Effect of physiological and environmental factors on mosquito wingbeat frequency

Wingbeat frequency may serve as a distinctive physical signature for identifying mosquito species. However, variation in wingbeat frequency within species may compromise reliability of wingbeat frequency-based mosquito identification. We examined the impact of mosquito density (number of females), time of day (day or night), gravid status, and age (days post-emergence) on the wingbeat frequency of three important vector mosquito species using infrared optical sensors. Wingbeat frequency of Culex quinquefasciatus was significantly higher (6.2% and 9.5%) for single females compared to groups of five and ten females, respectively, and 9.4% higher during the daytime compared to nighttime. Wingbeat frequency was also significantly higher for gravid Cx. quinquefasciatus (9.4%) and Aedes aegypti (1.4%) than nongravid conspecifics. Within a short age range (five to seven days post-emergence), wingbeat in Cx. quinquefasciatus did not vary significantly. Our results highlight that both extrinsic (density and time of day) and intrinsic (gravid status) factors contribute to wingbeat variation, potentially posing challenges for development of wingbeat profile libraries and the classification of unknown specimens. Traps that aim to use wingbeat frequency and target specific cohorts of the population (i.e., host-seeking or gravid females) will need to account for differences in wingbeat frequency due to multiple factors.

Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity

For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.

Rapid Identification of Medicinal Polygonatum Species and Predictive of Polysaccharides Using ATR-FTIR Spectroscopy Combined With Multivariate Analysis

INTRODUCTION

Medicinal Polygonatum species is a widely used traditional Chinese medicine with high nutritional value, known for its anti-fatigue properties, enhancement of immunity, delays aging, improves sleep, and other health benefits. However, the efficacy of different species varies, making the quality control of medicinal Polygonatum species increasingly important. Polysaccharides are important in medicinal Polygonatum species because of their potential functional properties, such as antioxidation, hypoglycemia, protection of intestinal health, and minimal toxicological effects on human health, as well as high polysaccharide levels.

OBJECTIVE

This study developed a qualitative medicinal Polygonatum species model and a polysaccharides predictive model based on attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) combined with a multivariate analysis approach.

MATERIALS AND METHODS

ATR-FTIR spectral information of 334 medicinal Polygonatum species samples was collected and the spectral information of different modes was analyzed. The ATR-FTIR spectral differences of three medicinal Polygonatum species were studied by multivariate analysis combined with four spectral preprocessing and three variable selection methods. For the prediction of polysaccharides in Polygonatum kingianum Collett & Hemsl. (PK), we initially determined the actual content of 110 PK polysaccharide samples using the anthrone-sulfuric acid method, then established partial least squares regression (PLSR) and kernel PLSR models in conjunction with attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy.

RESULTS

In the visualization analysis, the orthogonal partial least squares-discriminant analysis (OPLS-DA) model based on second-order derivative (SD) preprocessing was most suitable for medicinal Polygonatum species species binary classification, spectral differences between Polygonatum cyrtonema Hua (PC) and other species are evident; in the hard modeling, SD preprocessing improves the accuracy of non-deep learning models for the classification of three medicinal Polygonatum species. In contrast, residual neural network (ResNet) models were the best choice for species identification without preprocessing and variable selection. In addition, the partial least squares regression (PLSR) model and Kernel-PLSR model can quickly predict PK polysaccharides content, among them, the Kernel-PLSR model with SD pretreatment has the best prediction performance, residual prediction deviation (RPD) = 7.2870, Rp = 0.9905.

