Search Results (1,358)

Background/Objectives: Illicium verum Hook. f. and Illicium difengpi K. I. B.et K. I. M. are two important medicinal plants which grow in the mountainous areas of Guangxi, China. Their similar morphological characteristics frequently lead to their misidentification. Chloroplast genome (cp)-based barcode technology has been used to effectively identify two closely related species; however, at present, there is no systematic comparative study of the cp genome sequences between I. verum and I. difengpi. Methods: Here, the cp genomes of the two plants were sequenced and analyzed. Results: The cp genome sizes were 142,689 and 142,689 bp for I. verum and I. difengpi, respectively. Each of the cp genomes annotated 122 genes, with 79 protein coding genes, 8 ribosomal RNA genes, and 35 transfer RNA genes. Amino acid frequencies of 1.17–10.19% (I. verum) and 1.18–10.17% (I. difengpi) were found in the coding genes. There were also 104 and 96 SSRs as well as 26 and 25 long repeats identified in I. verum and I. difengpi, respectively, among which the most common were A/T base repeats. Both cp genomes had SSC/IRa junctions located in gene ycf1-trnN. The ycf1 and trnL-trnV-rps7 genes were positioned at the IRb/SSC and LSC/IR boundaries, respectively. A phylogenetic relationship was constructed and the two species were fully nested within the genus Illicium. Conclusions: The comparative cp genomes of I. verum and I. difengpi are presented in this study, and this provides valuable phylogenetic information for subsequent molecular marker development and research of I. verum and I. difengpi. Full article

Fisheries and aquaculture play a crucial role in global food security, yet species mislabeling remains a persistent challenge, undermining consumer trust and market transparency. Proper food labeling is essential for protecting public health due to the presence of unknown toxic or allergenic substances and preventing illegally sourced products from entering the market. Despite extensive research across Europe, seafood mislabeling in Croatia has remained unexplored. This study aims to provide the first comprehensive assessment of seafood labeling accuracy in Croatia, where fisheries are integral to the coastal economies and tourism. Using DNA barcoding of the COI gene, 109 seafood samples were collected over two years from various sources, including restaurants, markets, and fishing vessels, and analyzed for potential mislabeling. Results revealed a mislabeling rate of 3% among fish samples and 20% among cephalopods, with notable substitutions, such as the yellowfin tuna mislabeled as bigeye tuna and Bluefin tuna and the European squid mislabeled as Patagonian squid. Additionally, 38.5% of samples were partially labeled, while 32% lacked clear country-of-origin information, complicating traceability. While the findings align with the mislabeling rates in other European countries, this study underscores the ongoing challenges in seafood labeling compliance. Establishing standardized monitoring protocols will be essential for improving comparability and effectively addressing seafood fraud. Full article

Tetrigidae is one of the largest orthopteran families, but very few studies so far have integrated molecular and morphological data. Unsurprisingly, few species have been DNA barcoded, and the unresolved taxonomy makes Tetrigidae a difficult group to work with. Here, we examined a sample of 90 specimens collected as a part of the Costa Rican DNA barcoding project and identified 20 species assigned to 24 BINs, among which are 8 newly described species: Scaria bimaculata sp. nov., Lophotettix semicristatus sp. nov., Otumba auricarinata sp. nov., Otumba tenuis sp. nov., Otumba ignicula sp. nov., Metrodora mollilobata sp. nov., Metrodora ala sp. nov., and Platythorus inabsolutus sp. nov. We found that coloration and lateral lobe shape are species-specific among the examined species of Batrachideinae and Metrodorinae and that Lophotettiginae and Metrodora might be more closely related than previously assumed. Full article

NGS sequencing data are expanding exponentially, accompanied by a concomitant growth in non-target species contamination. Meanwhile, these seemingly undesirable sequences can actually provide valuable insights into the broad-scale diversity and distribution of their parasites or symbionts. In this study, we developed a pipeline called DBCscreen (DNA Barcode Contamination screen) to explore biodiversity and distribution across a broad range of living organisms, based on a DNA barcode contamination survey. We used DBCscreen to screen 39,302 eukaryotic assemblies in the NCBI TSA/WGS database, and after stringent filtering, we ultimately identified 110,880 contaminated contigs related to DNA barcodes in 10,717 assemblies. Subsequently, the taxonomic information of these contaminants was determined, and their heterogeneous distribution patterns revealed complex relationships between the hosts (assembly source) and their associated parasites or symbionts (contaminants). Finally, several application examples demonstrating the use of DBCscreen were described, such as identification of the most easily contaminated organisms associated with a specific host (ex. ticks), as well as the specification of which hosts are particularly prone to certain types of contamination (ex. Wolbachia and nematodes). Full article

