Search Results (6,460)

Background: The Taiwanese loach (Paramisgurnus dabryanus ssp. Taiwan, Dabry de Thiersant, 1872.) is an economically important aquaculture species in East Asia, and its body color directly affects its ornamental and market value. Our research group recently discovered a golden-red mutant, named “Gan Hong No. 1” (MR), within a wild-type (WT) population. During embryogenesis, MR individuals exhibit almost no melanophore deposition, and after hatching, xanthophores and erythrophores appear sequentially, suggesting that the body color variation likely originates from alterations in the gene regulatory network during early development. Objective: To systematically compare the transcriptomes of WT and MR-Taiwanese loach during early development, to identify the key regulatory pathways underlying red body color formation from a temporal perspective, to test whether the classical melanin synthesis pathway is impaired, and to provide a theoretical basis for selective breeding of body color traits. Methods: High-throughput transcriptome sequencing was performed on eight early developmental stages (0, 5, 10, 15, 20, 23, 28 and 43 h post-fertilization) of both loach types. Differential expression analysis, time-series trend analysis, and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment were used to systematically characterize gene expression dynamics. Transcriptomic data validation was performed using real-time PCR. Results: In MR, the core transcription factor mitfa was significantly downregulated, whereas the expression of melanin synthesis genes such as kita and dct showed no significant difference, indicating that the impairment of melanogenesis is caused by mitfa downregulation. Trend analysis and pathway enrichment revealed that in MR embryos, pathways related to oxidative stress, unsaturated fatty acid biosynthesis, C-type lectin receptor signaling, p53 signaling, and apoptosis were significantly activated, while the thyroid hormone synthesis pathway was markedly upregulated. In WT, these pathways showed the opposite trend. qRT-PCR results were consistent with the transcriptome data. Conclusions: This study demonstrates that downregulation of mitfa serves as the initial trigger for red body color variation in the Taiwanese loach. This mutation impedes melanin synthesis and concurrently activates a coordinated regulatory network involving oxidative stress, immune inflammation, and thyroid hormone signaling. Accumulation of unsaturated fatty acids alleviates oxidative damage and supports carotenoid deposition, while immune signals eliminate aberrant melanocytes and promote compensatory generation of red and yellow chromatophores. The upregulated thyroid hormone further fine-tunes pigment cell differentiation. For the first time in a cobitid species, this study elucidates the mitfa-mediated, multi-pathway synergistic molecular mechanism driving the transition from melanin-based to carotenoid/pteridine-based red coloration in fish, thereby providing a theoretical reference for molecular breeding of body color in aquaculture. Full article

(1) Background: Centella asiatica (L.) is a long-lived medicinal plant traditionally recognized for its wound-healing and anti-inflammatory properties. Despite the growing demand for diverse C. asiatica species in Korea, studies on genetic diversity remain limited. (2) Methods: Genome assembly data of C. asiatica from the NCBI database were utilized to develop genomic SSR markers. Genetic diversity and population structure were examined in 30 Korean native C. asiatica accessions using 90 SSR markers. (3) Results: Whole-genome sequencing revealed 376,751 SSR loci, from which 127,528 primer pairs were designed. Among 160 randomly selected primers, 90 showed consistent amplification and displayed high levels of polymorphism. Genetic analyses revealed that the MAF ranged from 0.15 to 1.00 (mean 0.55), the NA ranged from 1 to 15 (mean 5.6), the Ho ranged from 0.00 to 1.00 (mean 0.17), and the PIC values ranged from 0.00 to 0.88 (mean 0.52). Clustering analysis with 90 SSR markers revealed three clusters, whereas population structure analysis indicated two populations among the C. asiatica accessions. Furthermore, two minimum marker sets with five marker combinations were identified and proved useful to differentiate all C. asiatica accessions. (4) Conclusions: The newly developed SSR markers for C. asiatica hold promise for facilitating research endeavors pertaining to variety identification, genetic mapping, and marker-assisted selection. Full article

