Search Results (418)

Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts. Full article

The ongoing genetic erosion of natural Prunus armeniaca populations in their native habitats underscores the urgent need for targeted conservation and restoration strategies. This study provides the first comprehensive characterization of P. armeniaca populations in the Almaty region of Kazakhstan, integrating morphological descriptors (46 parameters), molecular markers, geobotanical, and remote sensing analyses. Geobotanical and remote sensing analyses enhanced understanding of accession distribution, geological features, and ecosystem health across sites, while also revealing their vulnerability to various biotic and abiotic threats. Of 111 morphologically classified accessions, 54 were analyzed with 13 simple sequence repeat (SSR) markers and four DNA barcoding regions. Our findings demonstrate the necessity of integrated morphological and molecular analyses to differentiate closely related accessions. Genetic analysis identified 11 distinct populations with high heterozygosity and substantial genetic variability. Eight populations exhibited 100% polymorphism, indicating their potential as sources of adaptive genetic diversity. Cluster analysis grouped populations into three geographic clusters, suggesting limited gene flow across Gorges (features of a mountainous landscape) and greater connectivity within them. These findings underscore the need for site-specific conservation strategies, especially for genetically distinct, isolated populations with unique allelic profiles. This study provides a valuable foundation for prioritizing conservation targets, confirming genetic redundancies, and preserving genetic uniqueness to enhance the efficiency and effectiveness of the future conservation and use of P. armeniaca genetic resources in the region. Full article

Members of the genus Nemipterus are economically important fish species distributed in the tropical and subtropical Indo-West Pacific region. The majority of species in this genus inhabit waters with sandy–muddy substrates on the continental shelf, although different species are found at slightly varying water depths. In this study, we sequenced seven species within the genus Nemipterus after identifying the specimens using complementary morphological analysis and DNA barcoding. Each species yielded over 40,000,000 clean reads, totaling over 300,000,000 clean reads across the seven species. A total of 276,389 unigenes were obtained after de novo assembly and a total of 168,010 (60.79%) unigenes were annotated in the protein database. The comprehensive functional annotation based on the KOG, GO, and KEGG databases revealed that these unigenes are mainly associated with numerous physiological, metabolic, and molecular processes, and that the seven species exhibit similarity in these aspects. By constructing a phylogenetic tree and conducting divergence time analysis, we found that N. bathybius and N. virgatus diverged most recently, approximately during the Neogene Period (14.9 Mya). Compared with other species, N. bathybius and N. virgatus are distributed in deeper water layers. Therefore, we conducted selection pressure analysis using these two species as the foreground branches and identified several environmental-responsive genes. The results indicate that genes such as aqp1, arrdc3, ISP2, Hip, ndufa1, ndufa3, pcyt1a, ctsk, col6a2, casp2 exhibit faster evolutionary rates during long-term adaptation to deep-water environments. Specifically, these genes are considered to be associated with adaptation to aquatic osmoregulation, temperature fluctuations, and skeletal development. This comprehensive analysis provides valuable insights into the evolutionary biology and environmental adaptability of threadfin breams, contributing to the conservation and sustainable management of these species. Full article

Barcodes are ubiquitous in manufacturing and logistics, but defects can reduce decoding efficiency and disrupt the supply chain. Existing studies primarily focus on a single barcode type or rely on small-scale datasets, limiting generalizability. We propose Y8-LiBAR Net, a lightweight two-stage framework for multi-type barcode defect detection. In stage 1, a YOLOv8n backbone localizes 1D and 2D barcodes in real time. In stage 2, a dual-branch network integrating ResNet50 and ViT-B/16 via hierarchical attention performs three-class classification on cropped regions of interest (ROIs): intact, defective, and non-barcode. Experiments conducted on the public BarBeR dataset, covering planar/non-planar surfaces, varying illumination, and sensor noise, show that Y8-LiBARNet achieves a detection-stage mAP@0.5 = 0.984 (1D: 0.992; 2D: 0.977) with a peak F1 score of 0.970. Subsequent defect classification attains 0.925 accuracy, 0.925 recall, and a 0.919 F1 score. Compared with single-branch baselines, our framework improves overall accuracy by 1.8–3.4% and enhances defective barcode recall by 8.9%. A Cohen’s kappa of 0.920 indicates strong label consistency and model robustness. These results demonstrate that Y8-LiBARNet delivers high-precision real-time performance, providing a practical solution for industrial barcode quality inspection. Full article

