SEARCH · PubMed Health
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
MOTIVATION: How population structure can shape genetic diversity is a longstanding problem in population genetics. While the use of geographic locations, when available, can help answer some of these questions, it is still difficult to determine population structure when such metadata are not available or when the potential population structure is not easily observed. Here, we present an updated version of treestructure, an R package that implements a statistical test based on coalescent theory to detect unobserved population structure in a time-scaled phylogenetic tree. AVAILABILITY: treestructure is available at CRAN at https://cloud.r-project.org/web/packages/treestructure/ and at https://emvolz-phylodynamics.github.io/treestructure/.
Explore the source record for details and available documents.
The Forkhead box (Fox) transcription factors are evolutionarily conserved regulators of development, cell cycle, and apoptosis across metazoans. This study provides the first comprehensive genome-wide analysis of the Fox gene family in the Asian green mussel (Perna viridis). We identified 28 Fox genes distributed across 10 chromosomes. Comparative analysis reveals the absence of the FoxI, FoxQ1, FoxR and FoxS subfamily, consistent with other bivalves and indicative of lineage-specific gene loss during molluscan evolution. Notably, gene duplications in the FoxAB, FoxD, FoxH, FoxN1-4, FoxQ2 and FoxQD subfamilies may reflect functional diversification associated with environmental adaptation. Exon-intron structural variability, including intron loss in several paralogues, suggests structural diversification and potential regulatory variation. Phylogenetic reconstruction confirmed the monophyly of core Fox classes while highlighting divergent expansion patterns in lophotrochozoans. Selection analyses showed strong purifying selection across duplicated Fox paralogs, supporting functional conservation after lineage-specific expansion. Gene Ontology enrichment linked Fox genes to stress response, apoptosis, and transcriptional regulation. By integrating phylogenetic, structural, and transcriptomic analyses, this study provides a genomic framework for understanding Fox gene organisation, evolution, and tissue-associated expression patterns in Perna viridis and establishes a comparative resource for future functional studies in bivalves.
Endocrine fibroblast growth factors (FGF19 subfamily) play a key role in regulating metabolic homeostasis in vertebrates. However, their functional diversification in salmonids remains poorly understood. In this study, we conducted an integrative characterisation of Fgf19 and Fgf21 signalling in rainbow trout (Oncorhynchus mykiss) by combining phylogenetic, structural and expression analyses. Phylogenetic analyses revealed the conservation of single fgf19 and fgf21 genes, despite the extensive expansion of receptors post-Ss4R (salmonid-specific fourth-round whole genome duplication). Structural modelling and molecular dynamics simulations demonstrated the stable interactions of both ligands to multiple Fgfr isoforms, with receptor-specific energetic profiles and conserved core interaction residues. Tissue expression profiling revealed clear differences from mammalian models, such as predominant hepatic fgf19 expression and the absence of hepatic fgf21 under basal conditions. In addition, there were complex and tissue-dependent distributions of fgfr and klotho transcripts. These findings support a receptor-driven diversification model of endocrine Fgf signalling in salmonids, suggesting enhanced endocrine plasticity associated with the retention of receptors following post-genomic duplication. Taken together, our findings provide new insights into the structural and regulatory organisation of endocrine Fgf signalling, as well as its potential role in metabolic regulation in rainbow trout.
Calcium signaling plays a central role in plant adaptation to abiotic stresses and is primarily mediated by calmodulin and its associated transcription factors. Calmodulin-binding transcription activators (CAMTAs) regulate stress-responsive gene expression, but their characteristics and functions remain largely unexplored in Aegilops tauschii Coss., the D-genome progenitor of bread wheat. In this study, a genome-wide identification and characterization of the CAMTA gene family was performed, followed by phylogenetic, structural, conserved domain, promoter cis-element, and expression analyses under drought stress. Five AetCAMTA genes were identified and classified into three phylogenetic groups. All proteins contained conserved CG-1 DNA-binding, ankyrin repeat (ANK), and IQ calmodulin-binding domains and exhibited similar exon-intron organization. Promoter analysis revealed abundant hormone- and stress-responsive cis-elements, particularly abscisic acid-responsive element (ABRE) and drought-responsive MYB-binding site (MBS) motifs, suggesting their involvement in drought-responsive signaling. Quantitative RT-PCR showed genotype- and stress-dependent expression patterns, with the drought-tolerant ecotype (TN-01-1747) exhibiting higher expression of AetCAMTA1, AetCAMTA2, and AetCAMTA3 than the drought-sensitive ecotype (TN-01-1559) under moderate drought stress. These findings provide new insights into the evolutionary and functional characteristics of AetCAMTA genes and identify promising candidates for improving drought tolerance in wheat through molecular breeding and biotechnological approaches.