Background: Oral squamous cell carcinoma (OSCC) remains a major public health challenge, particularly in South Asian populations where environmental exposures such as tobacco and areca nut consumption contribute significantly to disease burden. Although genomic studies have improved understanding of oral cancer biology, population-specific genomic data from high-risk Indian populations remain limited. This study aimed to characterize the genomic landscape of OSCC using whole-exome sequencing (WES) of fresh biopsy specimens obtained from patients residing along the southwest coast of Karnataka, India. Methods: Paired tumor and adjacent normal tissues from ten OSCC samples (total n = 20 samples) were subjected to WES to identify somatic and germline-associated variants. Matched tumor–normal comparative analysis, variant annotation, and population frequency assessment using established genomic databases, including gnomAD, were performed to characterize the mutational profile. The findings were further compared with a previously analyzed regional cohort comprising 66 OSCC patients to evaluate recurrence patterns and population relevance. Results: The analysis identified a broad background of recurrent germline-associated variants alongside a comparatively limited number of tumor-specific somatic mutations, consistent with the expected predominance of constitutional genetic variation relative to acquired coding alterations in tumor samples. Recurrent variants were observed in genes associated with DNA repair, immune signaling, inflammatory responses, and pharmacogenomic pathways, including XRCC1, ITPKB, ABCB1, and OPRM1, whereas somatic alterations were primarily detected in established cancer-associated genes such as TP53, CDKN2A, and TERT. Conclusions: Several recurrent variants demonstrated high frequencies in South Asian populations, suggesting that they may represent recurrent population-associated variants of potential biological or pharmacogenomic relevance that require validation in larger cohorts. KEGG pathway enrichment analysis identified pathways related to cancer, chemical carcinogenesis, metabolic regulation, and xenobiotic response. Overall, these findings provide preliminary insights into the population-specific genomic characteristics of OSCC in this regional cohort and highlight the need for larger validation studies to determine the biological significance and reproducibility of these findings. Full article

Global food production systems are increasingly challenged by population growth, climate change, water scarcity, and environmental degradation, necessitating the adoption of sustainable, resource-efficient food production strategies. Aquaponic systems integrate recirculating aquaculture with hydroponic crop cultivation, enabling nutrient recycling and improved water-use efficiency. Simultaneously, CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for precise genetic improvement of economically important aquaculture traits. This review critically evaluates current progress in CRISPR/Cas9 applications in aquaculture, with emphasis on Nile tilapia (Oreochromis niloticus). Evidence from peer-reviewed studies indicates that targeted modification of genes associated with growth regulation, disease resistance, nutrient metabolism, feed efficiency, and stress tolerance can significantly enhance fish productivity and physiological resilience. Genes involved in hypoxia adaptation and nitrogen metabolism may further improve environmental performance in intensive recirculating systems by reducing ammonia accumulation and enhancing nutrient utilization. However, most genome-editing studies have been conducted under laboratory or conventional aquaculture conditions, with limited information available regarding the long-term performance, ecological interactions, microbial dynamics, and biosafety of genome-edited fish in aquaponic environments. Technical limitations including off-target effects, mosaicism, delivery efficiency, regulatory uncertainty, and public acceptance continue to constrain large-scale implementation. In the short term, CRISPR/Cas9 applications are likely to focus on practical trait enhancement under controlled aquaculture systems, whereas longer-term research may explore fish lines specifically optimized for nutrient cycling, environmental resilience, and integrated aquaponic sustainability. Overall, CRISPR/Cas9-mediated genome editing represents a promising but still emerging strategy for improving sustainable aquaculture and aquaponic food production systems. Full article

