Search Results (231)

Distant hybridization is key to trait innovation and speciation, with Cyprinidae hybrid phylogeny helping to clarify diversification mechanisms. Yet, a major gap persists in Cyprinidae studies: the stabilization mechanisms of interspecific distant hybrid lineages. To address this, we systematically analyzed the molecular phylogeny of seven Cyprinidae distant hybrid lineages and their parental species, using an integrative genetic framework encompassing four mitochondrial genes (Cytb, COI, 16S rRNA, D-loop) and five nuclear genes (EGR2b, IRBP2, RAG1, RAG2, RH2). Homologous sequences of 41 representative Cyprinidae species (85 samples) were retrieved from GenBank to supplement the dataset. Phylogenies were reconstructed from concatenated sequences, complemented by haplotype networks. Intra-/interspecific divergence was quantified using two mitochondrial genes (COI, Cytb) and two nuclear (RAG1, RH2). The results showed that these hybrid lineages exhibited variation patterns analogous to other Cyprinidae species. Both ML and BI trees reconstructed exhibited congruent topologies with high support (bootstrap/BPP > 80%), resolving genus/species-level relationships. While most hybrids clustered intermediately between their parental species, they typically displayed maternal affinity. A notable exception was the 2nNCRC (a homodiploid hybrid from Cyprinus carpio ♀ × Megalobrama amblycephala ♂), which displayed convergent evolution toward Carassius auratus. COI-based K2P genetic distance analysis revealed 2nNCRC had a much closer relationship with C. auratus (0.0119) than with its parents (0.1249 to C. carpio, 0.1552 to M. amblycephala). These nine genes elucidate the genetic relationships between Cyprinid hybrid lineages and progenitors, serving as pivotal molecular markers for parentage tracing and genetic dissection of distant hybridization mechanisms. The integrated mitochondrial–nuclear marker system in this study advances understanding of cytonuclear coadaptation and the stabilization of interspecific distant hybrid lineages in Cyprinidae. Specifically, it provides a precise tool for parentage tracing, Cyprinid germplasm conservation, and targeted regulation of hybrid breeding—laying a foundation for exploring hybrid speciation and developing elite aquaculture germplasms. Full article

Cognitive impairments, particularly in the context of neurodegenerative diseases, are associated with disruptions in mitochondrial function and key metabolic pathways. This study investigates the impact of short-term scopolamine exposure on mitochondrial DNA (mtDNA) stability and the kynurenine pathway (KP) in the hippocampus, a brain region central to learning and memory. We analyzed the mitochondrial D-loop region for mutations and heteroplasmy levels in hippocampal tissue from rats exposed to scopolamine (1 mg/kg/0.4 mL/cc i.p. x 14 days). Additionally, the expression of the KP enzymes kynurenine aminotransferase (KAT I, KAT II) and kynurenine 3-monooxygenase (KMO) and receptors aryl hydrocarbon receptor (Ahr) and G protein-coupled receptor 35 (GPR35) was evaluated using quantitative PCR. Neither significant mutation nor heteroplasmy changes were observed in the mtDNA D-loop region between the scopolamine-treated and control groups. Similarly, the hippocampal expression levels of the kat I, kat II, kmo and ahr and gpr35 genes remained unchanged, indicating no activation of this metabolic pathway under short-term scopolamine exposure. These findings suggest that the mitochondrial genome in the hippocampus remains stable under acute pharmacological stress induced by scopolamine, with no significant activation of the KP. These results underline the distinction between transient, reversible cognitive deficits and chronic neurodegenerative processes, providing insights for therapeutic approaches targeting specific stages of cognitive change. Full article

The mammalian genome is hierarchically packaged into distinct functional units, including chromatin loops, topologically associating domains, compartments and chromosome territories. This structural organization is fundamentally important because it orchestrates essential nuclear functions that underpin normal cellular identity and organismal development. In this review, we synthesize current understanding of the intricate relationship between genome architecture and its critical biological roles. We discuss how hierarchical structures are dynamically established and maintained by architectural proteins, transcription factors, epigenetic regulators and non-coding RNAs via distinct mechanisms. Importantly, we focus on the functional consequences of three-dimensional (3D) genome organization and discuss how it modulates fundamental biological processes such as transcription, gene co-expression, epigenetic modification, DNA replication and repair. We also examine the dynamics of 3D genome organization during cellular differentiation, early embryonic development and organogenesis, followed by discussing how structural disruptions are mechanistically linked to various human diseases. Understanding the biological function of 3D genome organization is thus not only essential for deciphering fundamental nuclear processes but also holds significant promise for elucidating disease etiologies and developing effective therapeutics. Full article

