Search Results (163)

Chloroplast genomes are valuable tools for exploring plant evolution, photosynthesis, and molecular systematics due to their relatively conserved structure and gene content. Here, I present a comprehensive comparative analysis of complete chloroplast genomes from 20 taxonomically diverse plant species, focusing on 16 widely used barcoding genes to investigate patterns of genome structure, gene retention, codon usage bias, and phylogenetic relationships. Genome sizes ranged from ~121 kb in Marchantia polymorpha to over 160 kb in Vitis vinifera, with GC content largely conserved across species. A multi-gene Neighbor-Joining phylogenetic framework recovered major taxonomic groupings and revealed gene-specific topological differences, reflecting locus-specific evolutionary histories. Presence/absence profiling showed that 13 of the 16 barcoding genes were consistently retained across species and classified as core genes, while the remaining three exhibited more variable distributions and were considered accessory. This pattern reflects both broad conservation and lineage-specific gene loss across plastomes. Genome-wide similarity analysis revealed high identity among closely related taxa (e.g., Arabidopsis and Brassica) and greater divergence among bryophytes, gymnosperms, and angiosperms. Codon usage analysis revealed generally conserved patterns, with lineage-specific biases observed in Cucumis sativus and Brassica rapa, suggesting influences from mutational pressure and potential translational selection. This integrative analysis highlights the dynamic yet conserved nature of chloroplast genomes and underscores the value of combining multiple genomic features in plastome evolution studies. The resulting dataset and analytical pipeline offer a useful resource for future phylogenomic, evolutionary, and biodiversity research in plant science. Full article

As apex predators, felids (Felidae) face unresolved phylogenetic controversies due to their recent rapid speciation and remarkable morphological conservatism. Previous studies, often relying on a limited number of genetic markers, were constrained by insufficient data and conflicting phylogenetic signals, leaving these disputes unresolved. Therefore, establishing a robust phylogenetic framework based on larger-scale genomic data is crucial. This study integrated complete mitogenomes from 37 species representing all major felid genera to characterize genomic diversity, selection pressures, and phylogenetic relationships. Results revealed conserved gene content and arrangement patterns but significant intergenic variation in nucleotide composition, with the light-strand encoded ND6 exhibiting pronounced strand-specific bias. Nucleotide diversity was highest in ND4L (Pi = 0.132) and ATP6 (Pi = 0.131), suggesting their utility as novel markers for species delimitation and population studies. Selection pressure analysis indicated strong purifying selection on cytochrome oxidase subunits (e.g., COX1 Ka/Ks = 0.00327) but relaxed constraints on ATP8 (Ka/Ks = 0.12304). Phylogenies reconstructed from the complete 13PCGs + 2rRNAs dataset (showing high congruence between maximum likelihood and Bayesian methods) clearly delineated Felidae into two primary clades (Pantherinae and Felinae), confirming monophyly of all genera and positioning Neofelis nebulosa as the basal lineage within Pantherinae. Crucially, exclusion of ND6 (12PCGs + 2rRNAs) yielded topologies congruent with the complete 13PCGs + 2rRNAs dataset, whereas single-gene or limited multi-gene datasets produced inconsistent trees (particularly at genus-level nodes). This demonstrates that near-complete mitogenomic data (≥12PCGs + 2rRNAs) are essential for reconstructing robust felid phylogenetic frameworks. Our study provides insights into carnivoran mitogenome evolution. Full article

