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PubMed1992

Ontogeny and distribution of GABAA receptors in rat brainstem and rostral brain regions.

Previous studies from our laboratory and others have shown that there are major age-related differences in brainstem neuronal function. Since GABAA receptors are major targets for GABA-mediated inhibitory modulation and play a key role in regulating cardiorespiratory function, especially during O2 deprivation, we examined differences in GABAA receptor density and distribution during postnatal development. Using quantitative receptor autoradiography, the present study was performed to examine the postnatal expression of GABAA receptors in the rat brainstem and rostral brain areas at five ages, i.e. postnatal day 1 (P1), P5, P10, P21 and P120. Ten-micrometer brain sections at different brain levels were labelled with [3H]muscimol in Tris-citrate buffer. We found that (i) GABAA receptors appeared very early in almost all the brainstem as well as rostral areas; (ii) at P1, the brainstem had a higher GABAA receptor binding density than rostral areas and its density peaked at P5 or P10; and (iii) receptor densities of the cerebellum and rostral brain areas such as cortex, thalamus and dentate gyrus increased with age, especially between P10 and P21, but most other subcortical areas like caudate-putamen and hippocampal CA1 area did not increase remarkably after birth. We conclude that: (i) GABAA receptors exist in most brain areas at birth; (ii) there are several patterns of postnatal development of GABAA receptors in the CNS with dramatic differences between the brainstem and cortex; (iii) brainstem functions rely more on GABAA receptors in early postnatal life than at more mature stages. We speculate that GABAA receptors develop earlier in phylogenetically older structures (such as brainstem) than in newer brain regions (such as cortex).

Aging↗

PubMed2026

Evolutionary characterization and expression profiling of ACC and FASN genes in Chinese mitten crab Eriocheir sinensis.

Acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN) are rate-limiting enzymes in the fatty acid biosynthetic pathway, yet their evolutionary relationships, sequence features, and expression profiles remain poorly understood in crustaceans, particularly in the economically important Chinese mitten crab (Eriocheir sinensis). Here, we identified and systematically analyzed ACC and FASN genes in E. sinensis using comparative genomic analyses across 43 species. ACC was highly conserved as a single-copy gene in invertebrates, in contrast to the multiple paralogs observed in vertebrates. Similarly, FASN was generally maintained as a single-copy gene across most taxa but exhibited lineage-specific expansion in certain insect groups. Phylogenetic and structural analysis revealed strong conservation of both genes within crustaceans, supported by multiple conserved motifs and canonical functional domains. Expression profiling showed predominant expression in the hepatopancreas and midgut, suggesting their potential involvement in crustacean lipid metabolism. During the molting cycle, ACC and FASN exhibited higher expression levels during stages C and D, suggesting an increased capacity for fatty acid biosynthesis before molting. In addition, dietary lipid levels experiment revealed that ACC and FASN expression responded dynamically to dietary lipid availability, with increased expression at moderate lipid levels but reduced expression under excessive lipid supplementation, indicating a possible adaptive transcriptional response to lipid status. Collectively, this study provides insights into the evolutionary conservation and expression dynamics of ACC and FASN and improves our understanding of lipid metabolic adaptation in crustaceans.

Animals↗

PubMed2026

Zhiling Jiangya decoction treats hypertension in rats: An integrative study of network pharmacology, immune infiltration, molecular simulation, and 16S rDNA sequencing.