Basonuclin 2 (BNC2) is a highly conserved cysteine–histidine (C2H2)-type zinc-finger nuclear regulatory protein characterized by three pairs of zinc-finger domains, a putative nuclear localization signal, a serine-rich region, broad tissue distribution, and remarkable transcript diversity generated through alternative promoter usage, alternative splicing, and polyadenylation. Increasing evidence from human genetics, animal models, functional genomics, and transcriptomic studies indicates that BNC2 links nuclear regulatory mechanisms to tissue-specific developmental and disease phenotypes. In the nervous system, BNC2-positive neuronal populations and BNC2-derived circular RNAs have been implicated in energy-balance circuits and neuroinflammatory regulation. In the skeletal system, BNC2 contributes to osteochondral development, periosteal stem-cell activation, chromatin remodeling, fracture repair, and genetic susceptibility to adolescent idiopathic scoliosis. BNC2 variants have also been associated with congenital lower urinary tract obstruction, whereas its expression and regulatory landscape are closely related to germ-cell development, epithelial ovarian cancer susceptibility, pigmentation traits, fibrosis, and several tumor contexts. Mechanistically, BNC2-associated phenotypes appear to involve cysteine–histidine zinc-finger-mediated transcriptional regulation, non-coding enhancer activity, epigenetic alterations, RNA-processing-associated nuclear functions, and chromatin-remodeling-dependent control of cell proliferation, differentiation, and stromal activation. This review integrates current evidence on the molecular architecture and regulatory functions of BNC2, critically discusses its context-dependent roles across development and disease, and highlights unresolved questions regarding isoform-specific activity, cell-type-specific regulation, downstream target networks, and clinical translation. A clearer understanding of these mechanisms may support the future evaluation of BNC2 as a biomarker, genetic susceptibility locus, molecular stratification factor, and potential therapeutic regulatory node. Full article

Genomic sequencing can reveal potentially life-threatening clinically actionable secondary findings in healthy individuals. Little is known about the spectrum and frequency of secondary findings in healthy people in Russia. Here, we analyzed whole-genome sequences of 42,826 healthy volunteers from urban populations across Russia, focusing on known pathogenic and likely pathogenic variants of 81 genes associated with treatable or preventable monogenic diseases listed in the American College of Medical Genetics and Genomics’ Secondary Findings recommendations (ACMG SF v3.2). Based on the ClinVar 20250421 version, secondary findings were detected in 1186 (2.76%) participants. Cancer phenotypes were the most common category of secondary findings present in 565 (1.32%) participants, followed by cardiovascular phenotypes (454 individuals, 1.05%). Genes harboring the most frequent variants were BRCA1 (151 variants), BRCA2 (100), RYR1 (93), and LDLR (71). In addition, we found 238 potential loss-of-function variants in dominant ACMG SF v3.2 list genes in 280 (0.65%) participants, which, if confirmed by orthogonal methods, could increase the frequency of secondary findings to 3.41%. A study of such depth and scale was performed for the first time in the Russian population. Full article

A rare example of long-term elimination of Aedes aegypti occurred in Brisbane, where legislatively enforced removal of rainwater tanks led to its disappearance by the mid-1950s. However, widespread tank installation during a later drought reintroduced critical breeding habitat, enabling persistence in this subtropical region. With Ae. aegypti re-invading towns ~150 km north of Brisbane, we assessed the potential for sustained elimination. Using a genomics-informed simulation modeling framework, we integrated population genomic inference of connectivity and migration with entomological and environmental data to parameterize elimination scenarios. Genomic analyses revealed strong overall isolation among neighbouring populations in the region, with limited recent migration detected between the two southernmost populations, in Murgon and Wondai. We therefore focused simulations on these populations. Our results indicate that elimination is feasible with moderate releases of incompatible Wolbachia-infected (IIT) males (sorting error ≤ 10⁻⁶), provided non-compliant rainwater tanks are removed first. This combined strategy achieved >99% suppression and elimination in 35% of simulations in one town, whereas IIT alone resulted in moderate suppression (61–93%) and increased the risk of Wolbachia establishment at higher release ratios. Full article