Background: Traditional morphology-based classification of the Oriental Plover (Anarhynchus veredus) is inconsistent with molecular evidence, underscoring the necessity of incorporating molecular data to elucidate its evolutionary relationships within Charadriidae. Methods: Here, we present the first complete mitochondrial genome of A. veredus by Illumina NovaSeq Sequencing and explore its evolutionary implications within Charadriidae. Results: The mitogenome spans 16,886 bp and exhibits conserved structural features typical of Charadriidae, including gene order, overlapping coding regions, and intergenic spacers. Nucleotide composition analysis revealed a GC content of 44.3%, aligning with other Charadriidae species (44.5–45.8%), and hierarchical GC distribution across rRNA, tRNA, and protein-coding genes (PCGs) reflects structural and functional optimization. Evolutionary rate heterogeneity was observed among PCGs, with ATP8 and ND6 showing accelerated substitution rates (Ka/Ks = 0.1748 and 0.1352) and COX2 under strong purifying selection (Ka/Ks = 0.0678). Notably, a conserved translational frameshift in ND3 (position 174) was identified. Phylogenetic analyses (ML/NJ) of 88 Charadriiformes species recovered robust topologies, confirming that the division of Charadriidae into four monophyletic clades (Pluvialis, Vanellus, Charadrius, and Anarhynchus) and supporting the reclassification of A. veredus under Anarhynchus. Conclusions: This study resolves the systematic position of A. veredus and highlights the interplay between conserved mitochondrial architecture and lineage-specific adaptations in shaping shorebird evolution. Full article

Glutaredoxins (GRXs) are important proteins in plant development and environmental adaptation. Despite extensive characterization of GRX gene family members in various plant species, limited research has been conducted on the identification and functional analysis of GRXs in the economically important Solanaceae family pepper (Capsicum annuum). This study identified 35 typical GRX genes in pepper and categorized them into three distinct groups: CC-, CGFS-, and CPYC-type, based on the phylogenetic topology, which was consistent with motif or domain arrangement, and gene structures. Furthermore, the determination of ω values indicated that purifying selection was a significant factor in the evolutionary diversification of GRX genes in the eudicot family. Intra-genome investigations demonstrated that both segmental and tandem duplications were involved in the expansion of CaGRX genes. Moreover, examination of collinearity within the Solanaceae family revealed 53 orthologous pairs of GRX genes. Additionally, prediction of cis-regulatory elements and analysis of expression profiles revealed the significant involvement of GRX genes in plant stress response, specifically in relation to hypoxia and submergence. Subsequent subcellular localization examination suggested CaGRX may be involved in the endomembrane system and regulation of oxidative balance in plants. Collectively, these findings enhance our comprehension of the structural and functional properties of GRX in pepper, and establish a groundwork for subsequent functional characterization of the CaGRX genes. Full article

Objectives: Sillago japonica is a commercially important marine fish species in the Northwestern Pacific, and understanding its genetic diversity and population structure is crucial for germplasm resource conservation and elucidating population evolution mechanisms. This study specifically aimed to systematically explore the genetic diversity and population structure of S. japonica across five geographic regions (DJW, YSW, ST, ZS, and RS) in its distribution range. Methods: A total of 50 S. japonica individuals from the five geographic regions were analyzed using high-throughput mitochondrial genome sequencing data. We identified single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) loci, followed by comprehensive population genetic analyses including phylogenetic tree construction, principal component analysis (PCA), ADMIXTURE analysis, and calculation of genetic differentiation indices (Fst) and genetic diversity parameters. Results: A total of 2966 SNPs and 414 insertion-deletion loci were identified. Phylogenetic tree topology, PCA, and ADMIXTURE 1.3.0 analysis consistently showed low genetic differentiation among the five populations, a pattern supported by low pairwise Fst values ranging from 0.00047 to 0.05589, indicating extensive gene flow across regions. Genetic diversity parameters varied slightly among populations: observed heterozygosity (0.00001–0.00528), expected heterozygosity (0.04552–0.07311), percentages of polymorphic loci (19.41–30.36%), and nucleotide diversity (0.04792–0.07697). Conclusions: The low genetic differentiation and diversity observed in S. japonica populations may result from the combined effects of historical bottleneck-induced gene pool reduction and extensive gene flow. These findings provide essential theoretical support for formulating targeted conservation strategies for S. japonica germplasm resources and further studies on its population evolution mechanisms. Full article