Arid landscapes provide important systems for examining how geographic structure and environmental heterogeneity shape genomic differentiation. In topographically complex desert regions, however, it remains challenging to determine whether population structure primarily reflects landscape resistance, geographic distance, or contemporary environmental variation. Here, we use genome-wide SNP data to investigate population structure, phylogenetic relationships, historical gene flow, demographic history, and landscape correlates of genomic differentiation in the variegated racerunner (Eremias vermiculata), a widespread lacertid lizard across arid Eastern Central Asia. Analyses of 164 individuals recovered six geographically structured nuclear clusters associated with major desert basins and mountain-bounded regions. Nuclear phylogenies resolved two broad regional clades corresponding to northeastern and southwestern parts of the species' range, while PCA and ADMIXTURE analyses recovered six finer-scale genetic clusters. Mitochondrial phylogenies, based on combined NCBI-derived Cyt b and COI sequences from the same individuals, recovered four deeper maternal lineages. These patterns indicate overall phylogeographic agreement between nuclear and mitochondrial datasets, with genome-wide SNPs providing finer-scale resolution of population structure. Demographic reconstructions further uncovered regionally heterogeneous Late Pleistocene histories among clusters, including signals of expansion, stability, and decline. Landscape genomic analyses revealed that genomic differentiation is primarily associated with landscape resistance, particularly elevation and land cover, as well as geographic distance, whereas contemporary environmental variables explained comparatively little variation after controlling for spatial structure. Together, our results suggest that genomic differentiation in E. vermiculata reflects the interplay of persistent landscape configuration, historical connectivity, and region-specific demographic histories across arid Eastern Central Asia. More broadly, this study highlights the value of integrating phylogeographic and landscape genomic approaches for understanding population differentiation and evolutionary history in topographically heterogeneous desert ecosystems.
Current knowledge of class-I cytokine receptors comes primarily from studies in jawed vertebrates (gnathostomes), and their origin and evolution remain unresolved. In this study, we identified a leptin receptor-like sequence (LepRL) and three interleukin-6 receptor subunit b-like sequences (IL6RBL) from a jawless vertebrate (cyclostome), the sea lamprey (Petromyzon marinus). Based on structural, phylogenetic, and syntenic analyses, we deduced that these lamprey receptors are likely distinct ohnologs to gnathostome LepR and IL6RB-related receptors, respectively, that arose in the two rounds of vertebrate whole-genome duplication (1R and 2R). Notably, lamprey LepRL likely originated from a different 1R progenitor than the one giving rise to gnathostome LepR during cyclostome hexaploidization. Differential patterns in mRNA expression of LepRL and IL6RBLs were observed among adult tissues, during larval metamorphosis, and in response to juvenile feeding. Feeding stimulated hepatic expression of LepRL and IL6RBL (namely, IL6RBL1) mRNAs in correlation with upregulation of insulin-like growth factor mRNA, whereas brain LepRL and IL6RBL1 mRNA expression was correlated positively with neuropeptide Y but inversely with intestinal content in fed juveniles. Notably, these observations along with immunolocalization of LepRL in the hypothalamus suggest a role of leptin signaling in regulating energy balance that is conserved among vertebrates. Additionally, seawater exposure stimulated branchial LepRL expression coincident with increased expression of ion transporters in ionocytes, indicating a role of leptin signaling in osmoregulation. These findings provide new insight into the early evolution of class-I cytokine receptors and reveal diverse functions of the leptin signaling system in jawless vertebrate.