CONCLUSION

In this study, we employed ATR-FTIR spectroscopy and various treatments to discern different medicinal Polygonatum species. We also evaluated the effects of preprocessing methods and variable selection on the prediction of PK polysaccharides by PLSR and Kernel-PLSR models. Among them, the ResNet model can achieve 100% correct classification of medicinal Polygonatum species without complex spectral preprocessing. Furthermore, the Kernel-PLSR model based on SD-ATR-FTIR spectra had the best performance in polysaccharides prediction. In summary, by integrating ATR-FTIR spectroscopy with multivariate analysis, this research accomplished the classification of medicinal Polygonatum species and the prediction of polysaccharides. The methodology offers the benefits of speed, environmental sustainability, and precision, highlighting its significant potential for practical applications. In future research, on the one hand, it can be further investigated using a portable infrared spectrometer, and on the other hand, infrared spectroscopy can also be applied to the prediction of other chemical components of medicinal Polygonatum species.

Application of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Foodborne Pathogens: Current Developments and Future Trends

Foodborne pathogens have gained sustained public attention, exerted significant pressure on food manufacturers, and posed serious health risks to human. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been employed for quick and accurate identification of microorganisms in the prevention of foodborne epidemics in recent years. Herein, we first summarize the principle of MALDI and its workflow for foodborne pathogens. Subsequently, we review the recent progress and applications of MALDI-TOF MS in foodborne pathogen determination. Additionally, we outline the expanded utilization of MALDI-based techniques for the identification of closely related species. We also assess the current gaps and propose possible solutions to address the existing challenges. MALDI-TOF MS is a promising biotool for rapid and accurate identification of foodborne microbes at the species and genus level in food samples. Database expansion and direct quantification of spoilage microbes are two promising areas for future progress in MALDI-TOF MS applications.

A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany

Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination. In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. Our DNA barcode library comprises 824 high-quality cytochrome c oxidase I (COI) barcodes encompassing 76 crane fly species, counting for ca. 54% of the German tipulid fauna. Our results significantly increased the number of European tipulid species available in the Barcode of Life Data System (BOLD) by 14%. Additionally, the number of barcodes from European tipulid specimens more than doubled, with an increase of 118%, bolstering the DNA resource for future identification inquiries. Employing diverse species delimitation algorithms - including the multi-rate Poisson tree processes model (mPTP), Barcode Index Number assignments (BIN), Assemble Species by Automatic Partitioning (ASAP), and the TaxCI R-script - we successfully match 76-86% of the morphologically identified species. Further validation through neighbor-joining tree topology analysis and comparison with 712 additional European tipulid barcodes yield a remarkable 89% success rate for the species identification of German tipulids based on COI barcodes. This comprehensive DNA barcode dataset not only enhances species identification accuracy but also serves as a pivotal resource for ecological and biomonitoring studies, fostering a deeper understanding of crane fly diversity and distribution across terrestrial landscapes.

The First Report of Sphaerirostris picae Infection in the Oriental Magpie (Pica serica) in Beijing, China

Background: Sphaerirostris picae is a parasitic species known for its ability to infect and transmit between hosts in the gastrointestinal tracts of wild avian species. However, there is limited information on its presence and impact on urban avian populations, particularly in China. Materials and Methods: In this study, morphological observations were conducted to detect the presence of Sphaerirostris sp. within the intestinal tract of the Oriental Magpie (Pica serica) collected in Beijing, China. Further confirmation of the parasite's identity was achieved through phylogenetic analysis using COX1 gene sequencing to compare with previously documented Sphaerirostris picae isolates. Results: The morphological and molecular analyses confirmed the presence of Sphaerirostris picae in the Oriental Magpie. Phylogenetic analysis indicated a close relationship with known Sphaerirostris picae isolates. This represents the first reported case of Sphaerirostris picae infection in magpies from Beijing, China. Conclusion: The findings highlight the potential health hazards posed by Sphaerirostris picae to urban avian populations and public health. The study suggests that additional research and surveillance efforts are necessary to better understand the risks associated with this parasite and to develop effective mitigation strategies.

Identification and prevalence of ixodid ticks of cattle in case of Aleltu district, Oromia regional state, northern Ethiopia

BACKGROUND

In Ethiopia, ticks are the major threat to cattle productivity and production, leading to considerable economic losses. The current study was designed to estimate the prevalence of ixodid tick infestation, identify species, assess major risk factors associated with tick infestation and assess public awareness.