The white rhinoceros (Ceratotherium simum) offers a unique model for investigating the genomic consequences of extreme demographic bottlenecks. However, the fragmented southern white rhinoceros genome assembly has limited chromosome-scale structural and evolutionary comparisons with the functionally extinct northern subspecies. Here, we report a chromosome-scale genome assembly for the southern white rhinoceros by integrating Oxford Nanopore Technology long-read sequencing, Illumina short-read polishing and high-throughput chromosome conformation capture (Hi-C) scaffolding. The final assembly spans 2.48 Gb and achieves a contig N50 of 42.06 Mb, representing a 452-fold improvement in contiguity over the previous assembly. In total, 2.46 Gb of sequence was anchored to 40 autosomes plus the X and Y chromosomes. Genome annotation identified 1.13 Gb of repetitive elements (45.7% of the assembly), 22,593 protein-coding genes, and 100.68 Mb of segmental duplications. Inspection of the major histocompatibility complex class II gene region further supported the local assembly and annotation reliability, revealing conserved gene composition and order between the southern and northern white rhinoceroses. Whole-genome comparison with the northern white rhinoceros assembly indicated extensive chromosome-scale synteny, along with localized structural variants between the two subspecies, including 111 inversions spanning 33.48 Mb and 497 translocations spanning 36.48 Mb. Furthermore, coalescent demographic reconstruction indicated asynchronous Pleistocene population dynamics for southern and northern white rhinoceroses, reflecting divergent responses to historical climate oscillations. Both subspecies also exhibit lower recent effective population sizes than estimated Pleistocene ancestral levels, underscoring persistent conservation concern. This assembly provides a useful resource for evaluating the genomic consequences of historical bottlenecks, informing future genomic-rescue plans, and strengthening the comparative framework for rhinoceros conservation and evolutionary genomics. Full article

This study evaluates the vulnerability of Siberian larch (Larix sibirica L.) populations to future climate change using a genomic offset (GO) framework that integrates genome-wide SNP data with environmental variables. We analyzed 488 individuals from 37 populations across climatically diverse regions of Russia, genotyped by sequencing at over 20,000 SNP loci using the ddRADseq method. Gene–environment association (GEA) analyses (BayeScEnv, LFMM2, and RDA) identified candidate adaptive loci linked to six key bioclimatic variables. Based on these loci, GO was estimated using three approaches implemented in RONA–RDA, RDA, and Gradient Forest frameworks under multiple climate models (MIROC6, BCC-CSM2-MR, MRI-ESM2-0), scenarios (SSP2-4.5, SSP3-7.0, SSP5-8.5), and time periods (2041–2060, 2061–2080, and 2081–2100). Results revealed consistent spatial patterns of vulnerability, with northern and high-altitude populations, as well as populations from more continental and moisture-limited regions, exhibiting the highest GO and thus the greatest risk of maladaptation. In contrast, several central and southern populations showed relatively low vulnerability. The importance of temperature stability (isothermality) and precipitation of the driest month as key drivers of adaptive variation was highlighted. Despite differences in SNP datasets, population rankings remained highly consistent, supporting the robustness of predictions. Overall, our findings demonstrate substantial heterogeneity in climate vulnerability across the species range and provide a genomic basis for conservation strategies, including assisted gene exchange and climate-adaptive forest management. Full article

Arboviral diseases are emerging as important public health threats in Saudi Arabia, driven by rapid urbanization, climate variability, the expansion of Aedes aegypti populations, international travel, and large-scale religious mass gatherings. Dengue virus remains the most established arboviral infection in the Kingdom, particularly in the southwestern regions such as Jazan and the western urban centers of Makkah and Jeddah, where ecological and climatic conditions are conducive to sustained vector survival and transmission. This review synthesizes current evidence on the epidemiology, vector ecology, climatic determinants, diagnostics, and prevention strategies of arboviral diseases in Saudi Arabia. Particular attention is paid to the impacts of rising temperatures, changes in rainfall patterns, urban heat island effects, population mobility, and cross-border movement on vector expansion and disease emergence. The review also identifies gaps in surveillance, diagnostics, insecticide resistance monitoring, and integrated vector management programs. Emerging preparedness strategies include climate-informed early warning systems, Geographic Information System-based risk mapping, multiplex molecular diagnostics, genomic surveillance, and community-based vector control. The review emphasizes the importance of implementing a One Health approach that combines data on humans, the environment, entomology, and climate. Currently, sustained endemic transmission of chikungunya and Zika viruses has not been conclusively demonstrated in Saudi Arabia, but increased environmental suitability and connectivity with other areas highlight the need for proactive surveillance and preparedness. Full article