Sarcopenia and type 2 diabetes mellitus (T2DM) are chronic conditions that gradually affect the elderly, often coexisting and interacting in complex ways. Sarcopenia, which is characterized by the progressive loss of muscle mass and function, is frequently observed in individuals with T2DM. Although the clinical association is well known, the molecular mechanisms remain unclear. Gene expression datasets were retrieved from the Gene Expression Omnibus database. DEGs were identified using the limma package in R (R 4.4.0). Shared DEGs were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Protein–protein interaction networks were constructed using the STRING database and were visualized with Cytoscape. Hub genes were identified via six topological algorithms in the CytoHubba plugin. Pearson’s correlation analysis was conducted between hub genes and selected metabolic regulators. GO and KEGG enrichment analyses indicated that mitochondrial function, oxidative phosphorylation, and immune–inflammatory responses were significantly enriched. A PPI network revealed a mitochondrial hub of five key genes involved in energy metabolism, whose downregulation suggests mitochondrial dysfunction as a shared mechanism in sarcopenia and T2DM. Our results provide new insight into the molecular overlap between T2DM and sarcopenia, highlighting potential biomarkers and therapeutic targets for addressing both metabolic disruption and muscle decline. Full article

Diptera comprises more than 154,000 described species, representing approximately 10–12% of insects. Members have successfully colonized all continents and a wide range of habitats. However, higher-level phylogenetic relationships within Diptera have remained ambiguous. Mitochondrial genomes (mitogenomes) have been used as valuable molecular markers for resolving phylogenetic issues. To explore the effect of such markers in solving the higher-level phylogenetic relationship of Diptera, we sequenced and annotated the mitogenomes of 25 species, combined with 180 mitogenomes from 33 superfamilies of dipteran insects to conduct a phylogenetic analysis based on the PCGsrRNA and PCGs12rRNA datasets using IQ-TREE under the partition model. The phylogenetic analysis failed to recover the monophyly of the two suborders Nematocera and Brachycera. Two of six infraorders within the Nematocera—Tipulomorpha and Ptychopteromorpha—were monophyletic. The ancestral Deuterophlebiidae were a strongly supported sister group of all remaining Diptera, but Anisopodidae, as the closest relative of Brachycera, received only weak support. Three of four infraorders within Branchycera—Tabanomorpha, Xylophagomorpha, and Stratiomyomorpha—were, respectively, supported as a monophyletic clade, except Muscomorpha due to the strong long-branch attraction between Cecidomyiidae and Nycteribiidae. The inferred infraordinal relationships followed the topology Tabanomorpha + (Xylophagomorpha + (Stratiomyomorpha + Muscomorpha)). However, the proposed topology lacks strong statistical support, suggesting alternative relationships remain plausible. Based on mitogenome data alone, we infer that Diptera originated earlier than the Late Triassic at 223.43 Mya (95% highest posterior density [HPD] 166.60–272.02 Mya) and the earliest brachyeran Diptera originated in the mid-Jurassic (171.61 Mya). Full article

Background: Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD), are genetically complex and often linked to structural genomic variations such as copy number variants (CNVs). Current diagnostic strategies face challenges in interpreting the clinical significance of such variants. Methods: We developed a customized, gene-oriented chromosomal microarray (CMA) targeting 6026 genes relevant to neurodevelopment, aiming to improve diagnostic yield and candidate gene prioritization. A total of 39 patients with unexplained developmental delay, intellectual disability, and/or ASD were analyzed using this custom platform. Systems biology approaches were employed for downstream interpretation, including protein–protein interaction networks, centrality measures, and tissue-specific functional module analysis. Results: Pathogenic or likely pathogenic CNVs were identified in 31% of cases (9/29). Network analyses revealed candidate genes with key topological properties, including central “hubs” (e.g., NPEPPS, PSMG1, DOCK8) and regulatory “bottlenecks” (e.g., SLC15A4, GLT1D1, TMEM132C). Tissue- and cell-type-specific network modeling demonstrated widespread gene involvement in both prenatal and postnatal developmental modules, with glial and astrocytic networks showing notable enrichment. Several novel CNV regions with high pathogenic potential were identified and linked to neurodevelopmental phenotypes in individual patient cases. Conclusions: Customized CMA offers enhanced detection of clinically relevant CNVs and provides a framework for prioritizing novel candidate genes based on biological network integration. This approach improves diagnostic accuracy in NDDs and identifies new targets for future functional and translational studies, highlighting the importance of glial involvement and immune-related pathways in neurodevelopmental pathology. Full article