METHODS

A cross-sectional and questionnaire-based study was conducted from January 2022 to June 2022 in the Aleltu district. The study animals were selected using a simple random sampling method.

RESULTS

Of the 400 cattle examined, 303 (75.8%) were found to be infested by one or more tick species. Six species of ticks were identified that belonged to three genera: Amblyomma, Hyalomma and Rhipicephalus, and the subgenus Rhipicephalus (Boophilus). The most common tick species identified in terms of their prevalence and dominance were Rh. (Bo) decoloratus, Rh. evertsi, Am. variegatum, Hy. rufipes, Rh. bergeoni and Rh. praetextatus. In the present study, Rh. (Bo) decoloratus was the most prevalent (56.8%) in the study area. Among the risk factors considered, the prevalence of tick species had a statistically significant (p < 0.05) association with the age, production systems and body condition of animals. Out of 110 people interviewed, 107 (97.3%) believed there was a tick infestation in their village, and almost all farmers 103(93.6%) in the study area were unaware that ticks serve as vectors.

CONCLUSIONS

The present study provides preliminary information on the prevalence of tick infestation and the composition of ticks in the Aleltu district. Ticks are a major problem for the cattle in the study area. Therefore, the problem observed in the study area alarms the district and calls for a comprehensive control strategy.

Loop-Mediated Isothermal Amplification Assay to Detect Invasive Malaria Vector Anopheles stephensi Mosquitoes

Spread of the Anopheles stephensi mosquito, an invasive malaria vector, threatens to put an additional 126 million persons per year in Africa at risk for malaria. To accelerate the early detection and rapid response to this mosquito species, confirming its presence and geographic extent is critical. However, existing molecular species assays require specialized laboratory equipment, interpretation, and sequencing confirmation. We developed and optimized a colorimetric rapid loop-mediated isothermal amplification assay for molecular An. stephensi species identification. The assay requires only a heat source and reagents and can be used with or without DNA extraction, resulting in positive color change in 30-35 minutes. We validated the assay against existing PCR techniques and found 100% specificity and analytical sensitivity down to 0.0003 ng of genomic DNA. The assay can successfully amplify single mosquito legs. Initial testing on samples from Marsabit, Kenya, illustrate its potential as an early vector detection and malaria mitigation tool.

Exploring the landscape of automated species identification apps: Development, promise, and user appraisal

Two decades ago, Gaston and O'Neill (2004) deliberated on why automated species identification had not become widely employed. We no longer have to wonder: This AI-based technology is here, embedded in numerous web and mobile apps used by large audiences interested in nature. Now that automated species identification tools are available, popular, and efficient, it is time to look at how the apps are developed, what they promise, and how users appraise them. Delving into the automated species identification apps landscape, we found that free and paid apps differ fundamentally in presentation, experience, and the use of biodiversity and personal data. However, these two business models are deeply intertwined. Going forward, although big tech companies will eventually take over the landscape, citizen science programs will likely continue to have their own identification tools because of their specific purpose and their ability to create a strong sense of belonging among naturalist communities.

Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads

Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.IMPORTANCEDespite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.

Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species

The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources.

DNA Barcoding Unveils Novel Discoveries in Authenticating High-Value Snow Lotus Seed Food Products

Snow Lotus Seed (SLS), esteemed for its nutritional and market value, faces challenges of authentication due to the absence of appropriate testing standards and methods. This results in frequent adulteration of SLS sourced from Gleditsia sinensis (G. sinensis) with other plant seeds endosperm. Traditional chloroplast DNA barcoding methods are inadequate for species identification due to the absence of chloroplasts in G. sinensis seeds endosperm. In this study, the homology of 11 ITS genes among 6 common Gleditsia species was analyzed. Universal primers suitable for these species were designed and screened. A DNA barcoding method for distinguishing SLS species was developed using Sanger sequencing technology, leveraging existing GenBank and Barcode of Life Data System (BOLD) databases. Optimized sample pretreatment facilitated effective DNA extraction from phytopolysaccharide-rich SLS. Through testing of commercial SLS products, the species origin has been successfully identified. Additionally, a novel instance of food fraud was uncovered, where the Caesalpinia spinosa endosperm was used to counterfeit SLS for the first time. The study established that the developed DNA barcoding method is effective for authenticating SLS species. It is of great significance for combating food fraud related to SLS, ensuring food safety, and promoting the healthy development of the SLS industry.