OBJECTIVE: This study integrated network pharmacology, immune infiltration analysis, molecular docking, molecular dynamics simulation, ADMET prediction, 16S rDNA sequencing, and rat experiments to elucidate the potential mechanisms underlying the antihypertensive effects of Zhiling Jiangya Decoction (ZLJYD). METHODS: Active compounds and their potential targets were screened from the PubChem, TCMSP, NovoPro, and SwissTargetPrediction databases. Hypertension-related targets were retrieved from the OMIM and GeneCards databases, and overlapping targets were identified. The STRING database and Cytoscape 3.10.1 software were used to construct a protein-protein interaction network and a herb-component-target-disease network. Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed to identify the key biological processes and signaling pathways involved. Using the CIBERSORT algorithm combined with correlation analysis, we investigated the association between key targets and immune cell infiltration. Molecular docking, molecular dynamics simulations, and ADMET predictions were performed to assess the binding stability and pharmacokinetic properties of the main compounds with their corresponding targets. Finally, the antihypertensive efficacy of ZLJYD was validated using a spontaneously hypertensive rat model, and alterations in gut microbiota were analyzed using 16S rDNA sequencing. RESULTS: A total of 123 active compounds and 267 hypertension-related targets of ZLJYD were identified. Enrichment analysis revealed that these targets were primarily associated with the PI3K-Akt signaling pathway and lipid and atherosclerosis pathways. Immune infiltration analysis suggested that the therapeutic effects of ZLJYD may involve the regulation of follicular helper T cells, naïve B cells, and naïve CD4⁺ T cells. Molecular docking and dynamics simulations supported the stable binding of key compounds to their target proteins, while ADMET predictions indicated favorable pharmacokinetic properties and safety profiles. Rat experiments demonstrated that ZLJYD significantly reduced blood pressure in spontaneously hypertensive rats, partially alleviated gut microbiota dysbiosis, and altered microbial community structure and phylogenetic diversity. CONCLUSION: This study systematically elucidates the potential mechanisms underlying the antihypertensive effects of ZLJYD through multiple components, targets, and pathways, particularly immune regulation and gut microbiota remodeling. These findings provide mechanistic insights into its potential therapeutic application.

16S rDNA sequencing↗

PubMed2026

Functional characterization of SHC-like triterpene cyclase genes in azole response and virulence-related traits of Aspergillus fumigatus.

Aspergillus fumigatus is a major opportunistic fungal pathogen, and increasing azole resistance poses a challenge for aspergillosis treatment. Squalene is an upstream precursor of ergosterol biosynthesis and may also be utilized by SHC-like triterpene cyclases, suggesting a potential link between squalene-associated metabolism, membrane adaptation, and azole response. However, the roles of SHC-like triterpene cyclase genes in A. fumigatus remain unclear. Here, we characterized three candidates, shc1, shc2, and shc3, using comparative bioinformatic analysis, gene deletion, phenotypic assays, azole susceptibility testing, transcriptomics, and host-interaction models. Sequence, genomic-context, phylogenetic, and structural analyses suggested divergence among the three candidates. Individual shc deletion caused limited effects on vegetative growth, whereas loss of shc1 mildly reduced susceptibility to voriconazole and posaconazole, as reflected by twofold MIC increases and lower inhibition rates. Transcriptomic analysis revealed distinct remodeling patterns, with Δshc3 showing the broadest transcriptional changes despite no detectable MIC shift. Targeted metabolite profiling and PI uptake analysis further supported an association between shc deletion, sterol/hopane-type triterpenoid balance, and membrane-associated properties. shc deletion also altered epithelial cell interaction phenotypes, while Δshc1 showed reduced lethality in Galleria mellonella. In clinical isolates, elevated shc transcription was associated with azole-resistant backgrounds. These findings suggest functional diversification among SHC-like triterpene cyclase genes and indicate that shc1 may contribute to azole-associated adaptation and virulence-related traits in A. fumigatus.

Aspergillus fumigatus↗

PubMed2025

The emergence of sexually transmissible Shigella flexneri serotype 1b between 2019 and 2024 in England: a descriptive epidemiological study.

Background. Shigella species are pathogenic bacteria that cause gastrointestinal symptoms ranging from mild watery diarrhoea to bacillary dysentery. Transmission is faecal-oral and historically associated with international travel. Recently, sexual transmission has been documented among gay, bisexual and other men who have sex with men (GBMSM). Through routine surveillance, we observed an increase in notifications of S. flexneri serotype 1b. We investigated the emergence of this serotype and examined possible drivers of transmission.Methods. We used historical data and whole-genome sequencing data from S. flexneri 1b isolates submitted to the United Kingdom Health Security Agency (UKHSA) to determine the relatedness of isolates and describe the population structure using phylogenetics. We tested for associations with possible epidemiological, biological and genetic drivers.Results. Between 1 January 2004 and 30 June 2024, 1,672 isolates of S. flexneri 1b were identified. Prior to 2019, there was a median of 12.5 [interquartile range (IQR) 10-17] notifications per quarter, rising to a median of 39.5 (IQR 23-58) notifications from 2019 to 2024. The rise was predominantly among adult males, consistent with patterns seen in prior sexually transmitted shigellosis epidemics among GBMSM. Unlike previous outbreaks of shigellosis among GBMSM, the emergence of S. flexneri 1b showed no evidence of an association with the acquisition of antimicrobial resistance determinants.Conclusions. Shigellosis can have severe clinical outcomes, and the repeated emergence of Shigella variants among GBMSM highlights the significance of the sexual transmission pathway. Continued surveillance of Shigella subtypes is necessary to inform public health interventions aimed at preventing sexual transmission of enteric pathogens in the GBMSM community.

