Search Results (1,643)

Many biting midge species of the genus Culicoides Latreille are significant pests and vectors that transmit diverse parasites to humans and other animals. However, knowledge of these hematophagous insects in Laos remains limited, with the most recent information reported more than four decades ago. In this study, we investigated Culicoides species diversity, DNA barcoding and host blood sources using specimens collected across seven provinces in northern, central, and southern Laos. A total of 4592 specimens were collected, comprising 3095 females and 1497 males. Morphological identification, complemented by DNA barcode analysis, revealed 26 species (24 named and 2 unnamed), including five (three named and two unnamed) new country records. Culicoides peregrinus was the most abundant species, representing 25.7% (1179 individuals), followed by C. oxystoma at 23.8% (1093 individuals), and C. arakawae/C. mahasarakhamense, which together comprised 18.5% (849 individuals) of the total specimens. DNA barcode analysis demonstrated that this genetic marker is effective for species identification of Culicoides in Laos. Of the 115 COI sequences, 103 (89.6%) were successfully matched with conspecifics in the BOLD database. Cryptic genetic diversity was detected in three species, C. clavipalpis, C. palpifer, and C. huffi, with two, two, and three divergent lineages, respectively. Host blood meal analysis revealed that chickens and domestic water buffalo were the most common blood sources for the investigated Culicoides species. These findings provide important baseline information for future studies on the pest and vectorial roles of Culicoides in Laos. Full article

Two new cryptic species from central China, belonging to the Pholcus yichengicus species group, were identified using an integrative approach combining morphological and three molecular species delimitation methods, and incorporating data from five related previously described species. These two new species are named Pholcus chengkou sp. nov. and P. yanan sp. nov. DNA barcodes were generated for the two new species to calculate p-distances and K2P distances, thus confirming their identities alongside the five previously described species. Additionally, revised diagnoses for the five previously described species and a distribution map encompassing all the species discussed are provided. Full article

Introduction: Records of rare, deep-water, and non-indigenous fish species are of growing interest in marine biodiversity research because they refine regional inventories, improve taxonomic knowledge, and provide valuable evidence of ecological change. In regions supported by long-term monitoring programs, such findings are especially relevant, as they help detect unusual occurrences and document changes in species composition over time. Objective: The aim of this communication is to present recent records of fish species new to science and new to Spanish waters, together with a non-indigenous species, all from Galician and Cantabrian waters (northern Spain), while emphasizing the importance of scientific surveys and complementary local observations in their detection. Methodology: The material examined was collected during the annual demersal trawl surveys conducted by the Instituto Español de Oceanografía (IEO-CSIC) on the northern Spanish continental shelf (DEMERSALES), as well as during two multidisciplinary surveys carried out on the Galicia Bank in 2010 and 2011. An additional specimen was obtained from a local recreational fisher off Asturias. In all cases, species identification was based on an integrative taxonomic approach combining morphological examination and molecular analyses (COI barcoding). Results: Three species new to science were identified: Gaidropsarus gallaeciae (Gadiformes: Gaidropsaridae), Notacanthus arrontei (Notacanthiformes: Notacanthidae), and Neoscopelus serranoi (Myctophiformes: Neoscopelidae). In addition, Lyconus brachicolus (Gadiformes: Lyconidae) and Lipogenys hyalovelanum (Notacanthiformes: Notacanthidae) were recorded for the first time in Spanish waters. A specimen of Diapterus brevirostris (Perciformes: Gerreidae), native to the tropical and subtropical Pacific coast of America, was also identified off Asturias. Owing to its small size and to the proximity of the commercial port of Gijón, ballast water is considered the most plausible vector for its introduction into the Cantabrian Sea. Conclusions: These records illustrate the value of long-term oceanographic surveys for detecting rare and deep-water fishes and confirm the usefulness of integrative taxonomy for robust species identification. They also highlight the complementary role of fishers and citizen observers in documenting biodiversity change and detecting non-indigenous species in Spanish waters. 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

A nettle-feeding psyllid of the genus Trioza (Hemiptera: Triozidae) was discovered in Hokkaido, northern Japan. Although the European species Trioza urticae has been reported from Japan in several databases and publications, these records are based on erroneous literature citations rather than examined specimens. Adult and immature materials collected from Urtica platyphylla were examined morphologically and analysed using mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. The Japanese species is closely related to Palaearctic T. urticae and Nearctic T. albifrons but is consistently distinguishable by several adult and immature morphological characters. In addition, COI sequences show large interspecific divergence (≥12%) among the three species, supporting its distinct taxonomic status. The Japanese species is therefore described as Trioza miyatakei sp. nov., and Japan is formally excluded from the distribution range of T. urticae. These results indicate that records of T. urticae in East Asia surrounding Japan require re-examination using both morphology and DNA barcoding. A diagnostic key to all known Urtica-feeding species of Trioza worldwide is provided. Furthermore, the Chinese species Triozopsis huai Li, 2011 is transferred to Trioza as Trioza huai (Li, 2011) comb. nov. Full article

