Search Results (984)

The Bacillus anthracis pXO1 plasmid, encoding ~143 proteins, presents a compact model for exploring protein function and evolutionary patterns using protein language models. Due to the organism’s slow evolutionary rate, its limited amino acid variation enhances detection of physiologically relevant patterns in plasmid protein composition. In this study, we applied embedding-based analyses and machine learning methods to characterize pXO1 protein modules across diverse B. anthracis lineages. We generated protein sequence embeddings, constructed phylogenies, and compared plasmid content with whole genome variation. While whole genome and plasmid-based phylogenies diverge, the composition of proteins encoded along the pXO1 plasmid revealed lineage specific structure. Association rule mining combined with decision tree classification produced plasmid-encoded targets for assessing anthrax sublineage, which yielded functionally redundant protein modules that reflected geographic and phylogenetic patterns. A conserved DNA replication module exhibited both shared and B. anthracis lineage specific features. These results show that pXO1 plasmid protein modules contain biologically meaningful and evolutionarily informative signatures, exemplifying their value in phylogeographic characterizations of bacterial pathogens. This framework can be extended to study additional virulence plasmids across Bacillus and other environmental pathogens using scalable protein language model tools. Full article

Universal Stress Protein (USP) plays crucial roles in plant stress adaptation, yet their evolutionary dynamics, regulatory mechanisms, and functional diversification in rice (Oryza sativa) remain poorly understood. This study aimed to conduct a genome-wide identification and characterization of the OsUSP gene family to elucidate its role in abiotic stress responses using integrated bioinformatics approaches. Here, we identified 46 OsUSP genes that are unevenly distributed across 11 rice chromosomes and exhibit significant divergence in protein length, molecular weight, and subcellular localization. Phylogenetic analysis classified OsUSPs into three subfamilies, with conserved motif and domain architectures within groups but distinct structural variations across subfamilies. Evolutionary analysis revealed strong collinearity between rice and other monocots, which suggests functional conservation in grasses, whereas limited synteny with dicots indicates lineage-specific divergence. Cis-regulatory element analysis showed enrichment in ABA, MeJA, drought, and hypoxia response motifs, implicating OsUSPs in hormonal and stress signaling. Expression profiling indicated tissue-specific patterns, with subfamily III genes broadly expressed, while subfamily II members were anther-enriched. Stress response profiling revealed that 24 OsUSPs were significantly induced, while LOC_Os02g54590 and LOC_Os05g37970 emerged as particularly notable due to their broad-spectrum responsiveness, being upregulated under all tested stress conditions. Protein–protein interaction (PPI) analysis indicated that OsUSP proteins potentially interact with Leo1/TPR-domain proteins and are involved in stress response and phosphorylation signaling pathways. This study yields key insights into OsUSP-mediated stress adaptation in rice and pinpoints promising candidate genes to facilitate the breeding of climate-resilient rice. Full article

The success and impact of biological invasions depend on adaptations to novel abiotic and biotic selective pressures. However, the genetic mechanisms underlying adaptations in invasive species are inadequately understood. Taenioides sp. is an invasive worm goby, originally endemic to brackish waters in the estuaries of Southeastern China, and now colonizes multiple inland freshwaters of North China within decades as a byproduct of the East Route of South-to-North Water Transfer (ESNT) project. However, the molecular mechanisms underlying their adaptations to the climate of North China, especially the temperature regime, are unknown. Here, we performed genomic resequencing analysis to assess genetic diversity and population genetic structure, and further investigated the genomic signatures of local adaptation in the invasive population of Taenioides sp. during their northward invasion. We revealed that all invasive populations exhibited no genetic differentiation but low gene flow and an obvious signal of population bottleneck. Yangtze River estuary may serve as the source population, while Gaoyou Lake serves as a potential bridgehead of the invasion. Selective sweep analyses revealed 117 genomic regions, containing 673 candidate genes, under positive selection in populations at the invasive front. Redundancy analysis suggested that local temperature variables, particularly the monthly minimum temperature, represent critical evolutionary forces in driving adaptive divergence. Functional enrichment analyses revealed that multiple biological processes, including metabolism and energy production, substance transmembrane transport, and neural development and synaptic transmission, may play important roles in adaptation to regional temperature conditions. Our findings revealed a scenario of adaptive evolution in teleost species that underpins their regional climate adaptation and successful establishment of invasive populations in a human-facilitated invasion context. Proper management strategies should be established to manage Taenioides sp invasion as soon as possible. Full article