Description of five larvae of the genus Gnaptorina Reitter, 1887 from Xizang, China (Coleoptera, Tenebrionidae, Blaptinae), with molecular species delimitation and diagnoses

With 39 described species in three subgenera, the Gnaptorina is the second most species-rich genus in the subtribe Gnaptorinina (Tenebrionidae: Blaptinae). In this study, a phylogeny of Gnaptorina was reconstructed based on one nuclear (28S-D2) and three mitochondrial (COI, Cytb, and 16S) gene fragments; multiple molecular species delimitation approaches were also implemented to assess the taxonomic status of larval specimens based on COI gene fragment. Larvae of five known species of the subgenus Hesperoptorina are described and illustrated for the first time: Gnaptorinanigera Shi, Ren & Merkl, 2007, Gnaptorinatishkovi Medvedev, 1998, Gnaptorinabrucei Blair, 1923, Gnaptorinahimalaya Shi, Ren & Merkl, 2007, Gnaptorinakangmar Shi, Ren & Merkl, 2007. A key to larvae of four genera of the tribe Blaptini and a key to the known larvae of the genus Gnaptorina are provided. This study provides valuable morphological data for larval studies of the tribe Blaptini.

Identification of Diptera Puparia in Forensic and Archeo-Funerary Contexts

Diptera identification is fundamental in forensic entomology as well as in funerary archeoentomology, where the challenge is exacerbated by the presence of immature stages such as larvae and puparia. In these two developmental stages, specimens possess a very limited number of diagnostic features, and for puparia, there is also a lack of identification tools such as descriptions and identification keys. Morphological analysis, DNA-based techniques, and cuticular chemical analyses all show good potential for species identification; however, they also have some limitations. DNA-based identification is primarily hindered by the incompleteness of genetic databases and the presence of PCR inhibitors often co-extracted from the puparial cuticle. Chemical analysis of the cuticle is showing promising results, but this approach is also limited by the insufficient profile database and requires specific, expensive equipment, as well as trained personnel. Additionally, to ensure the repeatability of the analysis-a critical aspect in forensic investigations-and to preserve precious and unique specimens from museum collections, non-invasive protocols and techniques must be prioritized for species identification.

phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL.

Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids

Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.

Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade

Introduction. Commensal Neisseria spp. are highly prevalent in the oropharynx as part of the healthy microbiome. N. meningitidis can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify N. meningitidis, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).Hypothesis/Gap statement. N. meningitidis may be misidentified by MALDI-TOF MS.Aim. To conduct genomic surveillance of oropharyngeal Neisseria spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal Neisseria spp. genomes.Methodology. We analysed whole genome sequence (WGS) data from 119 Neisseria spp. isolates from a surveillance programme for oropharyngeal Neisseria spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) rplF gene species identification. WGS data were used to further characterize Neisseria species found with supplementary analyses of Neisseria cinerea genomes.Results. Based on genomic species identification, isolates from the oropharyngeal Neisseria surveilence study were composed of the following species: N. meningitidis (n=23), N. subflava (n=61), N. mucosa (n=15), N. oralis (n=8), N. cinerea (n=5), N. elongata (n=3), N. lactamica (n=2), N. bacilliformis (n=1) and N. polysaccharea (n=1). Of these 119 isolates, four isolates identified as N. meningitidis (n=3) and N. subflava (n=1) by MALDI-TOF MS, were determined to be N. polysaccharea (n=1), N. cinerea (n=2) and N. mucosa (n=1) by rMLST. Phylogenetic analyses revealed that N. cinerea isolates from the general population (n=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, n=2, cluster two). The latter contained genomes misidentified as N. meningitidis using MALDI-TOF MS. These two N. cinerea clusters persisted after the inclusion of published N. cinerea WGS (n=42). Both N. cinerea clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.Conclusion. This study provides insights into the importance of genomic genus-wide Neisseria surveillance studies to improve the characterization and identification of the Neisseria genus.

