ, confirming its identity as a type IV interferon, with minimal homology to classical type I, II, or III IFNs. Expression profiling revealed constitutive ChIFN-υ expression in mucosal and immune tissues of healthy chickens, exhibiting a distinct developmental shift: highest in trachea and small intestine in 1-day-old chicks, shifting to spleen and lung in 4-week-old chickens. ChIFN-υ expression was strongly upregulated following H9N2 AIV infection. Functionally, recombinant ChIFN-υ protein activated the interferon-stimulated response element (ISRE) and Mx promoter in a dose-dependent manner and significantly inhibited the replication of both vesicular stomatitis virus (VSV) and H9N2 AIV in DF-1 cells. In vivo, early treatment with exogenous ChIFN-υ significantly reduced pulmonary and tracheal viral loads and decreased oropharyngeal and cloacal virus shedding in H9N2-infected chickens. In conclusion, this study identifies and functionally characterizes the type IV interferon in chickens, elucidating the evolutionary status, regulated expression, and antiviral efficacy of ChIFN-υ. These findings highlight its potential as a candidate for developing interferon-based therapies against avian viral diseases.

Animals↗

PubMed2024

Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.

Animals↗

PubMed2026

Characterization and functional insights of histone deacetylases in bivalves: implications for temperature and immune response in Chlamys nobilis.

Histone deacetylases serve as pivotal epigenetic regulators that modulate chromatin remodeling and gene transcription, playing critical roles in immune defense and environmental stress responses in aquatic organisms. However, the evolutionary characteristics and functional roles of the HDAC family in bivalves remain poorly understood. In this study, genome-wide identification of the HDAC family across 30 bivalve species yielded 558 HDAC genes. Phylogenetic reconstruction categorized these genes into four conserved groups and revealed a unique, bivalve-specific SIRT8 clade. Using the noble scallop Chlamys nobilis as a representative model, expression profiling revealed distinct expression patterns among CnHDAC members. Class I and most Class III members were predominantly expressed in the gonads, while Class II members were enriched in immune-related tissues, implying their potential involvement in bivalve immunity. Upon temperature stress, CnHDAC1/2, CnHDAC11-1, CnHDAC11-2, CnSIRT2-1, CnSIRT4, CnSIRT6, and CnSIRT8-3 were significantly induced, highlighting their critical roles in temperature adaptation. Upon Vibrio exposure, CnHDAC1/2, CnHDAC8, CnSIRT4, and CnSIRT6 were upregulated, while CnHDAC4/5/7/9, CnHDAC6/10, CnSIRT2-2, CnSIRT5, CnSIRT7, and CnSIRT8-3 were downregulated, suggesting a coordinated epigenetic regulatory mechanism underlying host immune defense. In conclusion, this study systematically elucidates the evolutionary landscape of the HDAC family and underscores its potential involvement in environmental resilience and host immunity, providing a theoretical basis for the breeding of disease-resistant and stress-tolerant aquaculture bivalves.

Animals↗

PubMed2026

Genetic diversity, phylogenetic relationships, and marker development between Hydrangea serrata and H. macrophylla based on plastome and 45S nrDNA.

Ornamental hydrangeas (genus Hydrangea) are cultivated worldwide for their diverse flower colors and attractive morphology. Here, we assembled the complete plastid genome (plastome) and 45S nuclear ribosomal DNA (45S nrDNA) sequences of 22 individuals representing H. serrata, H. macrophylla, and related species (H. arborescens, H. paniculata, H. petiolaris, and H. hydrangeoides). The plastomes contained up to 2,344 single-nucleotide polymorphisms (SNPs) and 367 insertions/deletions (InDels) within the genus, whereas the assembled 45S nrDNA sequences showed 119 SNPs and 10 InDels. Phylogenetic analyses based on plastome and 45S nrDNA sequences clearly separated H. serrata and H. macrophylla from the other Hydrangea species. In the plastome-based tree, H. petiolaris was placed in the same clade as H. arborescens, whereas in the 45S nrDNA-based tree it showed a close relationship to H. hydrangeoides. The H. serrata and H. macrophylla samples were not always separated according to their species boundaries, as observed in samples Hse8-Hse12. Notably, one H. serrata sample (Hse8), collected from a wild mountainous region of Japan, exhibited a closer genetic relationship to H. macrophylla samples, indicating that cultivated hydrangeas may have originated from a specific wild lineage of H. serrata adapted to mountainous habitats. Using plastome-derived molecular markers, 66 Hydrangea samples were further classified into five groups, with Group II comprising both cultivated H. macrophylla and a subset of wild H. serrata samples, suggesting a close genetic affinity between this group and the ancestral gene pool of cultivated H. macrophylla. Based on these genomic resources, eight plastome-derived molecular markers were developed to differentiate cultivated hydrangeas from wild genotypes and to assess genetic diversity within H. serrata and H. macrophylla, providing practical tools for germplasm identification, breeding, and genetic resource management of Hydrangea species.

hydrangea↗

PubMed2025

A large-scale study across the avian clade identifies ecological drivers of neophobia.

Neophobia, or aversion to novelty, is important for adaptability and survival as it influences the ways in which animals navigate risk and interact with their environments. Across individuals, species and other taxonomic levels, neophobia is known to vary considerably, but our understanding of the wider ecological drivers of neophobia is hampered by a lack of comparative multispecies studies using standardized methods. Here, we utilized the ManyBirds Project, a Big Team Science large-scale collaborative open science framework, to pool efforts and resources of 129 collaborators at 77 institutions from 24 countries worldwide across six continents. We examined both difference scores (between novel object test and control conditions) and raw data of latency to touch familiar food in the presence (test) and absence (control) of a novel object among 1,439 subjects from 136 bird species across 25 taxonomic orders incorporating lab, field, and zoo sites. We first demonstrated that consistent differences in neophobia existed among individuals, among species, and among other taxonomic levels in our dataset, rejecting the null hypothesis that neophobia is highly plastic at all taxonomic levels with no evidence for evolutionary divergence. We then tested for effects of ecological factors on neophobia, including diet, sociality, habitat, and range, while accounting for phylogeny. We found that (i) species with more specialist diets were more neophobic than those with more generalist diets, providing support for the Neophobia Threshold Hypothesis; (ii) migratory species were also more neophobic than nonmigratory species, which supports the Dangerous Niche Hypothesis. Our study shows that the evolution of avian neophobia has been shaped by ecological drivers and demonstrates the potential of Big Team Science to advance our understanding of animal behavior.

Animals↗