Paulownia trees are grown globally for their robust timber, agroforestry, and effective carbon dioxide drawdown. China possesses rich Paulownia germplasm resources, offering favorable material for the genetic improvement. Understanding the taxonomy and phylogenetic relationships of Paulownia species is essential for the advancement of germplasm innovation. In this study, we re-sequenced 67 typical accessions of 11 species within the Paulownia genus. A total of 16,163,790 high-quality single nucleotide polymorphisms (SNPs) were identified. Based on these markers, these accessions were classified into three groups: P. fortunei and P. lampropylla (Group I); P. tomentosa, P. fargesii, and P. kawakamii (Group II); and P. taiwaniana, P. jianshiensis, P. catalpifolia, P. elongata, P. ichangensis, and P. albiphloea (Group III). Using maximum likelihood estimation, population genetic structure analysis revealed that the 11 species originated from four different ancestral populations. The two predominant breeding species—P. fortunei and P. tomentosa—exhibit divergent origins: P. fortunei arose from hybridization between two ancestral species followed by complex admixture, whereas P. tomentosa retains a predominantly singular ancestral lineage, with traces of P. kawakamii. The genetic diversity (π) of P. tomentosa was 0.002588, which was considerably lower than that of P. fortune (0.004181) suggesting that P. tomentosa is subjected to a stronger breeding selection during the evolution than P. fortune. A total of 59 selected regions and 65 genes were identified by selective sweep analysis. These genes may be involved in biological processes such as morphological development and response to abiotic stress and hormonal activity regulation. These findings provide valuable references for further research on the genetic differentiation and adaptive evolutionary mechanisms of Paulownia species, laying a foundation for future germplasm innovation and variety improvement. Full article

The genus Oxyuranus, which includes some of the most venomous snakes in the world, presents a complex venom composition with potent neurotoxic and procoagulant effects. This study provides a comparative proteomic analysis of the venom of Oxyuranus microlepidotus (Inland Taipan) and Oxyuranus scutellatus (Coastal Taipan), aiming to elucidate the molecular basis underlying their distinct toxicological profiles. Using high-resolution chromatographic fractionation and LC-MS/MS, we identified a core set of nine protein families shared between both species, including phospholipases A₂ (PLA₂), three-finger toxins (3FTx), natriuretic peptides (NTP), nerve growth factors (NGF), and prothrombin activators (PTA). O. microlepidotus venom exhibited greater diversity of 3FTxs and unique protein families, such as Waprin and 5′-nucleotidases, suggesting lineage-specific functional adaptations. Quantitative analysis revealed a greater relative abundance of PLA₂s in O. scutellatus (66%) compared to O. microlepidotus (47%), whereas 3FTXs were more prominent in O. microlepidotus (33% vs. 9%). These interspecific differences likely underlie the distinct clinical manifestations of envenomation and reflect evolutionary divergence in the venom composition. Our findings provide molecular insights into taipan venom complexity and highlight novel toxin candidates with potential biomedical applications in neurobiology, hemostasis, and anti-infective therapy. Full article

Biomphalaria pfeifferi snails serve as the major intermediate host for intestinal schistosomiasis in Sudan. The genetic structure and infection status of 163 B. pfeifferi collected from six localities in Gezira State, Sudan (East Gezira, Greater Wadmedani, Hasahisa, North Umelgura, South Gezira, and Managil) were characterized. Cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) mitochondrial genes were used for B. pfeifferi molecular identification and genetic diversity investigation. Schistosoma mansoni infection was detected using the traditional cercarial shedding and molecular methods (Sm^F/R primers). Five COI haplotypes and ten 16S haplotypes were identified, with haplotype diversity of 0.50 for COI and 0.11 for 16S. High evolutionary divergence was observed between groups (Fst = 0.94) for the COI, and low genetic divergence (Fst = 0.04) for the 16S, indicating genetic divergence among Sudanese B. pfeifferi, with the 16S showing lower divergence than the COI, consistent with a post-bottleneck population expansion. Cercarial shedding detected an overall infection prevalence of 3.6% (8/219), with only two snails from Hasahisa shedding S. mansoni cercariae. The Sm^F/R primers revealed a higher infection prevalence of 7.4% (12/163), with all S. mansoni positive samples found at the Hasahisa site. Findings highlight the value of molecular diagnostic tools for accurate surveillance and emphasize the need for site-specific control strategies. Full article