Humans↗

PubMed2026

Phytohormones in fungi: inter-kingdom modulators or fungal self-controlling elements?

SUMMARYLeveraging data from innovative experimental approaches, omics technologies, and bioinformatics, we offer new insights into how fungi communicate with and perceive their environment to achieve ecological success. By integrating comparative data from both the fungal and plant kingdoms, we critically reassessed the evolutionary, biochemical, and functional landscape of phytohormones in fungi, challenging the conventional notion that these molecules serve exclusively as plant regulators or as means of communication with them. Our analysis demonstrates that fungi not only synthesize a diverse array of phytohormones-including auxins, cytokinins, gibberellins, abscisic acid, ethylene, brassinosteroids, salicylic acid, and oxylipins-but also possess hormone-sensing and signal transduction mechanisms architecturally distinct from those of plants. Employing genomics, phylogenetics, and structural analyses, the review uncovers that many hormone biosynthetic and sensing pathways in fungi are evolutionarily ancient, sometimes predating their roles in plant-fungus interactions, and that some pathways show convergence rather than direct gene homology. Fungal phytohormones regulate development, growth, and metabolism, thereby playing key functions in their ecological context. The review emphasizes that, while biosynthetic pathways tend to be highly conserved, perception and signaling mechanisms in fungi are more varied and often remain poorly understood. We conclude that fungi have an intrinsic and autonomous hormonal physiology that underpins their ecological adaptability and success. Collectively, this analysis reframes fungal biology, highlighting the need for deeper investigation into the signaling and regulatory roles of phytohormones in fungi beyond their interactions with plants.

cell signaling↗

PubMed2026

Genomic characterization of efflux pumps and putative small multidrug resistance (SMR)-like transporters in disinfectant-tolerant coagulase-negative staphylococci from a Vietnamese hospital.

Coagulase-negative staphylococci (CoNS) are common inhabitants of healthcare environments and can serve as reservoirs of antimicrobial resistance determinants. However, the relationship among disinfectant tolerance, efflux-associated phenotypes, and multidrug resistance in environmental CoNS remains incompletely defined. Here, 51 staphylococcal isolates were recovered from high-touch hospital surfaces in Hanoi, Vietnam, and 14 isolates showed elevated MICs to at least one disinfectant, including benzalkonium chloride, chlorhexidine gluconate, or hydrogen peroxide, relative to Staphylococcus aureus ATCC 25923. These isolates also displayed multidrug-resistant phenotypes. Moreover, ethidium bromide accumulation assays revealed a clear efflux-associated phenotype, and representative isolates exhibited biofilm-forming ability. Whole-genome sequencing of three representative isolates reclassified SDH.B1 and SDH.B3 as Staphylococcus nepalensis-a CoNS species rarely documented in hospital AMR surveillance-and confirmed SDH.B7 as Staphylococcus haemolyticus. To our knowledge, this is among the first reports of S. nepalensis carrying mecA together with the disinfectant efflux gene qacG, and a set of putative small multidrug resistance (SMR)-like transporters in a hospital environment from Southeast Asia. In addition, six putative SMR-like proteins were identified. Phylogenetic and structural analyses suggested relatedness to YkkC/YkkD-like systems, although their transport activity remains to be experimentally verified. These findings identify environmental CoNS as reservoirs of disinfectant tolerance and multidrug resistance in hospital settings and provide a basis for future functional investigation of putative SMR-like transporters.IMPORTANCEHospital environmental CoNS are often dismissed as low-priority contaminants, yet they may persist under disinfectant pressure and carry clinically relevant resistance determinants. Here, disinfectant-tolerant CoNS recovered from a Vietnamese hospital combined multidrug resistance, efflux-associated phenotypes, and biofilm-related traits. Genome analysis further revealed known qac genes and six putative SMR-like proteins that merit functional testing. These findings support inclusion of environmental CoNS in infection-prevention surveillance and disinfectant stewardship programs.