Imaging-based spatial transcriptomics has advanced from low-plex single-molecule fluorescence in situ hybridization to a diverse set of highly multiplexed platforms, with recent multimodal and pathology-compatible capabilities. Despite major differences in chemistry, coding, and imaging strategies across different platforms, their biological interpretation often converges on a few notable computational biology problems. This review examines imaging-based spatial transcriptomics through the lens of data interpretation and applications, focusing on the analytical framework that converts raw fluorescence signals or accompanying in situ sequencing data into molecule-, cell-, and tissue-level representations. We discuss the key challenges in preprocessing, registration, restoration, feature detection, barcode decoding, molecule calling, cell segmentation, transcript assignment, probabilistic cell typing, spatial-domain inference, and atlas integration. We also highlight how optical crowding, tissue thickness, panel bias, and multimodal complexity increase computational difficulty. Finally, we summarize applications of imaging-based spatial transcriptomics techniques, ranging from subcellular RNA localization to atlas-scale and pathology-aware spatial analysis. Full article

South Korea is a highly import-dependent food economy and therefore offers a useful case for examining how an integrated national food control system can be built under trade openness, limited domestic agricultural capacity and changing consumer risk perceptions. This article presents a structured narrative review, rather than a causal impact evaluation, of South Korea’s transition from multi-agency food safety regulation toward an integrated, risk-based food control system. The review is organized through the FAO/WHO national food control system framework and maps Korean legal, institutional and operational evidence onto six analytical dimensions: legal foundations, institutional coordination, risk-based official controls, import supervision, traceability and recall, and risk communication. Examples of embedded risk-analysis principles include the Positive List System for pesticide residues with a default limit of 0.01 mg/kg for substances without a Korean MRL, inspection orders and risk-ranked import controls, barcode-linked recall blocking through the Hazardous Food Sales Prevention System, and public disclosure of unsafe directly purchased overseas products. Quantitative evidence is used descriptively: Korea’s agricultural and food imports reached USD 45.3 billion in 2024, hepatitis A notifications fell from 17,598 in 2019 to 3989 in 2020 after the salted-clam outbreak, and MFDS reported that 12 of 544 overseas direct-purchase products tested in the first half of 2020 contained restricted substances. These indicators suggest improvements in coordination and crisis response capacity, but they do not prove that institutional integration alone reduced foodborne disease incidence. The review finds that South Korea’s model is strongest in institutional consolidation, import-oriented technical standards and digital recall communication, while key challenges remain in small-business compliance burden, scientific independence, data transparency, cross-border e-commerce and novel foods such as cell-cultured food ingredients. Full article

To test the performance of COI-based DNA barcoding in species delimitation, we amplified and sequenced the mitochondrial COI gene from six Schizothoracine fishes endemic to Xinjiang, China. We then characterized the COI gene dataset, quantified genetic divergence, and inferred phylogenetic relationships using distance-based approaches. Morphological examination supported clear phenotypic differentiation among taxa. In particular, Diptychus maculatus can be readily distinguished from the densely scaled Schizothorax species by having a single pair of barbels and relatively sparse scales. The COI gene sequences showed an evident AT bias (55.1%), consistent with patterns reported for teleost mitochondrial genomes. Across all samples, 11 haplotypes were identified. Pairwise comparisons indicated a maximum interspecific divergence of 15.296%, whereas the smallest interspecific distance (0.262%) occurred between Schizothorax barbatus and Schizothorax irregularis. Species-delimitation analyses and phylogenetic reconstruction supported D. maculatus and A. laticeps as distinct mitochondrial lineages, whereas S. biddulphi, S. eurystomus, S. irregularis, and S. barbatus were not fully resolved by COI gene. The shared haplotypes and low genetic distances among the four Schizothorax species may reflect recent divergence, incomplete lineage sorting, or historical gene flow. Overall, COI gene barcoding is effective for distinguishing the major lineages in this dataset, especially D. maculatus and A. laticeps. Full article