Since the appearance of the Severe Acute Respiratory Syndrome (SARS) virus, there has been increased interest in understanding the role of bats in the maintenance and circulation of coronaviruses. This study aimed to describe the phylogenetic and evolutionary relationships and antigenic architecture of a new coronavirus detected in bats in the Department of Córdoba. In a surveillance study of pathogens of interest to public health, a bat Phyllostomus hastatus was captured. Rectal swabs samples were collected from the bats, and RNA was extracted and sequenced using NGS with MGI-G50 equipment. The results were analyzed using bioinformatics software. A contig of 28,619 nucleotides associated with the Coronaviridae family was obtained. Phylogenetic and molecular clock analyses of the ORF1ab gene revealed a novel divergent Alphacoronavirus that originated directly from an ancestral node. The analysis of the spike (S) protein and receptor-binding domain (RBD) is similar to that of humans (HCoV-229E) and porcine coronaviruses. In silico analysis suggests potential RBD interaction sites with human and pig cellular receptor aminopeptidase N. There is a possible risk of interspecies jumping of the new AlphaCoV/P. hastatus in humans and pigs. This is the first study to perform phylogenetic, evolutionary, and antigenic characterization of bat coronaviruses in Colombia. Full article

The concept of a genome signature broadly refers to characteristic patterns in DNA sequences that enable the identification and comparison of species or individuals, often without requiring sequence alignment. Such signatures have applications ranging from forensic identification of individuals to cancer genomics. In comparative genomics and evolutionary biology, genome signatures typically rely on statistical properties of DNA that are species-specific and carry phylogenetic information reflecting evolutionary relationships. We propose a novel genome signature based on the compositional structure of DNA, defined by the distributions of strong/weak, purine/pyrimidine, and keto/amino ratios across DNA segments identified through entropic segmentation. We observe that these ratio distributions are similar among closely related species but differ markedly between distant ones. To quantify these differences, we employ the Jensen–Shannon distance—a symmetric and robust measure of distributional dissimilarity—to define a genome-to-genome distance metric, termed Segment Compositional Distance ($\mathcal{D}$). Our results demonstrate a clear correlation between $\mathcal{D}$ and species divergence times, and also that this metric captures a strong phylogenetic signal. Our method employs a genome-wide approach rather than tracking specific mutations; thus, $\mathcal{D}$ offers a coarse-grained perspective on genome compositional evolution, contributing to the ongoing discussion surrounding the molecular clock hypothesis. Full article

K-mer analysis is a powerful tool for understanding genome structure and evolution. A “k-mer” refers to a short DNA sequence made up of k nucleotides (where k is a specific integer), while an “m-mer” is a similar concept but with a shorter sequence length. The functional mechanisms of CG-containing k-mers, as well as their potential role in evolutionary processes, remain unclear. To explore this issue, we analyzed 8-mers in several species with varying genomic complexities and evolutionary divergences: Homo sapiens, Saccharomyces cerevisiae, Bombyx mori, Ciona intestinalis, Danio rerio, and Caenorhabditis elegans, which were grouped by CG dinucleotide content (0CG, 1CG, and 2CG). We examined the relative frequencies of shorter m-mers (with m = 3 and 4) within each CG-defined group, using information-theoretic, distance-based, and angular metrics. Our results show that 0CG motifs follow random patterns, while 1CG and 2CG motifs display significant deviations, likely due to functional constraints such as nucleosome-binding and CpG island association. The observed unimodal distribution of 8-mers arises from the convergence of the three CG-defined groups. Among them, the 2CG group shows the highest divergence in m-mer composition, followed by 1CG, reflecting varying degrees of selective pressure. Furthermore, species-specific differences in CG-classified 8-mer patterns could provide valuable insights into phylogenetic relationships. Through extensive comparison, we explore how CG content and sequence composition influence genomic organization and contribute to evolutionary divergence across different taxa. These findings deepen our understanding of short motif functions, genome organization, and sequence evolution. Full article