Humulus lupulus L. (hop) is a multipurpose crop valued for its essential role in beer production and for its bioactive compounds with recognized medicinal properties. Otherwise, climate change represents a major challenge to agriculture, particularly impacting the cultivation of crops with stenoecious characteristics, such as hop. This highlights the urgent need to enhance crop resilience to adverse environmental conditions. The phytohormone abscisic acid (ABA) is a key regulator of plant responses to abiotic stress, yet the ABA signaling pathway remains poorly characterized in hop. Harnessing the publicly available hop genomics resources, we identified eight members of the PYRABACTIN RESISTANCE 1 LIKE ABA receptor family (HlPYLs). Phylogenetic and gene structure analyses classified these HlPYLs into the three canonical ABA receptor subfamilies. Furthermore, all eight HlPYLs are likely functional, as suggested by the protein sequence visual analysis. Expression profiling indicates that ABA perception in hop is primarily mediated by the HlPYL1-like and HlPYL8-like subfamilies, while the HlPYL4-like group appears to play a more limited role. Structure modeling and topology predictions of HlPYL1b and HlPYL2 provided insights into their potential functional mechanisms. To assess the physiological relevance of ABA signaling in hop, we evaluated the impact of exogenous ABA application during the ex vitro acclimatization phase. ABA-treated plants exhibited more robust growth, reduced stress symptoms, and improved acclimatization success. These effects were associated with reduced leaf transpiration and enhanced stomatal closure, consistent with ABA-mediated drought tolerance mechanisms. Altogether, this study provides the first comprehensive characterization of ABA receptor components in hop and demonstrates the practical utility of ABA in improving plant performance under ex vitro conditions. These findings lay the groundwork for further functional studies and highlight ABA signaling as a promising target for enhancing stress resilience in hop, with broader implications for sustainable agriculture in the face of climate change. Full article

The yak (Bos grunniens) has exceptional hypoxia resilience, making it an ideal model for studying high-altitude adaptation. Here, we investigated the effects of oxygen concentration on yak cardiac fibroblast proliferation and the underlying molecular regulatory pathways using RNA sequencing (RNA-seq) and metabolic analyses. Decreased oxygen levels significantly inhibited cardiac fibroblast proliferation and activity. Intriguingly, while the mitochondrial DNA (mtDNA) content remained stable, we observed coordinated upregulation of mtDNA-encoded oxidative phosphorylation components. Live-cell metabolic assessment further demonstrated that hypoxia led to mitochondrial respiratory inhibition and enhanced glycolysis. RNA-seq analysis identified key hypoxia adaptation genes, including glycolysis regulators (e.g., HK2, TPI1), and hypoxia-inducible factor 1-alpha (HIF-1α), with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses highlighting their involvement in metabolic regulation. The protein–protein interaction network identified three consensus hub genes across five topological algorithms (CCNA2, PLK1, and TP53) that may be involved in hypoxia adaptation. These findings highlight the importance of metabolic reprogramming underlying yak adaptation to hypoxia, providing valuable molecular insights into the mechanisms underlying high-altitude survival. Full article

In China, Anostostomatidae is represented by a single tribe, Anabropsini; two genera; and 33 species. Although extensive research has been conducted on Anabropsini, the monophyly of this tribe within Anostostomatidae remains unverified. Furthermore, the phylogenetic relationships within Anabropsis remain under debate. To address these gaps, we sequenced and annotated the mitochondrial genomes of five Anabropsini species to investigate their mitochondrial characteristics and phylogenetic positions and clarify the relationships among Anabropsis subgenera. The total mitochondrial length of the five species ranged from 15,985 bp to 16,423 bp and contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 1 control region. A grouped analysis of selection pressure on Anabropsis revealed that the Ka/Ks values for alate and apterous forms are not significantly different, suggesting that using wing length alone as the basis for dividing subgenera within Anabropsis may be unreliable. Tertiary structure modeling of proteins showed that the variable sites were concentrated in α-helix regions. Phylogenetic trees were reconstructed using the Bayesian inference and maximum likelihood methods and were based on two better datasets, namely, PCG123 (all codon positions of the PCGs) and PCG123 + 2R (all codon positions of PCGs, 12SrRNA, and 16SrRNA). The results indicate that the Chinese Anabropsini is paraphyletic, whereas Anabropsis is monophyletic, with a stable subgeneric topology. Full article