Mosquito-borne diseases pose a significant public health concern globally; however, data on mosquito population dynamics in Taipei, Taiwan are limited and outdated. Updated information on species composition and seasonal abundance is crucial for enhancing vector surveillance and informing effective control strategies. In this study, to investigate the seasonal dynamics of mosquito populations in Taipei, Taiwan, adult females were collected biweekly from June 2023 to May 2025 using CDC light traps baited with ultraviolet light and dry ice. Species identification was performed based on morphological characteristics, and morphologically challenging Culex mosquito species were further confirmed using cytochrome c oxidase I barcoding. Mosquito surveillance from June 2023 to May 2025 yielded 1926 females representing 31 species. Of these, Culex quinquefasciatus, Culex pipiens molestus, Aedes albopictus, and Culex tritaeniorhynchus accounted for over 90% of all specimens. These dominant species exhibited distinct seasonal patterns: Cx. quinquefasciatus occurred year-round, Cx. pipiens molestus predominated during winter and spring, while Ae. albopictus and Cx. tritaeniorhynchus populations peaked in summer. Furthermore, spatial heterogeneity in both mosquito abundance and species composition was noted among the study sites. Monitoring the composition and seasonal dynamics of mosquito species is essential for understanding the epidemiology of mosquito-borne pathogens. These insights can inform more effective and targeted vector control strategies for reducing disease transmission. Such ecological insights can also support One Health approaches by linking human, animal, and environmental factors that influence the transmission of mosquito-borne diseases. Full article

Long-read sequencing technologies provide portable and flexible service, making them attractive for small-scale sequencing studies. However, many existing RNA-sequencing analysis frameworks are designed for transcriptome-wide analyses and require substantial computational resources. Here we present a lightweight and reproducible computational pipeline for targeted long-read transcriptomic profiling using Oxford Nanopore Technologies (ONT) cDNA sequencing data. The pipeline was evaluated using targeted long-read transcriptomic datasets generated from formalin-fixed paraffin-embedded (FFPE) colorectal carcinoma samples previously classified as microsatellite instability—high (MSI-high) by PCR-based testing. Libraries were sequenced on the Oxford Nanopore MinION platform using R10.4.1 flow cells. Application of the workflow enabled rapid quantification of mismatch repair gene expression and detection of immune-related transcripts including CD8A, PDCD1, and HAVCR2 across multiplexed barcode samples. The pipeline performs targeted alignment of long-read sequencing data to a custom transcript reference panel using minimap2, followed by gene-level read counting and normalization using reads-per-million (RPM). Optional modules enable immune marker profiling, detection of reads aligning to multiple genes, exploratory variant analysis, and visualization of expression patterns. By combining simplicity, reproducibility, and minimal computational overhead, the present pipeline provides an accessible framework for targeted transcriptomic analysis of long-read sequencing data. It may facilitate adoption of ONT-based transcriptomic profiling in settings with restricted computational resources. Full article

Fusarium spp. are active producers of mycotoxins that enter the food chain and pose risks to human health. Identifying pathogenic agents is a key step in developing disease management strategies. For the first time in Bulgaria, we identified eight Fusarium species in wheat, harvest 2024–2025, through the application of DNA barcoding. For a genetic marker and construction of phylogenetic tree, the protein-coding gene β-tub was chosen. Among 26 identified isolates, F. sporotrichioides (42.3%) dominated, followed by F. proliferatum (23.1%), F. avenaceum (7.7%), F. armeniacum (7.7%), and F. poae (7.7%). F. tricinctum (3.8%), F. oxysporum (3.8%), and F. equiaseti (3.9%) were weakly expressed. Phylogenetic analysis classified the isolates into five species complexes: FSAMSC, FFSC, FTSC, FIESC, and FOSC and highlighted the genetic distances between them. Molecular genetic analysis showed that 84.6% of the wheat samples contained only one species of Fusarium, and in 15.4% the co-presence of two species was established. The largest share was in samples with a low infestation of 2–4%, which represented 35% (n = 32) of all positives. No statistically significant difference was found between varieties and contamination level, but a statistically significant positive correlation was demonstrated by the preceding crop (rapeseed, sunflower, and maize). Full article