Throughout the 20th century, coyotes (Canis latrans) expanded from their historical geographic range west of the Mississippi River to a current range of almost all of North America. Over the course of this expansion, coyotes have demonstrated diverse and variable omnivorous diets that change with the food resources available. This study examined the stomach contents of 25 coyotes in an area where they are relatively new, the Qualla Boundary in North Carolina, to better understand the diets of coyotes in this area. A combination of morphological identification and DNA barcoding was used to characterize the stomach contents of coyotes. Both plant and animal material were identified from anthropogenic and natural sources, the latter including native mammals. This study provides one example of the breadth and flexibility of coyote diets and helps build an understanding of how coyotes can adapt to new conditions. Full article

Prior to this study, Myanmar was known to host 15 species of snakehead fishes (genus Channa) distributed across Southeast Asia. The region, characterized by its confluence of diverse river systems and two biodiversity hotspots, is presumed to have notable gaps in its biodiversity assessments. Recently, a new snakehead species, Channa shingon, was discovered in China, with its potential distribution in Myanmar warranting further investigation. This study focused on exploring Channa species in Kachin State and examined collected specimens using an integrated approach. The specimens were identified as C. shingon based on their distinct morphological characters, with a maximum standard length of 99.2 mm. Additionally, mitochondrial COI sequence data were generated, and species confirmation was achieved through nucleotide BLAST searches, genetic distance estimations, and phylogenetic analyses. The DNA sequences of C. shingon showed a mean inter-species genetic distance of 7.97% to 27.41% compared with other Channa species in the dataset, while the intra-species genetic distance between the Burmese and Chinese populations was 0.27%. Both Bayesian and maximum-likelihood phylogenetic analyses distinctly separated C. shingon from other congeners through a monophyletic clustering pattern, revealing its sister relationship with C. rubora. Overall, this study provides the first report of C. shingon from Myanmar and suggests its speciation from a common ancestor with C. rubora, likely driven by geographical barriers such as the Irrawaddy River. Furthermore, the study contributes a robust DNA barcode dataset encompassing 85.7% of the global Channa species diversity, which can serve as a valuable resource for further species identification, discovery, and diversity assessments of snakeheads from South and Southeast Asia. Full article

Micropterigidae and Eriocraniidae are poorly investigated in Southern Europe. Despite the richness of the Italian territory, studies devoted to investigating their molecular diversity are lacking. Furthermore, knowledge concerning the diversity and species distribution of these families in southern Italian regions is very poor. The aim of this paper is to contribute to filling the gaps in knowledge on the diversity of Micropterigidae and Eriocraniidae in southern Italian regions by analysing, through DNA barcoding, the samples collected in this geographic area by the authors in recent years. In total, 37 specimens were submitted to DNA barcoding analysis. The sequences were subsequently identified by comparing them with those available in the Barcoding of Life Data Systems. The results provided the first record and the first sequences of the Eriocraniidae family for southern Italy, the first record in continental Italy of a formerly Sicilian endemic species, the first sequences of an endemic species, and the first sequence belonging either to a previously described but unsequenced species or to an undescribed species. In conclusion, DNA barcoding of these families in southern Italy provided very interesting insights, improving their molecular libraries and the knowledge on the fauna of this territory. Daytime studies can further improve these results, but addressing the gaps concerning immature stages should be the major goal of future research. Full article

According to the World Health Organization, the global population is aging, with cognitive and memory functions declining from the age of 40–50. Individuals aged 65 and older are particularly prone to dementia. Therefore, we developed an interactive system for visual cognitive training to prevent dementia and delay the onset of memory loss. The system comprises three “three-dimensional objects” with printed 2D barcodes and near-field communication (NFC) tags and operating software processing text, images, and multimedia content. Electroencephalography (EEG) data from a brainwave sensor were used to interpret brain signals. The system operates through interactive games combined with real-time feedback from EEG data to reduce the likelihood of dementia. The system provides feedback based on textual, visual, and multimedia information and offers a new form of entertainment. Thirty participants were invited to participate in a pre-test questionnaire survey. Different tasks were assigned to randomly selected participants with three-dimensional objects. Sensing technologies such as quick-response (QR) codes and near-field communication (NFC) were used to display information on smartphones. Visual content included text-image narratives and media playback. EEG was used for visual recognition and perception responses. The system was evaluated using the system usability scale (SUS). Finally, the data obtained from participants using the system were analyzed. The system improved hand-eye coordination and brain memory using interactive games. After receiving visual information, brain function was stimulated through brain stimulation and focused reading, which prevents dementia. This system could be introduced into the healthcare industry to accumulate long-term cognitive function data for the brain and personal health data to prevent the occurrence of dementia. Full article