Magnoliids represent one of the most basal lineages within angiosperms, and their ancestral floral morphology provides crucial insights into the evolution of flowers in angiosperms. MCM1-AGAMOUS-DEFICIENS-SRF (MADS)-box transcription factors play crucial roles in specifying floral organs. To understand their evolutionary history and functional divergence in magnoliids, we identified MADS-box genes, and conducted phylogenetic and expression analysis in 33 magnoliids and 8 other angiosperm plants. A total of 1310 MADS-box genes were identified and classified into Type I and Type II. The expansion of MADS-box genes in magnoliids mainly arose from whole-genome duplication events. In Liriodendron chinensis and Chimonanthus praecox, we identified floral homeotic MADS-box genes that are orthologous to the ABCDE model genes of floral organ identity determination. The broad expression pattern of A and B genes in floral organs and overlapping activity of ABCDE-model genes are consistent with the “shifting−fading borders” scheme proposed in basally diverging angiosperm lineages. Our results not only elucidate the driving forces underlying the diversification of MADS-box genes in magnoliids, but also shed light on the evolutionary models of floral development in angiosperms. Full article

Eyespots are functionally complex and highly variable elements of butterfly wing patterns. The Meadow Brown, Maniola jurtina, is a classic model species studied for variation in eyespots as an index of evolutionary divergence and adaptation. However, the role of fine-scale ecogeographic conditions on eyespot variation remains poorly understood. In this study, we examined hindwing eyespot number, distribution, and combination patterns in male M. jurtina across climatically and topographically diverse north-western Balkans. Compared to the species average, males in this region displayed greater spottiness and phenotypic diversity. While the typical two-spot phenotype was dominant and stable, in some populations, three-spotted and even four-spotted males occurred at similar frequencies. Rare six-spotted individuals were recorded only at mountain localities above 1200 m. Geographic and climatic factors together influenced this variation: higher altitudes and cooler, thermally stable environments promoted increased eyespot number and greater phenotypic plasticity than warmer, more variable environments. This pattern contrasts with large-scale latitudinal trends previously described for the species, emphasizing the importance of local climatic heterogeneity. Our findings suggest the north-western Balkans as a possible transitional zone where environmental complexity promotes elevated eyespot variability, contributing to the understanding of adaptive morphological plasticity in M. jurtina. Full article

Duck viral hepatitis, caused by Duck Hepatitis A Virus Type 3 (DHAV-3), remains a major threat to young ducklings. Although DHAV-3 has circulated in China since the 1999s, the complete genomic architecture, exact virulence parameters, and evolutionary distance between early Yunnan isolates and current field strains have remained undefined. This study investigated six DHAV-3 strains isolated in Yunnan Province, China, between 2004 and 2006, to elucidate their genetic and biological characteristics. Full-genome sequencing and phylogenetic analysis revealed >99.5% nucleotide and >99.6% amino acid identity among the strains, suggesting a common ancestral origin. In vivo challenge assays showed rapid onset of clinical signs and >90% mortality in ducklings within 36 h post-inoculation. Embryonic deaths began at 24 h post-infection and peaked by 90 h. Viral replication was efficient in DEF, DEK, Vero, and BHK-21 cells, but absent in chicken fibroblasts (DF-1). Comparative genomic analysis between the YN/LR/2005 strain and recent field isolates (2022–2024) revealed substantial nucleotide divergence in structural regions, with 32 unique amino acid substitutions—all five located in the immunodominant VP1 region that may influence viral antigenicity and host interaction—alongside changes in N-glycosylation sites and alterations in protein secondary structure. Histopathological examination confirmed characteristic hepatic lesions. These findings demonstrate that while DHAV-3 has undergone genetic evolution, it retains high virulence, underscoring the need for ongoing molecular surveillance and supporting future vaccine and diagnostic development. Full article