Staphylococcus haemolyticus↗

PubMed2026

Evidence for dual pathways of Tc1/mariner domestication in Drosophila.

BACKGROUND: The domestication of transposable elements is a key source of evolutionary innovation, yet the pathways by which their functional modules are repurposed by the host remain poorly understood. The Tc1/mariner superfamily is a widespread group of DNA transposons, but the prevalence and patterns of their domestication are underexplored. RESULTS: We performed a systematic genomic screen across 43 drosophilid species using stringent criteria for molecular domestication. This analysis identified five high-confidence, evolutionarily conserved genes derived from Tc1/mariner transposases. Phylogenetic and structural analyses suggest domestication via two distinct molecular pathways: co-option of the DNA-binding module and co-option of the catalytic domain. The DNA-binding module pathway includes CG4570, the previously known genes cag and toy (the latter fused with a homeodomain), and a lineage-restricted gene in the Drosophila obscura group that exhibits signatures of recent domestication. In contrast, the catalytic domain pathway is represented solely by CG14478. Structural modeling reveals that CG14478 protein preserves a canonical DDE endonuclease fold. Co-expression network analysis suggests potential cellular roles of these genes: CG14478 is linked to RNA/chromatin-related processes, CG4570 to cell cycle/chromosome functions, cag to ciliary and nuclear functions, and toy to neuronal development. CONCLUSIONS: This study establishes a stringent framework for identifying domesticated TEs, demonstrating that Tc1/mariner elements are co-opted via two distinct pathways: retention of either catalytic or DNA-binding modules. Our findings suggest that domestication is a dynamic continuum, ranging from recent, lineage-specific events to ancient, conserved genes, and underscore how genomic conflict with TEs can drive eukaryotic evolution and regulatory complexity.

Animals↗

PubMed2026

Genome-Wide Characterization of the Apple HD-Zip IV Gene Family and Functional Validation of MdHDZIV3 Under PEG-Induced Osmotic Stress.

The homeodomain-leucine zipper IV (HD-Zip IV) transcription factor subfamily plays essential roles in epidermal development, cuticle formation, lipid metabolism, and environmental adaptation in plants. Despite its biological importance, the HD-Zip IV family has not been systematically characterized in apple (Malus domestica). Here, we identified 17 apple HD-Zip IV genes and named them MdHDZIV1-MdHDZIV17 based on their locations on the chromosomes. The 17 genes showed a nonuniform distribution on eight chromosomes, while the occurrence of both tandem and segmental duplications indicated that family expansion involved more than one duplication mechanism. All MdHDZIV proteins contained the conserved HD, LZ, START, and SAD domains but lacked the MEKHLA domain, consistent with typical HD-Zip IV structural features. Phylogenetic analysis classified MdHDZIV proteins into five groups together with HD-Zip IV members from Arabidopsis thaliana and rice, indicating evolutionary conservation of this subfamily. Collinearity and Ka/Ks analyses revealed that duplicated MdHDZIV gene pairs were mainly subjected to purifying selection. Promoter scanning revealed diverse cis-regulatory motifs associated with hormonal signaling, environmental stress, light response, and epidermal regulation, including ABRE, ARE, W-box, MYC, G-box, and L1-box motifs. Integration of transcriptomic profiling with qRT-PCR validation revealed pronounced tissue-dependent differences in the expression of MdHDZIV genes in leaf, fruit skin, and branch bark. Under PEG6000-induced osmotic stress and NaCl-induced salt stress, 10 candidate MdHDZIV genes displayed gene-specific and stress type-specific expression patterns, with MdHDZIV3 showing strong induction under PEG6000 treatment. Functional validation in apple calli showed that MdHDZIV3 overexpression enhanced PEG tolerance, increased fresh weight, elevated SOD and POD activities, and reduced MDA accumulation under osmotic stress. These findings provide a genome-wide framework for understanding the apple HD-Zip IV gene family.

abiotic stress↗

PubMedDate not supplied

[Neuronal reactions of the olfactory centers of the forebrain during stimulation of the hypothalamic structures in rabbits].

During stimulation of phylogenetically ancient parts of the hypothalamus (the anterior and lateral), neuronal reactions have been recorded in the prepyriform lobe and tuberculum olfactorium. These reactions are characterized by a short latent period (6-25 msec) and high stability to rhythmic stimulation. Neuronal reactions in the same olfactory centers during stimulation of phylogenetically more recent hypothalamic structures (the posterior and medial) exhibit a long latent period (30-120 msec) and are readily exhausted by rhythmic stimulation.