The complete chloroplast genome sequences of nine melon varieties (Cucumis melo L.): lights into comparative analysis and phylogenetic relationships

Melon (Cucumis melo L.) is one of the most extensively grown horticulture crops of the world. Based on the morphological characters, melon was formerly divided into two subspecies, Cucumis melo ssp. melo and C. melo ssp. agrestis. However, the present methods are still inadequate to distinguish between them. The phylogenetic analysis based on chloroplast genome sequences could provide essential evidence for the classification of melon varieties. We sequenced the chloroplast genomes of nine different melon varieties by the Illumina Hiseq and performed bioinformatic analyses including repeat element analysis, genome comparison and phylogenetic analysis. The results showed that the melon chloroplast genome has a typical quadripartite structure that was conserved across the analyzed sequences. Its length ranges between 155, 558 and 156, 569 bp, with a total GC content varying from 36.7% to 37%. We found 127-132 genes in melon chloroplast genomes, including 85-87 protein-coding regions, 34-37 tRNA and 6-8 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) were mostly conserved among the nine sequenced genomes. Phylogenetic analysis showed that the chloroplast genome could clearly distinguish between C. melo ssp. melo and C. melo ssp. agrestis. This study not only provides valuable knowledge on melon chloroplasts, but also offers a theoretical basis and technical support for the genetic breeding of melons.

Organic-Acid-Sensitive Visual Sensor Array Based on Fenton Reagent-Phenol/Aniline for the Rapid Species and Adulteration Assessment of Baijiu

Baijiu is an ancient, distilled spirit with a complicated brewing process, unique taste, and rich trace components. These trace components play a decisive role in the aroma, taste, and especially the quality of baijiu. In this paper, the redox reaction between the Fenton reagent and four reducing agents, including o-phenylenediamine (OPD), p-phenylenediamine (PPD), 4-aminophenol (PAP), and 2-aminophenol (OAP), was adopted to construct a four-channel visual sensor array for the rapid detection of nine kinds of common organic acids in baijiu and the identification of baijiu and its adulteration. By exploiting the color-changing fingerprint response brought by organic acids, each organic acid could be analyzed accurately when combined with an optimized variable-weighted least-squares support vector machine based on a particle swarm optimization (PSO-VWLS-SVM) model. What is more, this novel sensor also could achieve accurate semi-quantitative analysis of the mixed organic acid samples via partial least squares discriminant analysis (PLSDA). Most importantly, the sensor array could be further used for the identification of baijiu with different species through the PLSDA model and the adulteration assessment with the one-class partial least squares (OCPLS) model simultaneously.

Evaluation of phenotypic and genotypic methods for the identification and characterization of bacterial isolates recovered from catheter-associated urinary tract infections

AIMS

Urinary tract infections are the most common hospital-acquired infection, 80% of which are associated with catheterization. Diagnostic methods may influence the reported identities of these pathogens, and phenotypic testing under laboratory conditions may not reflect infection phenotypes. This study aimed to evaluate the efficacy of diagnostic methods and whether medium composition alters phenotypes by characterizing catheter-associated urinary tract infection isolates from a UK hospital.