The Dalbergia genus, a morphologically diverse group within the Fabaceae family, encompasses species of significant value in furniture production and medicinal and aromatic applications. The taxonomy of Dalbergia has relied on morphological traits, chloroplast (cp) DNA fragments, and cp genomic data. However, genomic resources for tropical liana species within this genus remain scarce. In this study, we assembled and analyzed the cp genomes of 3 liana species—Dalbergia peishaensis, D. pinnata, and D. tsoi—and compared them with those of 26 other Dalbergia species to explore their cp genome characteristics and evolutionary patterns. We employed a combination of traditional cp genome analysis and methods adapted from plant whole-genome sequencing. Phylogenetic analysis revealed that D. peishaensis has a close relationship with D. cultrata, forming a recently diverged clade, whereas D. tsoi and D. pinnata are positioned within a basal clade of the Dalbergia genus, suggesting an earlier divergence. The Dalbergia cp genomes exhibit considerable variation in size, with evidence of pseudogenization, gene loss, and duplication observed in the three liana species. Notably, the infA gene, previously reported as absent in the chloroplast genomes of Dalbergia species, was identified in the cp genomes of these three liana Dalbergia species. A total of 4533 simple sequence repeats (SSRs) were identified, providing valuable insights into cp genome evolution and facilitating future population genetics studies, particularly when combined with the high structural variation observed in the genus through whole-genome analysis methods. Additionally, seven highly divergent regions were identified as potential DNA barcode hotspots. This study enhances the genomic characterization of liana Dalbergia species and offers a robust framework for future plant cp genome analyses by integrating methodologies originally developed for whole-genome studies. Full article

DNA metabarcoding is a powerful biodiversity monitoring tool, enabling simultaneous assessments of diverse biological communities. However, its accuracy depends on the reliability of reference databases that assign taxonomic identities to obtained sequences. Here we provide a DNA barcode dataset for aquatic fauna of the Panama Canal, a region that connects the Western Atlantic and Eastern Pacific oceans. This unique setting creates opportunities for trans-oceanic dispersal while acting as a modern physical dispersal barrier for some terrestrial organisms. We sequenced 852 specimens from a diverse array of taxa (e.g., fishes, zooplankton, mollusks, arthropods, reptiles, birds, and mammals) using COI, and in some cases, 12S and 16S barcodes. These data were collected for a variety of studies, many of which have sought to understand recent changes in aquatic communities in the Panama Canal. The DNA barcodes presented here are all from captured specimens, which confirms their presence in Panama and, in many cases, inside the Panama Canal. Both native and introduced taxa are included. This dataset represents a valuable resource for environmental DNA (eDNA) work in the Panama Canal region and across the Neotropics aimed at monitoring ecosystem health, tracking non-native and potentially invasive species, and understanding the ecology and distribution of these freshwater and euryhaline taxa. Full article

Accurate species identification of small aquatic insects remains challenging due to their morphological similarities. This study addresses this issue by developing a DNA barcode reference library for the globally distributed Brillia (Diptera: Chironomidae). We analyzed cytochrome c oxidase subunit I (COI) sequences of 241 specimens belonging to 13 Brillia species from 18 countries, including 56 newly generated and 185 publicly available COI barcodes. Our integrated approach included genetic distance analysis, haplotype network construction, and ecological niche modeling. The results revealed remarkable cryptic diversity, with sequences clustering into 30 Barcode Index Numbers and 158 unique haplotypes, most being region-specific. Notably, East Asian and North American populations showed complete genetic distinctness, suggesting long-term isolation. Environmental factors, particularly temperature and precipitation gradients, were identified as key drivers of this diversification. The study also corrected several misidentifications in existing databases. These findings significantly advance our understanding of Brillia diversity and provide a reliable molecular tool for freshwater ecosystem monitoring, with important implications for biodiversity conservation and environmental assessment. Full article