The consumption of edible insects is a promising approach to meet the increasing global demand for food. Commercialization of edible insects in the EU is regulated by the Novel Food regulation. To date, the yellow mealworm (Tenebrio molitor larva), the migratory locust (Locusta migratoria), the house cricket (Acheta domesticus), and the buffalo worm (Alphitobius diaperinus larva) have been authorized in the EU for human consumption. We aimed to develop a method based on DNA barcoding and high-resolution melting (HRM) analysis for the identification and differentiation of these four EU-authorized edible insect species in food. A primer pair previously designed for DNA metabarcoding, targeting a ~200 bp sequence of mitochondrial 16S rDNA, allowed discrimination between the four insect species in highly processed food. However, house cricket and migratory locust could not unambiguously be differentiated from tropical house cricket, desert locust, superworm, cowpea weevil, and sago worm, respectively. This problem could be solved by designing primers specific for house cricket and migratory locust. By combining these primers with the insect primers, additional polymerase chain reaction (PCR) products for house cricket and migratory locust were obtained, resulting in more complex melt curves compared to the unauthorized insect species. The optimized PCR-HRM assay is a very cost-efficient screening tool for authentication of EU-authorized edible insect species in food. Full article

Background/Objectives: Fish are vital in the Mediterranean diet, offering protein, nutrients, and ω-3 fatty acids. Greek consumers favor wild-caught, high-value fish like the dusky grouper (Epinephelus marginatus) classified as “vulnerable” and the white grouper (Epinephelus aeneus) classified as “near threatened” species, according to the IUCN Red List. Due to their premium prices and complex supply chains, these species are susceptible to fraud, especially through mislabeling. This practice not only deceives consumers but also poses health risks and encourages illegal fishing. DNA-based methods have shown effectiveness in accurately identifying species, even in processed samples. The aim of this study is to apply high-resolution melting analysis (HRM) as a rapid, effective method for monitoring the appropriate labeling of the two Epinephelus species in the Greek market. Methods: In this study, fresh fish from Greek catches as well as cooked, frozen, and filleted samples collected from the Greek market were identified using DNA barcoding. HRM analysis based on single nucleotide polymorphisms (SNPs) was used to differentiate between locally sourced E. marginatus and E. aeneus from their imported counterparts or from other species available in the Greek market that could be used in substitution incidents. Results: Using HRM analysis, cases of species mislabeling were identified and were also confirmed using sequencing. Conclusions: HRM analysis proved to be an accurate and cost-effective method for rapidly processing a large number of samples; therefore, it could serve as a valuable tool in extensive market controls as well as for bio-diversity conservation monitoring. Full article

Nanhaia speciosa is a valuable industrial crop known for its significant edible and medicinal properties, attributed to its abundance of secondary metabolites. This study aims to elucidate the genetic relationships among N. speciosa, enhance species identification accuracy, and select genetically stable, high-quality germplasms of N. speciosa. To achieve this, we conducted chloroplast gene amplification and sequencing, alongside an analysis of the agronomic traits of 19 N. speciosa germplasms. Additionally, non-targeted metabolomic profiling using UPLC-Q-Orbitrap/MS and chemometric methods was employed to assess their metabolic diversity and genetic relationships. The results revealed notable differences in DNA barcodes and secondary structures across the germplasms, with the atpF-atpH sequence successfully distinguishing all 19 germplasms into distinct varieties. Multivariate statistical analyses, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and hierarchical clustering, identified 12 key marker metabolites that effectively differentiated the germplasms, consistent with the observed phenotypic diversity. A clustering analysis integrating genetic, phenotypic, and metabolomic data further validated the utility of DNA barcoding for species identification. The results of the comprehensive analysis showed that NDL-2 and NDL-18 exhibited relatively good edible and medicinal properties, while NDL-1 and NDL-19 exhibited relatively poor edible and medicinal properties. This study provides crucial insights for the breeding and genetic improvement of N. speciosa and related species, offering a valuable reference for the identification, conservation, and utilization of germplasm resources within the N. speciosa. Full article