Recent studies with comparative data on base sequences of homologous DNA's or amino acid sequences of homologous proteins indicate that simultaneous estimation of phylogenetic structure and time of divergence is often cumbersome and time consuming. On the other hand, when the topology of an evolutionary tree is known, it is shown in this paper that the least squares theory may be applied to obtain simple estimates of the relative time lengths for each segment of the tree under the assumption of uniform random substitutions in each segment. The method is illustrated with amino acid sequence data on various globin molecules and cytochrome c. The evolutionary significance of some of the estimates is also discussed.
While the key aspects of genetic evolution and their clinical implications in clear cell renal-cell carcinoma (ccRCC) are well-documented, how genetic features co-evolve with the phenotype and tumor microenvironment (TME) remains elusive. Here, through joint genomic-transcriptomic analysis of 243 samples from 79 patients recruited to the TRACERx Renal study, we identify pervasive non-genetic intratumor heterogeneity, with over 40% not attributable to genetic alterations. By integrating tumor transcriptomes and phylogenetic structures, we observe convergent evolution to specific phenotypic traits, including cell proliferation, metabolic reprogramming and overexpression of putative cGAS-STING repressors amid high aneuploidy. We also uncover a co-evolution between the tumor and the T cell repertoire, as well as a longitudinal shift in the TME from an anti-tumor to an immunosuppressive state, linked to the acquisition of recurrently late ccRCC drivers 9p loss and SETD2 mutations. Our study reveals clinically-relevant and hitherto underappreciated non-genetic evolution patterns in ccRCC.
Chloroplast genomes provide important insights into plant phylogeny, genome evolution, and molecular marker development. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of two endemic species from Uzbekistan, Astragalus nuratensis and Oxytropis pseudorosea. Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively. The chloroplast genomes were 122,316 bp in A. nuratensis and 122,708 bp in O. pseudorosea. Both genomes encoded 110 unique genes, including 76 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Consistent with members of the inverted repeat-lacking clade of Fabaceae, both species lacked the typical inverted repeat regions, resulting in a single-copy genome structure. Phylogenetic analysis based on 119 complete chloroplast genomes resolved major lineages within Astragalus and related genera with strong support. Astragalus nuratensis was placed within the Phaca clade, while Oxytropis pseudorosea formed part of a distinct Oxytropis lineage. These results provide new genomic resources for understanding evolutionary relationships and plastome evolution in Central Asian legumes.
The Mediterranean population of tomato leaf curl New Delhi virus (ToLCNDV-ES) is characterized by a high genetic uniformity, distinguishing it from its Asian counterparts. ToLCNDV-ES is thought to have a monophyletic origin, likely resulting from a single recombination event, prior to its spread throughout the Mediterranean region. Following its first detection in southeastern France in 2020, ToLCNDV-ES re-emerged in France in 2022. Our analysis based on advanced long-read sequencing, circular DNA profiling, and phylogeny indicates both local persistence of French ToLCNDV-ES and multiple independent introduction events. Signatures of positive selection were identified in French ToLCNDV-ES populations, whereas no clear evidence of recombination was found. Bayesian time-structured phylogenetic analyses suggest that introductions in France occurred between 2018 and 2021 from the major ToLCNDV-ES clade, while several Italian ToLCNDV-ES isolates diverged prior to the virus introduction in the Mediterranean basin. Overall, this study demonstrates the value of an optimized long-read sequencing approach for resolving circular DNA virus diversity, and sheds light on the complex evolutionary history of ToLCNDV-ES in the Mediterranean Basin, particularly in southeastern France.