Camphora officinarum Nees constitutes a pivotal tree species within the evergreen broad-leaved forests of East Asia, endowed with significant economic, ornamental, and ecological importance. Nevertheless, previous research has markedly underestimated the genetic diversity of this species, thereby hindering our efforts in conserving resources and enhancing genetic breeding. The current study generated 155 chloroplast genomes from specimens of C. officinarum obtained from six provinces/regions in China. The results reveal the identification of seven distinct clades (I–VII), with Clades II, III, V, and VII exhibiting genome expansions, primarily influenced by lineage-specific elongation of inverted repeats (IRs), whereas Clades I, IV, and VI maintained conserved IR lengths. Despite the structural plasticity, the GC content remained highly conserved. Geographic patterns indicated gene flow between adjacent regions (e.g., Hunan and Hubei with identical IR lengths), but genetic isolation in Fujian. High-polymorphism regions (psba-matK, ycf1, ycf2, and ndhF) were identified as superior phylogenetic markers, enhancing intraspecies-level resolution. Simple sequence repeats (SSRs) varied significantly among clades, dominated by A/T-rich mononucleotide repeats. These repeats, along with divergent repeat types (e.g., absence of reverse repeats in Clades V/VI), serve as robust tools for resource identification and evolutionary trajectory inference. Phylogenetically, samples from Fujian formed a distinct lineage, while samples from other regions, especially Guangdong, were mixed, with this finding probably being a reflection of historical cultivation and anthropogenic translocation. This study offers a framework for the genetic breeding and investigation of the evolutionary history of C. officinarum. Full article

Olfaction plays a crucial role in fish feeding behaviors and ecological adaptation. However, systematic studies on its transcriptional regulation and molecular evolutionary mechanisms in herbivorous and carnivorous fishes remain scarce. In this study, we analyzed four Xenocyprididae species: two herbivorous (Ctenopharyngodon idella and Megalobrama amblycephala) and two carnivorous (Elopichthys bambusa and Culter alburnus), using olfactory rosette transcriptome sequencing and cross-species comparisons. The number of unigenes per species ranged from 40,229 to 42,405, with BUSCO completeness exceeding 89.2%. Functional annotation was performed using six major databases. Olfactory-related candidate genes were identified based on Pfam domains (7tm_4) and KEGG pathways (ko04740), revealing 8–19 olfactory receptor genes per species. These candidate genes were predominantly enriched in the olfactory transduction and neuroactive ligand–receptor interaction pathways. A total of 3681 single-copy orthologous genes were identified, and their expression profiles exhibited clear interspecific divergence without forming strict clustering by dietary type. High-threshold differentially expressed trend genes (|log₂FC| ≥ 4) were enriched in pathways related to RNA processing, metabolite transport, and xenobiotic metabolism, suggesting that the olfactory system may participate in diverse adaptive responses. Ka/Ks analysis indicated that most homologous genes were under purifying selection, with only 0.87–2.07% showing positive selection. These positively selected genes were enriched in pathways related to immune response and neural regulation, implying potential roles in adaptive evolution associated with ecological behavior. Furthermore, the olfactory-related gene oard1 exhibited Ka/Ks > 1 in the E. bambusa vs. C. idella comparison. qRT-PCR validation confirmed the reliability of the RNA-Seq data. This work is the first to integrate two complementary indicators—expression trends and evolutionary rates—to systematically investigate the transcriptional regulation and molecular evolution of the olfactory system in Xenocyprididae species under the context of dietary differentiation, providing valuable reference data for understanding the perceptual basis of dietary adaptation in freshwater fish. Full article

Background/Objectives: The mutational dynamics of microsatellites over deep evolutionary timescales are poorly understood. This study aims to elucidate the life history of trinucleotide microsatellites by tracing orthologous loci across divergent vertebrate lineages and characterizing their mutational pathways. Methods: We developed a bioinformatic framework for identifying orthologous microsatellite loci using conserved flanking sequences. This approach was applied to three trinucleotide microsatellites located in exonic, intronic, and intergenic regions, respectively. These loci were amplified and sequenced across 126 individuals representing 64 vertebrate species, whose divergence times range from 6 to 150 million years ago (MYA). Results: Flanking sequences proved essential for reliable orthology assignment, while repeat motifs revealed distinct mutational pathways. Microsatellite decay occurs through two primary mechanisms: the complete loss of dominant repeats or their progressive reduction to solitary units (≤1 repeat). This degeneration process is facilitated by cryptic simple sequences (CSS), which act as genomic catalysts promoting birth–death transitions. Large intra-motif deletions were identified as the key mutational event driving contractions and eventual locus degeneration. Furthermore, mutational patterns were highly locus-specific, influenced by genomic context. Conclusions: Although the study focused on only three loci, limiting broader generalizations, our findings provide mechanistic insights into microsatellite evolution. These results establish a foundation for modeling complex microsatellite life histories and highlight the role of CSS in facilitating evolutionary turnover. Full article