The genus Tulipa L. is a common group of ornamental plants, characterized by high morphological variability and a complex taxonomy. Despite considerable interest in this group, assessments of its species composition remain inconclusive, as evidenced by discrepancies between contemporary taxonomic sources. The number of recognized taxa varies across major taxonomic databases, including Plants of the World Online, World Flora Online, and Euro+Med PlantBase, reflecting ongoing taxonomic revisions and differences in species concepts. In terms of distribution patterns, 7.6% are widely distributed taxa across transcontinental regions, 28.0% occur across multiple countries within a continent, and 66.9% are range-restricted taxa. The latter group includes 4.2% transnational endemics, 44.1% single-country endemics, 8.5% single-region endemics, and 10.2% single-site endemics. Recent taxonomic and evolutionary studies of Tulipa increasingly rely on molecular approaches, particularly DNA barcoding and chloroplast genome analyses, which have improved phylogenetic resolution and species delimitation in several cases. However, truly comprehensive studies combining morphological, cytogenetic, and molecular datasets remain limited and are typically restricted to individual taxa or species complexes rather than the genus as a whole. Modern molecular genetic studies demonstrate the high informativeness of both nuclear and plastid markers for studying the phylogeny, systematics, and genetic diversity of Tulipa species. Natural populations of Tulipa are under pressure from anthropogenic factors and climate change, resulting in reduced range and habitat degradation. According to the International Union for Conservation of Nature Red List of Threatened Species, among 118 taxa of the genus Tulipa, T. sprengeri Baker is classified as Extinct in the Wild, 5.9% as Critically Endangered, 5.9% as Endangered, 8.5% as Vulnerable, 11.9% as Near Threatened, and 11.0% as Least Concern. The use of exclusively national assessments to determine species extinction risk may be insufficiently objective, whereas global assessments provide a more informative and reliable approach for evaluating conservation status. In this review, we combine investigations of the morphology, taxonomy, and geographic diversity; population genetic structure and molecular diversity; and molecular phylogenetics and plastome-based genomics of the genus Tulipa. Furthermore, the review examines current challenges and future research prospects, emphasizing that studies of the genus Tulipa should integrate morphological, genomic, and ecological approaches to refine taxonomy and conserve genetic resources. Full article

Background/Objectives: Antimicrobial resistance (AMR), driven by high-risk bacterial pathogens, is a major healthcare threat. This scoping review mapped artificial intelligence/machine learning (AI/ML) and computational approaches integrated with whole-genome sequencing (WGS), genomic surveillance, rapid typing, epidemiological data, or clinical metadata for early warning of AMR outbreak clones. Methods: Following PRISMA-ScR guidance and the Population–Concept–Context (PCC) framework, PubMed/MEDLINE, Scopus, and Web of Science were searched for English-language studies published between 2010 and 2026. Eligible studies addressed AI/ML or computational approaches for AMR outbreak detection, clone surveillance, transmission analysis, or infection prevention and control (IPC). Results: Thirty-eight studies were grouped into five domains: genomic surveillance; rapid typing; resistance, risk-factor, and lineage prediction; transmission reconstruction; and IPC-oriented genomic epidemiology. AI/ML supported automation, isolate prioritization, typing triage, prediction, transmission modelling, and electronic health record (EHR)-linked route identification. Conclusions: AI/ML may enhance WGS-based AMR surveillance, but validation, dataset dependence, heterogeneity, and limited IPC outcome reporting remain key gaps. Full article

The misuse of antibiotics is causing widespread antibiotic resistance, creating an urgent need for new treatment options such as nanoparticle-based therapies. This study aimed to compare silver nanoparticles (AgNPs) produced via green synthesis methods with those made through traditional chemical processes. Furthermore, the study investigated and contrasted the bacterial responses to these two types of AgNPs over a 21-day period of selection pressure using experimental evolution techniques. Analysis using scanning electron microscopy and transmission electron microscopy revealed a consistent, uniform morphology among the AgNPs produced via chemical methods. In contrast, AgNPs synthesized through green methods displayed an irregular morphology. Despite these morphological differences, all nanoparticles from both synthesis approaches were under 100 nm in diameter. These findings were further supported by the absorption spectrum data, which showed a maximum absorption peak between the 400 and 500 nm wavelength range. E. coli exposed to green synthesized AgNPs for 21 days adapted to their presence, exhibiting both enhanced resistance to the green synthesized AgNPs themselves and the development of cross-resistance to ionic silver, a pattern not observed in chemically synthesized AgNP-selected populations. Populations selected using chemical synthesized AgNPs did not develop increased resistance to either chemically or green synthesized AgNPs; however, they showed a slight increase in resistance to ionic silver. Genomics analysis identified polymorphism in genes in a green synthesized AgNP-resistant line including but not limited to the multidrug efflux transporter system (EmrAB), DUF4756 family protein (D1792_RS05680), putative zinc-binding protein YnfU/cold shock-like protein (ynfU/cspB) and imcF-related family protein (D1792_RS10035). Bacterial resistance to chemical AgNPs involves specific polymorphisms in key bacterial components like the RNA polymerase sigma factor (RpoE) and the EmrAB efflux pump. Collectively, the method used to synthesize the AgNPs influences their antibacterial efficacy and the likelihood of bacteria developing resistance. Understanding this interaction is vital for developing effective and resistance-controlled applications of AgNPs across medicine, environmental science, and industry. Full article