Complete chloroplast genome sequences are widely used in the analyses of phylogenetic relationships among angiosperms. As a species-rich genus, species diversity centers of Saxifraga L. include mountainous regions of Eurasia, such as the Alps and the Qinghai–Tibetan Plateau (QTP) sensu lato. However, to date, datasets of chloroplast genomes of Saxifraga have been concentrated on the QTP species; those from European Alps are largely unavailable, which hinders comprehensively comparative and evolutionary analyses of chloroplast genomes in this genus. Here, complete chloroplast genomes of 19 Saxifraga species were de novo sequenced, assembled and annotated, and of these 15 species from Alps were reported for the first time. Subsequent comparative analysis and phylogenetic reconstruction were also conducted. Chloroplast genome length of the 19 Saxifraga species range from 149,217 bp to 152,282 bp with a typical quadripartite structure. All individual chloroplast genome included in this study contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs. The IR boundaries keep relatively conserved with minor expansion in S. consanguinea. mVISTA analysis and identification of polymorphic loci for molecular markers shows that six intergenic regions (ndhC-trnV, psbE-petL, rpl32-trnL, rps16-trnQ, trnF-ndhJ, trnS-trnG) can be selected as the potential DNA barcodes. A total of 1204 SSRs, 433 tandem repeats and 534 Large sequence repeats were identified in the 19 Saxifraga chloroplast genomes. The codon usage analysis revealed that Saxifraga chloroplast genome codon prefers to end in A/T. Phylogenetic reconstruction of 33 species (31 Saxifraga species included) based on 75 common protein coding genes received high bootstrap support values for nearly all identified nodes, and revealed a tree topology similar to previous studies. Full article

The non-random usage of synonymous codons encoding the same amino acid—referred to as codon usage bias (CUB)—varies substantially across genomes and significantly affects translational efficiency by modulating transcriptional and post-transcriptional processes. In chloroplast genomes, the optimization of CUB is critical for improving the efficacy of genetic engineering approaches. However, comprehensive analyses of CUB in Fagopyrum chloroplast genomes remain scarce. In this study, we performed an in-depth comparative analysis of codon usage patterns in the chloroplast genomes of nine Fagopyrum species. Our results revealed a marked AT-rich nucleotide composition, with base content in the order T > A > C > G. We identified 23 optimal codons and 29 high-frequency codons, most of which ended with A or U. Correlation analyses demonstrated that codon usage is strongly influenced by nucleotide skewness (GC and AT skews), protein properties (such as amino acid composition and the number of synonymous codons), and gene expression levels. Neutrality plot analysis (PR2 bias) and evaluations based on the effective number of codons (ENc) indicated that both mutational pressure and natural selection contribute to shaping CUB, with natural selection identified as the predominant evolutionary force. Comparative analyses with four model organisms indicated that Arabidopsis thaliana shares the highest codon usage compatibility with Fagopyrum chloroplast genomes, highlighting its suitability as a potential heterologous expression system. Phylogenetic reconstruction based on codon usage profiles yielded a fully resolved topology with 100% bootstrap support at all nodes, reinforcing the utility of codon usage data in evolutionary inference. This study elucidates the evolutionary determinants of codon usage variation in Fagopyrum plastomes and provides a robust methodological foundation for codon optimization in chloroplast-based synthetic biology. The validated codon adaptation metrics offer promising tools for improving heterologous protein expression and guiding transgene design in advanced breeding strategies. Full article