Background/Objectives: Circulating cell-free DNA (cfDNA) consists of genomic DNA (cf-nDNA) and mitochondrial DNA (cf-mtDNA) fragments released from cells primarily through apoptosis and necrosis. In healthy individuals, the main source of cfDNA is apoptosis, whereas in cancer patients, necrosis predominates. Considering that in vitro cfDNA models are valuable research tools, this study presents an in vitro characterization of cf-mtDNA patterns released into the culture medium by four human cell lines: normal dermal fibroblasts (Hs27), induced pluripotent stem cells (iPSCs), melanoma cells (BMel), and prostate cancer cells (PC3). Furthermore, as fetal bovine serum (FBS)—a widely used supplement in cell culture media—has been shown to contain bovine cfDNA, species-specific primers were employed to eliminate potential artifacts arising from this contamination in in vitro experiments. Methods: Fragmentation analysis of cf-mtDNA was conducted by amplifying the human MT-CYB gene and the D-loop region in four cell lines using species-specific primers. Two indices, Q and λ, were employed to quantify fragmentation. Results: These indices reveal that cancer cells exhibit the highest degree of fragmentation compared to fibroblasts, whereas stem cells show the lowest degree of fragmentation. This study identified species-specific primers for the human and bovine MT-CYB gene, confirming the presence of bovine cf-mtDNA in cell culture media supplemented with FBS. Conclusions: in vitro cellular models are useful for studying the mechanisms of cfDNA release and fragmentation; designed primers provide a reliable tool for assessing contamination across different growth time points minimizing interference errors and non-specific amplifications. Full article

Complete mitochondrial DNA genome annotation of an ecologically and commercially important fish species Cirrhinus cirrhosus was executed with next-generation sequencing (NGS) for nucleotide and phylogenetic analyses. The findings of this study showed that the Cirrhinus cirrhosus mitochondrial genome contained 16,593 bp, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and a D-loop region. The overall base composition was 32% adenine, 25% thiamine, 16% guanine, and 27% cytosine. This mitochondrial DNA exhibits an AT biasness, with 56% AT content in its genome. Significant fluctuations were identified in the AT and GC skew values of the ND6 gene, indicating that the selection and mutation forces acting on this gene might be different from those acting on other genes. The Ka/Ks ratios of most protein-coding genes were less than 1, indicating very strong natural selection pressure. Phylogenetic analysis of Cirrhinus cirrhosus with Cirrhinus mrigala and Bangana tungting suggested a closer evolutionary relationship among these species, which might have shared a more recent common ancestor. It has been also found that the genera Labeo and Cirrhinus are not monophyletic. Full article

Enhancer-promoter interactions occur in the chromatin loci delineated by the CCCTC-binding zinc-finger protein CTCF. CTCF binding is frequently perturbed in genetic disorders and cancer, allowing for misregulation of genes. Here, we developed a panel of chimeric proteins consisting of either full-length or truncated CTCF fused with programmable DNA-binding module dCas9 and fluorescent tracker EGFP. We found that the recruitment of a chimeric protein based on the CTCF N-terminal domain and two zinc-finger domains to the human HOXD locus leads to the de novo formation of a spatial contact with a nearby cohesin/CTCF-bound region, anchoring several chromatin loops. This chimeric protein did not show binding to CTCF motifs and did not affect the epigenetic and transcription profile of the locus. Recruitment of this chimeric protein is also able to restore chromatin loops, lost after deletion of an endogenous CTCF-binding site. Together, our data indicate that the ectopic recruitment of the CTCF N-terminal part could be an appropriate tool for 3D genome engineering. Full article