INTRODUCTION: Candidozyma auris is an emerging healthcare-associated fungal pathogen with a high propensity for nosocomial transmission and development of antifungal resistance. This study aimed to identify resistance-associated genomic variants and characterize the phylogenetic structure of clinical C. auris isolates circulating in Russia. METHODS: We analyzed 82 isolates collected between 2017 and 2023 from 18 hospitals in the Northwestern and Central Federal Districts of the Russian Federation. Antifungal susceptibility testing was combined with whole-genome sequencing, targeted FCY2 sequencing, and comparative phylogenomic analysis using publicly available international genomes. RESULTS: All isolates analyzed in this study belonged to clade I and showed a highly conserved profile of elevated azole MICs. The consistent detection of ERG11 (K143R), TAC1B (A640V), and CDR1 (V704L) suggests that reduced azole susceptibility in this population is associated with both target-gene alteration and efflux-mediated mechanisms. All isolates remained susceptible to echinocandins in vitro, and no resistance-conferring mutations were detected in FKS1, consistent with the absence of an echinocandin-resistant phenotype. Decreased susceptibility to flucytosine was mainly associated with the FCY2 (L383*) nonsense mutation, which was confirmed by targeted Sanger sequencing in additional isolates. Phylogenomic reconstruction showed that the Russian isolates represented a restricted segment of global clade I diversity and revealed two major geographically structured lineages corresponding to two large metropolitan areas in European Russia. DISCUSSION: The distribution of closely related isolates across hospitals supports local persistence and inter-hospital dissemination of genetically related strains. These findings provide important insights into the molecular epidemiology, antifungal resistance mechanisms, and transmission dynamics of C. auris in Russia.
Nelumbo nucifera Gaertn. is an economically and ecologically important aquatic plant, but its growth and productivity are severely constrained by soil salinization and alkalization. AP2/ERF transcription factors are key regulators of plant abiotic stress responses; however, their roles in salt-alkali tolerance in N. nucifera remain largely unclear. In this study, we performed a genome-wide identification and characterization of the AP2/ERF gene family in N. nucifera, followed by phylogenetic, structural, and physicochemical analyses. A total of 101 AP2/ERF genes were identified and classified into five subfamilies, showing both evolutionary conservation and species-specific divergence compared with Arabidopsis thaliana. Physiological analyses during seed germination under salt-alkali stress revealed significant changes in malondialdehyde content, proline accumulation, and antioxidant enzyme activities, suggesting activation of oxidative stress defense and osmotic adjustment mechanisms. Transcriptome profiling of seedlings treated with 150 mM salt-alkali solution for 5 and 10 days identified 7,350 differentially expressed genes, including 29 AP2/ERF members responsive to stress. Among them, 13 genes, including AP2-9, ERF23, ERF15, ERF31, ERF34, and DREB21, were consistently upregulated under both treatments, indicating their potential roles in stress adaptation. qRT-PCR validation further confirmed the sustained upregulation of key genes AP2-9, ERF23, ERF34, and DREB21, consistent with transcriptome data. Overall, this study provides the first comprehensive overview of the AP2/ERF gene family in N. nucifera and identifies candidate regulators involved in salt-alkali stress responses, offering valuable insights into the molecular mechanisms of stress adaptation and potential genetic resources for breeding salt-alkali tolerant aquatic plants.
Genes encoding DUF568 domain-containing proteins participate in plant stress adaptation. To elucidate the functional role of DUF568 domain-containing genes in Trichoderma-induced wheat defense responses against wheat Fusarium crown rot, we performed a genome-wide identification and characterization of the TaDUF568 gene family in hexaploid wheat (Triticum aestivum L.). In this study, a total of 33 TaDUF568 family genes were systematically identified and characterized at the genome-wide level, exhibiting uneven chromosomal distribution and diverse physicochemical properties. Phylogenetic, structural, and collinearity analyses revealed conserved family characteristics among monocot species. Segmental duplication was verified as the primary driver of gene family expansion. Expression profiling revealed divergent tissue-specific expression patterns among TaDUF568 family members, among which TaDUF568.18 was strongly induced by Trichoderma M2. Subcellular localization assays confirmed that TaDUF568.18 is a plasma membrane-localized protein. Functional validation via stable transgenes demonstrated that overexpression of TaDUF568.18 restricted lesion expansion, improved agronomic traits, and enhanced disease resistance. This study is the first to characterize the wheat DUF568 family and confirm that TaDUF568.18 (annotated as TaAIR12) acts as a positive regulator of Trichoderma-mediated wheat defense, providing a valuable gene resource for wheat disease-resistance breeding.