Objective: To elucidate the molecular targets and mechanisms by which Acorus tatarinowii exerts therapeutic effects in major depressive disorder (MDD) using network pharmacology and molecular docking approaches. Methods: Bioactive compounds of Acorus tatarinowii were identified from comprehensive pharmacological databases. MDD-related targets were sourced from extensive genomic repositories. Overlapping targets were determined and subjected to network topology and protein–protein interaction (PPI) analyses to identify core targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to reveal pertinent biological processes and signaling pathways. Molecular docking simulations validated the interactions between key bioactive compounds and core targets. Results: A total of 57 bioactive compounds were identified in Acorus tatarinowii, including apigenin, heterotropan, and isoelemicin. Integrative analysis revealed 700 compound-related targets and 2590 MDD-associated targets, with 150 intersecting targets. Network analyses pinpointed five core targets: TP53, STAT3, AKT1, PIK3CA, and PIK3R1. GO enrichment identified 858 significant biological processes, while KEGG pathway analysis highlighted 155 enriched pathways, notably the PI3K-Akt, cAMP, and MAPK signaling pathways. Molecular docking studies demonstrated strong binding affinities between key compounds and their respective targets. Conclusions: This study delineates the multifaceted polypharmacological mechanisms through which Acorus tatarinowii may confer protective effects against major depressive disorder, underscoring its potential as a promising therapeutic agent. Full article

This research proposes to systematically investigate the cardioprotective mechanisms of Pericarpium Trichosanthis injection (PTI) against acute myocardial ischemia through an integrated approach combining ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) constituent profiling, UNIFI database-assisted component identification, network pharmacology-guided target prediction, molecular docking verification, and in vivo experimental validation. The multimodal methodology is designed to comprehensively uncover the therapeutic benefits and molecular pathways underlying this traditional Chinese medicine formulation. Methods: UPLC-Q-TOF/MS and the UNIFI database were used in conjunction with a literature review to screen and validate the absorbed components of PTI. Using network pharmacology, we constructed protein-protein interaction (PPI) networks for pinpointing prospective therapeutic targets. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to identify potential signaling pathways. In vivo experiments were conducted to investigate the mechanisms by which PTI ameliorated isoproterenol-induced myocardial injury in rats. All animal experiments have adhered to ARRIVE guidelines. Results: UPLC-Q-TOF/MS revealed 11 core active components in PTI. Network pharmacology prioritization identified pseudoaspidin, ciryneol C, cynanoside M, daurinol, and n-butyl-β-D-fructopyranoside as central bioactive constituents within the compound-target interaction network. Topological analysis of the protein interactome highlighted AKT1, EGFR, MMP9, SRC, PTGS2, STAT3, BCL2, CASP3, and MAPK3 as the most interconnected nodes with the highest betweenness centrality. Pathway enrichment analysis established the PI3K/Akt signaling cascade as the principal mechanistic route for PTI’s cardioprotective effects. Molecular docking simulations demonstrated high-affinity interactions between characteristic components (e.g., cynanoside M, darutigenol) and pivotal targets including PTGS2, MAPK3, CASP3, and BCL2. In vivo investigations showed PTI treatment markedly attenuated myocardial tissue degeneration and collagen deposition (p < 0.05), normalized electrocardiographic ST-segment deviations, and suppressed pro-inflammatory cytokine production (IL-6, TNF-α). The formulation concurrently reduced circulating levels of cardiac injury indicators (LDH, cTnI) and oxidative stress parameters (ROS, MDA), Regarding apoptosis regulation, PTI reduced Bax, caspase-3, and caspase-9, while elevating Bcl-2 (p < 0.05), effectively inhibiting myocardial cell apoptosis with all therapeutic outcomes reaching statistical significance. These findings highlight PTI’s protective effects against myocardial injury through multi-target modulation of inflammation, oxidation, and apoptosis. Conclusions: PTI exerts its therapeutic effects in treating acute myocardial ischemia by regulating and suppressing inflammatory responses, and inhibiting cardiomyocyte apoptosis. Full article