The taxonomy of genus Ambulyx Westwood, 1847 from China is reviewed based on analysis of wing morphology, male and female genitalia and phylogenetic relationships derived from DNA barcodes. A new species, Ambulyx wukong sp. nov. is described from NW Yunnan, China. A male of the rare species, A. zhejiangensis from Yintiaoling Nature Reserve, Chongqing, China is examined and its male genitalia illustrated for the first time. Two taxa are newly recorded from China, A. tattina tattina from Xishuangbanna, Yunnan, and A. semiplacida montana from Pingbian, Yunnan. Distribution maps, biological notes, and ecological records are also given. Full article

The genus Cymbidium, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among Cymbidium species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (matK, rbcL, trnL-F, psbA-trnH) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of Cymbidium species. The comparison of genetic distance variations showed that psbA-trnH, ITS + psbA-trnH, and ITS + matK + psbA-trnH exhibit minimal overlap and significant genetic variation within Cymbidium species. The phylogenetic analysis indicated that the combination, ITS + matK + psbA-trnH, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids. Full article

Environmental DNA from bulk materials can be analyzed to gain an understanding of the bacterial, fungal, plant, and/or arthropod communities present. DNA metabarcoding is widely used to characterize these biological communities, by amplifying “barcode” regions and sequencing these amplicons via next-generation sequencing. The Earth Microbiome Project (EMP) adopted the use of indexed primers, PCR primers containing Illumina^® adapter sequences and a unique 12-nucleotide Golay barcode to simplify the identification of bacterial taxa via the 16S barcode. We sought to develop a wet laboratory workflow utilizing indexed primers that could cost-effectively reduce bench time while simultaneously targeting multiple DNA barcode regions to characterize bacterial (16S), fungal (ITS1), plant (ITS2, trnL p6 loop), and arthropod (COI) communities. The EMP primer constructs for 16S were modified to accommodate our DNA barcode regions of interest while also permitting successful demultiplexing following sequencing. A single indexed primer pair was designed for ITS1 and trnL p6 loop, and two primer pairs were developed for ITS2 and COI. To test the workflow, a total of 648 soil and 336 dust samples were processed, with key steps including DNA isolation, total DNA quantification, amplification with indexed primers, library purification and quantification, and Illumina MiSeq sequencing. Based on raw read counts and analysis of positive controls, the trnL p6 loop and ITS2 a primer pairs performed comparably to the originally designed 16S primers. Both COI primers pairs, ITS1 and ITS2 b primers, had lower raw reads compared to the other three primer pairs. The combination of the three plant targets successfully recovered all plant taxa in the positive controls except for Nephrolepis exaltata [Nephrolepidaceae] and the COI primers recovered all arthropod taxa except for the beetle. Notably, none of the taxa in the fungal positive control were recovered using ITS1. For environmental samples, sequencing was successful for all primers except COI c, and primer biases were observed for all three plant primers, in which a small number of families were uniquely amplified for each primer pair. This workflow can be applied to many disciplines that utilize DNA metabarcoding given its customizability and flexibility with Illumina sequencing chemistry. Full article

The Danube Clouded Yellow (Colias myrmidone) has experienced one of the most dramatic declines among European butterflies. To estimate genetic diversity in the last population in Poland that has survived in the Knyszyn Forest (KF), we analyzed mitochondrial (COI) and nuclear (EF-1α) polymorphisms in individuals sampled in 2014 and 2022. The results were compared with genetic data obtained in 2014 from a recently extirpated nearby population (Czerwony Bór, CB). Because mtDNA polymorphisms in insects can be modulated by endosymbionts, the samples were screened for Wolbachia. The polymorphism of EF-1α indicated that diversity was gradually decreasing. The KF experienced rapid demographic processes, manifested by a significant change in allele frequency. The small differentiation in nuclear markers between the KF and CB in 2014 suggests that the regional population used to be genetically uniform. Four COI haplotypes that were identified in this study probably belong to two different haplogroups. Wolbachia was detected only in individuals with one specific haplotype, and the prevalence was female-biased, suggesting the induction of two reproductive manipulations. The most common COI haplotype found in Poland was the same as that reported from other parts of Europe, not only for C. myrmidone but also C. caucasica. These results allow us to question the distinctiveness of each taxa. Full article