Although diverse and abundant, the phylum Bryozoa has been the subject of few studies in Costa Rica. Nearly 50 years have passed since Banta and Carson identified, described, and published twenty-four bryozoan species, including scanning electron microscope (SEM) images. To expand the knowledge of bryozoan diversity in the region, we sampled shallow coastal waters along the northern Pacific coast of Costa Rica and extracted tissue for DNA barcoding using the mitochondrial COI marker. Photographs of living specimens and SEM images were taken for morphological identification. We identified fifteen individuals belonging to nine bryozoan species from the orders Cyclostomatida and Cheilostomatida. Five of these species represent new records for Costa Rica (Savignyella lafontii, Bugula neritina, Watersipora arcuata, Smittipora levinseni, and Biflustra tenuis), while the remaining four (Disporella sp., Parasmittina crosslandi, Cigclisula sp., and Biflustra sp.) had been previously reported. Full article

Complete chloroplast genome sequences are widely used in the analyses of phylogenetic relationships among angiosperms. As a species-rich genus, species diversity centers of Saxifraga L. include mountainous regions of Eurasia, such as the Alps and the Qinghai–Tibetan Plateau (QTP) sensu lato. However, to date, datasets of chloroplast genomes of Saxifraga have been concentrated on the QTP species; those from European Alps are largely unavailable, which hinders comprehensively comparative and evolutionary analyses of chloroplast genomes in this genus. Here, complete chloroplast genomes of 19 Saxifraga species were de novo sequenced, assembled and annotated, and of these 15 species from Alps were reported for the first time. Subsequent comparative analysis and phylogenetic reconstruction were also conducted. Chloroplast genome length of the 19 Saxifraga species range from 149,217 bp to 152,282 bp with a typical quadripartite structure. All individual chloroplast genome included in this study contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs. The IR boundaries keep relatively conserved with minor expansion in S. consanguinea. mVISTA analysis and identification of polymorphic loci for molecular markers shows that six intergenic regions (ndhC-trnV, psbE-petL, rpl32-trnL, rps16-trnQ, trnF-ndhJ, trnS-trnG) can be selected as the potential DNA barcodes. A total of 1204 SSRs, 433 tandem repeats and 534 Large sequence repeats were identified in the 19 Saxifraga chloroplast genomes. The codon usage analysis revealed that Saxifraga chloroplast genome codon prefers to end in A/T. Phylogenetic reconstruction of 33 species (31 Saxifraga species included) based on 75 common protein coding genes received high bootstrap support values for nearly all identified nodes, and revealed a tree topology similar to previous studies. Full article

Mangrove-associated fungi represent a diverse but understudied group of eukaryotic organisms, especially in the Neotropics. The Colombian Pacific region, with approximately 1300 km of coastline covered with 194,880 ha of mangrove forests that remain largely unexplored for macrofungal diversity, is recognized as a global biodiversity hotspot. This study aimed to catalog the macrofungi associated with mangrove ecosystems in Colombia, integrating morphological characterization and molecular phylogenetics, focusing on three Valle del Cauca Pacific coast localities. A total of 81 specimens were collected from both living trees and decaying wood. Detailed macroscopic and microscopic analyses were conducted, and DNA sequences from two ribosomal DNA barcode regions (ITS and LSU) were generated for 43 specimens. Three new species—Neohypochnicium manglarense, Phlebiopsis colombiana, and Porogramme bononiae—were documented. In addition, eight species were reported as new records for both Colombia and mangrove ecosystems, including Microporus affinis, Paramarasmius palmivorus, Phlebiopsis flavidoalba, Porogramme brasiliensis, Resinicium grandisporum, Trametes ellipsospora, T. menziesii, and T. polyzona. Although previously recorded in Colombian terrestrial ecosystems, Lentinus scleropus and Oudemansiella platensis are globally reported here for the first time from mangrove habitats. Furthermore, Fomitopsis nivosella and Punctularia strigosozonata were documented for the first time in Colombia. This study addresses the first exploration of mangrove-associated macrofungi in the country and provides new insights into the hidden fungal diversity and potential of mangrove ecosystems as a latent niche for basidiomycete dispersal along Colombia’s Pacific coast. Full article