The tufted deer (Elaphodus cephalophus), a Near-Threatened (NT) species endemic to China and Myanmar, requires robust genetic data for effective conservation. However, the genetic landscape of key populations, such as those in Chongqing, remains poorly understood. This study aimed to comprehensively evaluate the genetic diversity, population structure, gene flow, and demographic history of tufted deer across this critical region. We analyzed mitochondrial DNA (mtDNA) from 46 non-invasively collected fecal samples from three distinct populations: Jinfo Mountain (JF, n = 13), Simian Mountain (SM, n = 21), and the Northeastern Mountainous region (NEM, n = 12). Genetic variation was assessed using the cytochrome b (Cyt b) and D-loop regions, with analyses including F_st, gene flow (N_m), neutrality tests, and Bayesian Skyline Plots (BSP). Our results revealed the highest genetic diversity in the SM population, establishing it as a genetic hub. In contrast, the JF population exhibited the lowest diversity and significant genetic differentiation (>0.23) from the SM and NEM populations, indicating profound isolation. Gene flow was substantial between SM and NEM but severely restricted for the JF population. Demographic analyses, including BSP, indicated a long history of demographic stability followed by a significant expansion beginning in the Middle to Late Pleistocene. We conclude that the SM/NEM metapopulation serves as the genetic core for the species in this region, while the highly isolated JF population constitutes a distinct and vulnerable Management Unit (MU). This historical demographic expansion is likely linked to climatic and environmental changes during the Pleistocene, rather than recent anthropogenic factors. These findings underscore the urgent need for a dual conservation strategy: targeted management for the isolated JF population and the establishment of ecological corridors to connect the Jinfo Mountain and Simian Mountain populations, ensuring the long-term persistence of this unique species. Full article

As distant hybridization has profound implications for evolutionary biology, aquaculture, and biodiversity conservation, this study aims to elucidate patterns of maternal inheritance, genetic divergence, and phylogenetic relationships by synthesizing mitochondrial genome (mitogenome) data from 74 distant hybrid fish species. These hybrids span diverse taxa, including 48 freshwater and 26 marine species, with a focus on Cyprinidae (n = 35) and Epinephelus (n = 14), representing the most frequently hybridized groups in freshwater and marine systems, respectively. Mitogenome lengths were highly conserved (15,973 to 17,114 bp); however, the genetic distances between hybrids and maternal species varied from 0.001 to 0.17, with 19 hybrids (25.7%) showing distances >0.02. Variable sites in these hybrids were randomly distributed but enriched in hypervariable regions, such as the D-loop and NADH dehydrogenase subunits 1, 3 and 6 (ND2, ND3, and ND6) genes, likely reflecting maternal inheritance (reported in Cyprinus carpio × Carassius auratus). Moreover, these genes were under purifying selection pressure, revealing their conserved nature. Phylogenetic reconstruction using complete mitogenomes revealed three distinct clades in hybrids: (1) Acipenseriformes, (2) a freshwater cluster dominated by Cypriniformes and Siluriformes, and (3) a marine cluster comprising Centrarchiformes, Pleuronectiformes, Scombriformes, Cichliformes, Anabantiformes, Tetraodontiformes, Perciformes, and Salmoniformes. The prevalence of Cyprinidae hybrids underscores their importance in aquaculture for hybridization, where traits such as rapid growth and disease resistance are enhanced. In contrast, marine hybrids are valued for their market value and adaptability. While mitogenome data robustly support maternal inheritance in most cases, exceptions suggest complex mechanisms, such as doubly uniparental inheritance (DUI), in distantly related crosses. Moreover, AT-skew of genes in hybrids revealed a paternal leakage of traits in mitogenomes. This study also highlights ecological risks, such as genetic swamping in native populations, emphasizing the need for responsible hybridization practices. These findings advance our understanding of the role of hybridization in fish evolution and aquaculture, providing a genomic framework and policy recommendations for optimizing breeding programs, hybrid introduction, and mitigating conservation challenges. Full article

Carassius auratus var. suogu, an endemic fish in southern China, is a natural triploid crucian carp mutant. In this study, the characteristics of mitochondrial DNA sequences were analyzed to understand their taxonomic status and genetic background at the gene level. The complete mitochondrial genome of C. auratus var. suogu (length, 16,580 bp) comprises 37 genes (13 protein-coding genes, 22 transfer RNA (tRNAs) genes, and 2 ribosomal RNA (rRNAs) genes) and a non-coding control region. The RSCU of the mtDNA of Carassius was similar. Ka/Ks analyses showed the ND4 gene had the highest evolutionary rate. Moreover, the whole mitogenome sequences and D-loop region were employed to examine phylogenetic relationships among C. auratus var. suogu and other closely related species. The result indicated that Carassius auratus suogu var clustered with Carassius auratus auratus and divided Carassius into four clades, providing new insights and data support for the taxonomic status of Carassius. Full article