Background/Objectives: Melophagus ovinus is an economically important ectoparasite of small ruminants with a broad global distribution. Although mitochondrial genomes are widely used in population genetic studies, the D-loop region of M. ovinus remains poorly characterized because its high AT content and repetitive structure complicate amplification, assembly, and sequencing. Methods: We sequenced the mitochondrial genome of M. ovinus collected from Qinghai using an integrative approach combining Illumina paired-end sequencing, targeted PCR amplification, and Nanopore long-read sequencing. Comparative genomic analysis was performed against published mitogenomes from Gansu (MH024396) and Xinjiang (NC_037368). Results: The Qinghai mitochondrial genome contained the typical 37 mitochondrial genes within a 14,728 bp conserved region. Comparative analysis revealed exceptionally high conservation (>99.6% sequence identity) among Qinghai, Gansu, and Xinjiang isolates outside the D-loop region. Notably, the D-loop exhibited length polymorphism, with different assembly strategies or samples yielding lengths ranging from 317 bp to 2385 bp. Targeted long-read sequencing of ten individuals identified a predominant D-loop variant of approximately 844 bp in nine samples and a markedly shorter variant of approximately 164 bp in one sample. The short variant was characterized by extensive deletions and a novel 45 bp insertion. Support for this variant was obtained from independent Illumina DNA-seq, RNA-seq, Nanopore sequencing, and de novo assembly analyses. Conclusions: This study provides preliminary evidence for D-loop structural heterogeneity in M. ovinus, suggesting remarkable length polymorphism and complex indel patterns that require further validation. These findings significantly expand the genomic resources available for this important veterinary parasite and establish a foundation for future population genetic and evolutionary studies. Full article

Neolissochilus heterostomus, a cyprinid fish endemic to Yunnan Province, China, is highly valued for both ornamental and edible purposes, yet its wild populations are currently declining and classified as endangered. In this study, we present a chromosome-level genome assembly of N. heterostomus, utilizing the PacBio HiFi and Hi-C strategies. The assembled genome spans 1793.99 Mb and is anchored to 50 chromosomes, comprising a total of 50,203 genes. Genomic features and chromosomal karyotype data recorded in the present study are consistent with an allotetraploid origin for N. heterostomus. Comparative genomics shows that N. heterostomus shares a close phylogenetic relationship with another allotetraploid fish, the common carp Cyprinus carpio. In total, 4687 expanded and 1365 contracted gene families were identified in N. heterostomus. Further enrichment analyses indicated an overrepresentation of metabolism-related pathways among the expanded and positively selected gene families, whereas the contracted gene families were enriched in reproduction- and embryonic development-related pathways. Reproductive observations further indicate that N. heterostomus produces fewer eggs than other cyprinid species characterized by relatively long embryonic development periods (106.1 h; accumulated temperature: 2260.6 °C·h), including common carp, goldfish (Carassius auratus), grass carp (Ctenopharyngodon idella), pond loach (Misgurnus anguillicaudatus), and blunt snout bream (Megalobrama amblycephala). These findings suggest a potential association between metabolism-related genomic features and reproductive traits, although functional validation remains necessary. Overall, this study may offer insights into the polyploidization, metabolic, and reproductive traits of N. heterostomus, thereby providing genomic and biological resources that may support future studies relevant to the conservation and management of this endangered species. Full article