Pumpkin (Cucurbita spp.) is a globally significant vegetable crop known for its high nutritional value and remarkable phenotypic diversity. Yet, the surge in new cultivar releases has overwhelmed traditional morphological descriptors, creating critical gaps in variety purity control and breeders’ rights enforcement. Despite the established utility of SNP markers as the gold standard for genetic analysis, a dedicated high-resolution molecular database for modern pumpkin cultivars remains unavailable. To address this gap, we conducted whole-genome resequencing (WGS) on 94 representative pumpkin cultivars (spanning C. moschata, C. maxima, and C. pepo). Clean reads were mapped to the Cucurbita maxima reference genome. We employed a stringent pipeline to identify genomic variants and utilized STRUCTURE software, Principal Component Analysis (PCA), and Neighbor-Joining (NJ) trees to evaluate population stratification. Linkage disequilibrium (LD) decay and DNA fingerprinting barcodes were also developed. A total of 8,873,150 high-quality variants were identified, including 7,345,007 SNPs and 1,528,143 InDels, with an average SNP density of 21,281.50 SNPs/Mb. Population analysis consistently categorized the 94 cultivars into two primary subpopulations (G1 and G2). The first two PCs accounted for 74.06% of the total genetic variance. Further analysis revealed that G1 possessed a more complex genetic architecture and slower LD decay compared to G2, suggesting distinct selection histories. Finally, we screened for highly informative biallelic SNPs to construct a DNA fingerprinting database, enabling precise sample discrimination through unique chromatic barcodes. This study fills a critical gap in pumpkin genomics by establishing a high-density SNP database and a robust fingerprinting system. These resources provide a definitive tool for variety certification, seed purity testing, and the advancement of molecular-assisted breeding in pumpkin. Full article

Urbanization can act as a powerful ecological filter, restructuring biodiversity through species loss, replacement, and altered resource pathways. While urban green spaces (UGS) are recognized as potential biodiversity refuges, the effectiveness and mechanisms for conserving insect diversity across the urban-to-natural gradient remain poorly understood. Here, we combine full-season Malaise trapping (April–November) with MinION-based DNA barcoding to test two predictions about how urbanization reshapes Diptera communities across five sites in Haidian District, Beijing, ranging from residential areas and urban parks to a nearby shallow mountain reserve (BWM). Based on 5528 barcoded individuals, we identified 686 putative species from 39 families. As predicted, β-diversity between urban and mountain sites was overwhelmingly driven by species turnover rather than nestedness, demonstrating that cities do not simply receive subsets of the surrounding fauna but actively reassemble communities. This filtering effect was, however, trophic-guild specific. Detritivores showed the highest replacement, consistent with a shift from natural to anthropogenic resource subsidies, while predators/parasitoids exhibited significant nested loss, aligning with their hypothesized sensitivity at higher trophic levels. Vegetation structure further clarified these patterns: vegetation density, not plant species richness, was the primary bottom-up driver for herbivore and predator/parasitoid diversity, whereas detritivores were decoupled from living plant biomass. These findings demonstrate that urban and near-natural habitats maintain distinct species pools via guild-specific assembly pathways, highlighting the need for guild-specific conservation strategies for urban biodiversity conservation. Extending beyond compositional analysis, we propose a temporal-abundance framework, classifying species by persistence and abundance, as a diagnostic tool for assessing ecological integrity and guiding conservation in urbanizing landscapes. Full article

In situ hybridization (ISH) has undergone a rapid evolution from a low-throughput histological staining technique to a diverse family of modern methods for sensitive, specific and multiplexed molecular detection in intact cells and tissues, and to a cornerstone technology for image-based spatial transcriptomics. This transformation has been driven by advances in probe design, signal amplification, cyclic imaging, combinatorial barcoding, automated fluidics and computational decoding, which together allow RNA molecules to be measured within preserved cellular and tissue architecture. In this review, we examine the molecular and engineering principles that underlie modern ISH methods and their extension into ISH-based spatial profiling, with emphasis on hybridization chain reaction, branched-DNA amplification, SABER-FISH, rolling-circle-amplification-based approaches, seqFISH, MERFISH, RAEFISH and selected commercial implementations. We discuss how sensitivity, specificity, tissue compatibility, optical crowding, imaging burden, cost, reproducibility and computational uncertainty shape the practical use of each method. Sequencing-based spatial capture platforms are not reviewed comprehensively, but are considered where comparative benchmarks help clarify trade-offs in spatial resolution, transcriptome breadth, tissue area or analytical interpretation. We also consider how recent benchmarking and standardization efforts are beginning to define quantitative criteria for comparing platforms, and how advances in segmentation, barcode decoding, spatial integration and cell–cell communication analysis convert raw images into biological insight. Finally, we highlight applications in targeted transcript detection, tissue-based validation, neuroscience, cancer, developmental biology, non-model organisms and spatial functional genomics, where modern ISH methods and ISH-based spatial profiling provide information that bulk and dissociated single-cell approaches cannot capture. Together, these developments trace how ISH has expanded from targeted molecular visualization into a broad methodological framework for in situ detection and spatially resolved transcriptomic analysis. Full article