Castor fiber birulai is a subspecies of the Eurasian beaver that has a relatively small population size compared to other Castor subspecies. There is limited genetic research on this subspecies. In this study, mitochondrial cytochrome b (Cytb) and D-loop sequences were analysed in genetic samples obtained from 19 individuals residing in the Buergen River Basin, Xinjiang, China. The Cytb region presented a single haplotype, whereas three haplotypes were identified in the D-loop region. The genetic diversity within the Chinese population was low (D-loop Hd = 0.444; Pi = 0.0043), markedly lower than that observed in other geographical populations of C. fiber. Phylogenetic reconstructions and haplotype network analyses revealed substantial genetic differentiation between C. f. birulai and other Eurasian lineages (Fst > 0.95), supporting the status of C. f. birulai as a distinct evolutionary lineage. Although the genetic distance between the Chinese and Mongolian populations was relatively small (distance = 0.00269), significant genetic differentiation was detected (Fst = 0.67055), indicating that anthropogenic disturbances—such as hydraulic infrastructure and fencing along the cross-border Bulgan River—may have impeded gene flow and dispersal. Demographic analyses provided no evidence of recent population expansion (Fu’s Fs = 0.19152), suggesting a demographically stable population. In subsequent studies, we recommend increasing nuclear gene data to verify whether the C. f. birulai population meets the criteria for Evolutionarily Significant Unit classification, and strengthening cross-border protection and cooperation between China and Mongolia. Full article

Brain muscle ARNT-like1 (Bmal1) is a transcriptional factor, consisting of basic helix–loop–helix (bHLH) and PER-ARNT-SIM (PAS) domains, that plays a central role in circadian clock activity. However, the precise roles of the BMAL1-PAS domain, a circadian rhythm-regulating structure, remain unexplored in monocytes. Here, we highlight the BMAL1-PAS domain as a key structure in monocyte pleiotropic functions by using human monocytic cell line THP-1. THP-1 cells lacking the BMAL1-PAS-B domain (THP-1#207) abrogated the circadian expression of core clock genes. THP-1#207 cells exhibited less proliferation, glycolysis and oxidative phosphorylation activity, and LPS-induced IL-1β production, but exhibited more production of LPS-induced IL-10 than THP-1 cells. A quantitative proteomics analysis revealed significant expression changes in ~10% metabolic enzymes in THP-1#207 cells compared to THP-1 cells, including reduction in a rate-limiting enzyme hexokinase2 (HK2) in the glycolytic pathway. Importantly, treatment of THP-1 with 2-deoxy-D-glucose (2-DG), an HK2 inhibitor, largely recapitulated the phenotypes of THP-1#207 cells. These findings suggest that the BMAL1-PAS-B domain is an important structure for the regulation of proliferation, cellular energetics, and inflammatory response in THP-1 cells, at least in part, via the control of glycolytic activity. Thus, the BMAL1-PAS-B domain may become a promising pharmacological target to control inflammation. Full article

Chionea is classified within the Tipuloidea superfamily and predominantly inhabits cold regions. However, its phylogenetic relationships remain contentious. In this study, the first three mitogenomes of Chionea (Diptera: Limoniidae) sampled in northeastern China (Jilin region) were sequenced, and their phylogenetic relationships were reconstructed by integrating these sequences with 30 additional Tipuloidea mitogenomes retrieved from NCBI. Unlike other Tipuloidea species, which are predominantly distributed in relatively warmer regions, this research investigates whether positive selection has acted on the mitogenomes of these three Chionea species due to environmental pressures, thereby elucidating key evolutionary drivers for Chionea. The three mitogenomes of Chionea exhibit characteristic features typical of insect mitogenomes, comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA genes (tRNA), and a single non-coding control region (D-loop). Notably, the secondary structure of trnS1 lacks the DHU arm in all three samples, and UUA (Leu) emerges as the most frequently utilized codon. Furthermore, the COX2 and ND5 genes utilize incomplete stop codons “T”. Utilizing these 13 PCGs, we reconstructed the internal phylogenetic relationships within Tipuloidea, revealing that Chionea tianhuashana and C. sphaerae form sister branches, while (C. tianhuashana + C. sphaerae) constitutes a sister branch to C. crassipes. Moreover, our analysis confirms the monophyly of Tipulidae, Tipula, and Nephrotoma as well as the polyphyly of Tipulinae, Chioneinae, and Limoniidae. In the branch site model analysis, three positively selected sites were detected when Chionea was designated as the foreground branches: COX3 (at position 242), ND5 (at position 535), and ND6 (at position 138). Full article