A detailed understanding of the molecular mechanisms governing the flowering time of Amomum villosum Lour., a medicinal plant within the Zingiberaceae family, is currently lacking. In modern plants, the florigen activation complex (FAC), which includes PEBP, FD/bZIP, and GRF proteins, is known to regulate flowering. In this study, we identified 13 PEBP, 5 FD, and 19 GRF genes within the A. villosum genome and conducted phylogenetic, structural and promoter analysis. Notably, cross-species protein-protein interaction predictions and yeast two-hybrid assays uncovered an unexpected interaction pattern: an AREB3-like FD protein (AvFD5) and a GRF protein (AvGRF13) directly interact with specific PEBP members, whereas canonical FD-like proteins (AvFD1 and AvFD4) did not, which contrasts with the classical rice FAC model (Hd3a-14-3-3-OsFD1). These results imply that FAC assembly in A. villosum may involve alternative components or regulatory mechanisms, potentially indicating lineage-specific divergence within monocots. This research represents the first systematic characterization of FAC core gene families in A. villosum and Zingiberaceae, laying the groundwork for understanding flowering time regulation and facilitating future molecular breeding efforts in this economically significant plant.
Derivatives of one triterpene family, the hopane family, are widely distributed in prokaryotes; they may be localized in membranes, playing there the same role as sterols play in eukaryotes, as a result of their similar size, rigidity, and amphiphilic character. Their biosynthesis embodies many primitive features compared to that of sterols and could have evolved toward the latter once aerobic conditions had been established. Membrane reinforcement appears to be achieved in other prokaryotes by other mechanisms, involving either approximately 40-A-long rigid hydrocarbon chains terminated by one polar group acting like a peg through the double-layer or similar chains terminated by two polar groups acting like tie-bars across the membrane. These inserts can be tetraterpenes (e.g., carotenoids). The biophysical function of membrane optimizers appears to have evolved toward sterols by changes limited to only a few enzymatic steps of the same fundamental biosynthetic processes.
While advances in molecular epidemiology and computational modeling have enhanced our capacity to track pathogen evolution, the accurate reconstruction of spatiotemporal transmission dynamics remains essential for developing epidemic preparedness frameworks and implementing outbreak response measures. Structured coalescent models offer a phylogeographic framework by restricting lineage coalescence events to geographically proximate host populations. Although the Bayesian structured coalescent approximation (BASTA) provides a tractable approach, contemporary phylogeographic analyses involving dozens of geographic localities and hundreds to thousands of viral genomes substantially exceed the computational capacity of existing implementations. The BASTA likelihood scales cubically with deme count and quadratically with sequence count due to matrix exponentiation and pairwise coalescent probability calculations. Here, we introduce a comprehensive algorithmic restructuring of the structured coalescent likelihood that eliminates redundancies, optimizes memory access, and exposes parallelization opportunities. Our approach reorganizes computations along three dimensions: (i) independent calculation of deme-transition probability matrices across time intervals; (ii) simultaneous evaluation of partial likelihood vectors within temporal slices; and (iii) concurrent aggregation of coalescent probabilities. Algorithmic restructuring cuts average coalescent likelihood computation by 7-8 fold, and parallelization further boosts performance to 10-26 fold, enabling joint phylogeographic analyses of dengue virus across 10 South American countries and H5N1 avian influenza across 20 Eurasian regions to finish in a fraction of prior time. This computational efficiency also enables comparison between backward-in-time structured coalescent approximations and forward-in-time phylogeographic methods, revealing that the former provides appropriately conservative posterior estimates, particularly at intermediate phylogenetic depths. We integrate our implementation into the popular BEAST X and BEAGLE software packages, with an accompanying interface in BEAUti X to easily set up the analyses, providing researchers with an accessible and scalable tool for real-time phylogeographic surveillance of rapidly evolving pathogens.