METHODS AND RESULTS

We compared five bacterial identification methods, including biochemical testing, matrix-assisted laser desorption/ionization biotyping, and genome sequencing, finding differences in genus- or species-level identifications. Antibiotic susceptibility comparisons between phenotypic assays and genomic predictions showed high agreement only in multidrug-resistant strains. To determine whether growth rate and biofilm formation were affected by medium composition, strains were grown in both planktonic and biofilm states. Low planktonic growth and significant biofilm formation were observed in artificial urine compared to rich laboratory media, underscoring the importance of assay design.

CONCLUSIONS

This study highlights the risks of relying on a single diagnostic method for species identification, advocating for whole-genome sequencing for accuracy. It emphasizes the continued importance of phenotypic methods in understanding antibiotic resistance in clinical settings and the need for characterization conditions that mirror those encountered by pathogens in the body.

Sequence variation of commercially available kratom products at universal DNA barcode regions

Mitragyna speciosa, commonly known as kratom, is a narcotic plant that is used for its unique mood-enhancing and pain-relieving effects. It is marketed throughout the United States as a 'legal high' and has gained popularity as an alternative to opioids. However, kratom's increasing involvement in accidental overdoses, especially among polydrug users, has prompted warnings from the Drug Enforcement Agency (DEA) and the Food and Drug Administration (FDA). Despite these warnings, kratom remains legal federally, although it is banned in six states. This legal disparity complicates monitoring and enforcement efforts in states where kratom is illegal. Common forensic techniques using morphology or chemical analysis are beneficial in some instances but are not useful in source attribution because most seized kratom is powdered and the alkaloid content of samples can vary within products, making sourcing unreliable. This study focused on developing a DNA barcoding method to access sequence variation in commercial kratom products. It evaluated the utility of one nuclear barcode region (ITS) and three chloroplast barcode regions (matK, rbcL, and trnH-psbA) in assessing sequence variation across commercially available kratom products. Novel polymorphisms were discovered, and the ITS region showed the greatest variation between samples. Among the 15 kratom products tested, only two haplotypes were identified across the four barcoding regions. The findings highlight the potential of DNA barcoding as a forensic tool in the traceability and enforcement against illegal kratom distribution. Nonetheless, the limited haplotypic diversity points to a need for further development and expansion of the M. speciosa DNA sequence database.

DNA barcoding is currently unreliable for species identification in most crayfishes

DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.

Establishment and Validation of a Multiplex PCR Detection System for the Identification of Six Common Edible Meat Components

OBJECTIVES

To establish a rapid, accurate, and sensitive multiplex PCR detection method for the simultaneous identification of the six common edible meats (beef, lamp, chicken, pork, goose, duck), and to evaluate its application value in meat adulteration identification.

METHODS

Based on complete mitochondrial genomic sequences of six species in the GenBank database, DNA sequences (cattle：16S rRNA; sheep：COX-1; chickens：Cytb; pig：COX-1; goose：NADH2; duck：16S rRNA) with intra-species conservation and inter-species specificity were screened, and species-specific primers were designed to construct a multiplex PCR detection system that can simultaneously detect the meat of six common species. The species specificity, sensitivity and reproducibility of the system were studied, and the simulated mixture sample detection was performed.

RESULTS

This study successfully constructed a multiplex PCR detection system that can detect the meats of six common species simultaneously. The system was not effective in DNA amplification of non-target species. When the DNA template sizes were 0.062 5-2 ng/μL, the amplified products of all six species could be detected. The duck component was still detected when the mixing ratio of duck and beef was as low as 0.5%.

CONCLUSIONS

This study constructs and establishes a multiplex PCR detection system with strong specificity, high sensitivity, and good reproducibility. It can accurately identify the components of animal origin in common edible meats and provide a simple and practical method for identifying adulteration of common edible meats and meat products in China.

A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project

Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.

DNA barcoding of terrestrial invasive plant species in Southwest Michigan

Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA-based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH-psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR-and-sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH-psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH-psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual-barcode approaches (e.g., ITS + trnH-psbA) might be the efficient and cost-effective method in DNA-based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.