Animals↗

PubMed2025

Inference of Cytochrome P450 Evolutionary History Using Structural and Physicochemical Metrics.

Cytochrome P450s are a superfamily of heme-binding monooxygenases involved with the detoxification of intrinsic and extrinsic toxins. They are near ubiquitous within biological domains and are found in all domains. Members of families within the superfamily are defined based on amino acid identity thresholds, with thresholds as low as 40% in some families. Relationships among Cytochrome P450 families have proven elusive due to sub-Twilight Zone interfamily identities (<30%) that result in poor multiple sequence alignment quality and thus low levels of support for downstream phylogenetic reconstructions. Despite the low identities, Cytochrome P450 structures are remarkably well conserved both within and among families. In such cases, structural phylogenetics has the potential to unveil elusive relationships because the selectively favored physicochemical properties giving rise to the structure and function of the proteins persist despite sequence-level divergence. Recently, in two separate publications, we demonstrated that by utilizing physicochemical vectors, dynamic time warping, and hierarchical clustering (PCDTW), large swaths of protein domain families and betacoronavirus receptor-binding domain clades were congruent with validated functional/structural relationships. These were important findings because anomalous sequence alignment-based maximum likelihood phylogenetic findings, which were not congruent with the known functional relationships, were resolved. That also validated the use of physicochemical vectors in making inferences about structural/functional homology. Additionally, it illuminated that the same methods might be applied to other protein families with relationships that are difficult to resolve from sequence data alone. Herein, we used Molecular Weight and Hydrophobicity Physicochemical Dynamic Time Warping (MWHP PCDTW) along with structural and sequence alignment-based phylogenetic methodologies to analyze all of the Cytochrome P450s found both in the high-fidelity Structural Classificaction of Proteins (SCOP) database and the reviewed sequences with both experimentally resolved and de novo predicted structures in the Protein Data Bank and the AlphaFold (AF) Protein Structure Database, respectively. We compared the resulting phylogenetic topologies and found that in some cases, structure-based methods may be less able to resolve random/convergent similarity than physicochemical and sequence-based methodologies. This finding agrees with previous findings that demonstrate the usefulness of physicochemical properties in resolving both random structural similarity and potentially convergent relationships.

Cytochrome P-450 Enzyme System↗

PubMed2026

Mitochondrial genomes of Dactylogyrus wunderi (Monopisthocotyla: Dactylogyridae): structural features, codon usage patterns, and phylogenetic implications.

BACKGROUND: Codon usage bias (CUB) is a common phenomenon reported among many species and genes, but its unique characteristics in the mitochondrial genome of class Monopisthocotyla remain unknown. METHODS: The complete mitochondrial genome of Dactylogyrus wunderi was sequenced and characterized, and the mitochondrial genome compositions and CUB of six Dactylogyrus species and 35 Monopisthocotyla species were analyzed using bioinformatics methods. RESULTS: The mitochondrial genome of D. wunderi is a typical circular structure in length of 14,920 bp. The A + T contents of the six Dactylogyrus species (58.4% ± 5.7%) were significantly lower than that of Monopisthocotyla species (71.0% ± 5.80%, p < 0.01). Neutrality plot analysis showed slopes of 0.3136 and 0.389 in the six Dactylogyrus and the 35 Monopisthocotyla species, respectively. Furthermore, 98.3% and 77.4% of the genes in the six Dactylogyrus and the Monopisthocotyla species, respectively, had effective number of codons (ENC) higher than 35, but 23.3% and 0.5% genes of ENC ratio ranged from - 0.05 to 0.05 in the six Dactylogyrus and Monopisthocotyla species. Phylogenetic analysis revealed that, within the context of the sampled taxa, the families of Monopisthocotyla were monophyletic groups, except for Ancyrocephalidae. CONCLUSIONS: The nucleotide composition had AT base bias in Monopisthocotyla, and natural selection was the main factor affecting CUB in the mitochondrial genomes of Monopisthocotyla species. These results provided insights into the factors affecting CUB in Monopisthocotyla species and deepened our insight of phylogeny, evolution, and codon usage of Monopisthocotyla.