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP) is the only freshwater cetacean species that remains in the Yangtze River, China. Poyang Lake is connected to the main stream of the Yangtze River, and the number of YFPs in Poyang Lake constitutes approximately half of the total species population. To implement effective conservation measures and formulate scientific genetic management strategies for the YFPs in Poyang Lake, we conducted population genetic analyses on 125 blood samples from the Poyang population and 46 tissue samples from the Anqing population, utilizing mitochondrial DNA D-loop and microsatellite loci. The genetic diversity analysis revealed two haplotypes in the Poyang population, with mitochondrial genetic diversity indices of Hd = 0.481 ± 0.020 and Pi = 0.00078 ± 0.00030. Microsatellite markers further demonstrated indices of Ho = 0.610 and He = 0.655. The genetic differentiation analysis indicated that the two populations exhibited moderate genetic differentiation (0.05 < Fst < 0.15). Upon excluding the dead samples from the Anqing population, the genetic differentiation between the two populations increased and the gene flow diminished. This indicated that certain dead samples from the Anqing population might have originated from Poyang Lake or had a background of Poyang Lake–Yangtze River migration and gene exchange. This finding was further corroborated by STRUCTURE analysis, which revealed genetic admixture between the two populations. We assessed the current genetic diversity of the Poyang population and its genetic differentiation from the Anqing population. This study provides fundamental data for formulating a conservation program for YFPs in Poyang Lake. Full article

Macrobrachium rosenbergii, commonly known as giant freshwater prawns (GFPs), is an economically and nutritionally important decapod crustacean species in China. Understanding the genetic diversity of selective breeding populations is crucial in breeding plans for selecting genetically diverse broodstocks and maintaining genetic diversity. The genetic structure of six breeding populations (Hefu (HF), Nantaihu No.2 (NTH), Jiaxin (JX), Shufeng (SF), Taiwan (TW), and Guangxi (GX)) of GFP in China was examined using 16 newly developed microsatellite loci and the mitochondrial control region (D-loop). The microsatellite data revealed that all 16 loci have high diversity, with all values of polymorphism information content (PIC) more than 0.5. The average expected heterozygosity (He, 0.89) and the number of alleles (Na, 18.25) of SF were the highest, followed by He (0.89) and Na (14.75) of the JX, and GX has the lowest He (0.83) and Na (11.31). The average PIC value for the six stocks ranged from 0.80 to 0.87. Pairwise comparisons revealed that Fst ranged from 0.03541 to 0.09637 and was significant (p < 0.05) between most populations, indicating from low to moderate genetic differentiation among the six populations. The D-loop analysis identified 114 variable sites and 29 haplotypes, with an average haplotype diversity (Hd) and nucleotide diversity (π) of 0.640 and 0.01247, respectively. Genetic differentiation among the six populations based on the D-loop was from moderate to high, with Fst values of 0.05603–0.80788, and all p < 0.05. This study demonstrates that selective breeding stocks of M. rosenbergii in China show moderate to high genetic diversity and have the potential for further selective breeding, providing a theoretical basis for conserving and utilizing M. rosenbergii genetic resources. Full article

Millipedes (Diplopoda) are crucial decomposers in soil ecosystems, as they play a vital role in organic matter degradation while also holding potential as bioindicators of environmental health. This study deciphered the complete mitogenomes of four millipede species (Diplopoda: Spirostreptida and Spirobolida) using next-generation sequencing technology, thus revealing evolutionary relationships among diplopod taxa and characterizing mitochondrial genomic features. The full mitochondrial sequences of Agaricogonopus acrotrifoliolatus, Bilingulus sinicus, Paraspirobolus lucifugus, and Trigoniulus corallinus, ranged in size from 14,906 to 15,879 bp, with each containing 37 typical genes and one D-loop region. Notably, the D-loop regions of A. acrotrifoliolatus and B. sinicus were positioned atypically, thus indicating structural rearrangements. A nucleotide composition analysis revealed pronounced AT-skews, with tRNA sequences exhibiting the highest A+T content. Ka/Ks ratios demonstrated that the ND5 gene experienced the weakest purifying selection pressure, thus suggesting its potential role in adaptive evolution. The results of the phylogenetic analysis showed genetic relationships between the three orders of ((Julida, Spirostreptida), Spirobolida), which was inconsistent with the previous conclusion regarding the three orders, obtained through morphological studies: ((Julida, Spirobolida), Spirostreptida). These findings highlight the role of the mitochondrial genome in resolving phylogenetic conflicts and provide important insights for further studies on millipedes. Full article