Genome, Mitochondrial↗

PubMed1992

Characterization of the Bacillus subtilis rpsD regulatory target site.

The Bacillus subtilis rpsD gene, which encodes ribosomal protein S4, is subject to autogenous regulation. Repression of rpsD expression by excess S4 protein was previously shown to be affected by mutations in the leader region of the gene. A large number of deletion and point mutations in the leader region were generated, and their effect on repression by S4 in vivo was tested. These studies indicated that the required region was within positions +30 to +190 relative to the transcription start point. Replacement of the rpsD promoter with a lac promoter derivative which is expressed in B. subtilis had no effect, indicating that repression by S4 occurs at a level subsequent to transcription initiation. The rpsD leader region was isolated from several Bacillus species. Members of the B. subtilis group, as defined by analysis of 16S rRNA sequence, contained a leader region target site very closely related in structure to that of B. subtilis, despite considerable primary sequence variation; the B. brevis rpsD leader contained some but not all of the structural features found in the regulatory target sites of the other Bacillus species. Very little similarity to the Escherichia coli alpha operon S4 target site was found at either the primary-sequence or the secondary-structure level. Mutagenic and phylogenetic data indicate that the secondary structure of the leader region regulatory target site contains two large stem-loop domains. The first of these helices has a side loop which is essential for autoregulation, is highly conserved among Bacillus rpsD genes, and is similar to a region of 16S rRNA important in S4 binding.

Bacillus subtilis↗

PubMed1976

Possible phylogenetical significance of the corpus callosum with special reference to the dolphin brain (Stenella graffmani).

The surface area of the corpus callosum was measured in several animals as compared to the brain weight. A general consideration of the importance of this structure on the phylogenetic scale, with special reference to the corpus callosum of the dolphin, Stenella graffmani, is given. Some theoretical considerations about the significance of this structure upon some specialized features are mentioned.

Anatomy, Comparative↗

PubMed1976

[Lung structure of Sphenodon punctatus. A comparative anatomic study].

After a critical review of the literature, the authors describe the structure of the lung of Sphenodon, dealing with form, arteries, veins, and septation. The external form, circulatory pattern, degree of complication, height of the septa, vascular structure, and decrease in complication (?) are discussed from the standpoint of comparative anatomy. In an attempt to explain the unusual findings, the capacity for development of the central and subpleural type of differentiation is compared and contrasted. Obvious relations between the unusual lung structure and the phylogenetic age of the Sphenodon were sought, with the conclusion that the Sphenodon cannot be included in the Reptilian oders since its physical structure forms a class by itself.

Animals↗

PubMed2025

Landscape genomics analysis reveals the genetic basis underlying cashmere goats and dairy goats adaptation to frigid environments.

Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance. The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments, clarify the impact of environmental factors on genome diversity, and lay the foundation for breeding goat breeds to adapt to climate change. A total of 240 dairy goats were subjected to genome resequencing, and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated. By integrating multiple approaches such as phylogenetic analysis, population structure analysis, gene flow and population history exploration, selection signal analysis, and genome-environment association analysis, an in-depth investigation was carried out. Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds. Through signal analysis (θπ, FST, XP-CLR), we identified numerous candidate genes associated with cold adaptation in dairy goats (STRIP1, ALX3, HTR4, NTRK2, MRPL11, PELI3, DPP3, BBS1) and cashmere goats (MED12L, MARC2, MARC1, DSG3, C6H4orf22, CHD7, MYPN, KIAA0825, MITF). Genome-environment association (GEA) analysis confirmed the link between these genes and environmental factors. Moreover, a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds. This study contributes to understanding the genetic basis of cold adaptation, providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles, thereby ensuring sustainable animal husbandry.

Environmental adaptation↗

PubMed2026

Plastid genome evolution and phylogenomics with broad taxon sampling: insights into intrafamilial classification of Hamamelidaceae.

Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences (accD, ycf1, clpP, ndhF, and rpl22) and intergenic spacers (rpl33-rps18, the trnG-UCC intron, trnH-GUG-psbA, accD-psaI, and petA-psbJ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

Hamamelidaceae↗

PubMed2025

Genetic and phenotypic diversity of wine-associated Hanseniaspora species.

The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow-evolving lineage (SEL) and fast-evolving lineage (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 116 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO₂, and cold tolerance.

Wine↗