Insect mitochondrial genomes are vital to understanding evolutionary relationships and identifying species. This study focused on Microtendipes (Chironomidae), a genus with unresolved phylogenetic positioning and cryptic species challenges. We sequenced and analyzed eight mitogenomes from five Microtendipes species, integrating 23 published Chironominae mitogenomes to reconstruct phylogenies using Maximum Likelihood and Bayesian Inference. The mitogenomes exhibited conserved gene arrangements but variable control region lengths (338–1266 bp) and high AT content (94.14–96.42% in control regions). Our results show that Microtendipes species may be a separate group within the subfamily, while also supporting the monophyly of the Harnischia, Polypedilum, and Chironomus complexes. The monophyly of Microtendipes bimaculus was weakly supported, which may demonstrate the presence of two potential cryptic species. Notably, larval morphology-based species groupings conflicted with the molecular data, suggesting that classifications derived from larval morphological traits may be unreliable. This study advances the evolutionary understanding of Chironomidae and underscores the limitations of single-gene barcodes in species-rich genera. Full article

Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) is the only genus within its family endemic to Brazil, being present in the Atlantic Forest and sections of the Cerrado. Taxonomic knowledge of the genus is incomplete, especially for nymphs. An integrative approach to the description of species and semaphoronts is essential for further studies. We describe a new species of Kempnyia based on morphological and molecular data, associate and describe the nymphs of both the new species and Kempnyia umbrina Froehlich, 1988, as well as expand its distribution and correct past mistakes in identification of K. umbrina. Specimens were identified morphologically and sequenced for the barcode region of the cytochrome oxidase subunit I (COI) mitochondrial gene, resulting in eight new sequences for three species of the genus. Both morphological and molecular analyses revealed a new species, Kempnyia krenaki sp. nov. Its nymph and that of K. umbrina are also described. With our additions, the number of known Kempnyia species rises to 41, of which 26 have COI sequences available in GenBank. Although only 11 nymphs have been associated and described for the genus so far, as the Kempnyia sequence database continues to grow, studies associating and describing nymphs will become more common, gradually reducing the Haeckelian deficit. Full article

As close relatives of the vertebrates, cephalochordates have been the focus of significant evo–devo and genomic research; however, their biodiversity and systematics remain poorly known. In particular, few species have been documented in the eastern Pacific and there are few published observations for this region. Using sequences from COI and 16S DNA barcode markers and morphological observations from 16 animals collected incidentally during other studies, we document the presence of three species of amphioxus on the Pacific coast and one from the Caribbean coast of Panama. The high genetic diversity recovered from so few samples suggests that the application of molecular taxonomy to neotropical amphioxus would likely uncover additional species and could help to more easily delineate morphological differences among taxa. Full article

Molecular species identification plays an increasingly important role in forensic entomology and is centered on selecting appropriate DNA barcodes, which there are not yet enough of. Such identification is decisive in discovering a better DNA barcode for the identification of necrophilous fly species. Here, we analyzed 10 common necrophilous fly species found on Hainan Island; designed 12 pairs of fly-specific primers from different mitochondrial regions; screened two fly DNA barcodes with better results than those of published studies, which were used as controls; and employed a high-resolution melting (HRM) curve to construct PCR-HRM technology systems for rapid and efficient necrophilous fly species identification. The results showed that, among the 14 DNA barcoding PCR-HRM systems, the newly designed COXII-519/COXII-615 primer was the best, which identified 10 necrophilous fly species in one test. The second-best system was the C1-J-2495/C1-N-2800 primer published in the literature, which identified six fly species in one test. Moreover, since the COXII-519/COXII-615 primer system performed successfully in both stale (stored over two years) and larval samples due to its short amplificated fragment (shorter than 97 bp), it may serve as a new efficient DNA barcode for necrophilic fly species identification. The new DNA barcoding PCR-HRM system established in this study enables the rapid and accurate identification of necrophilic fly species. Full article

Background/Objectives: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding. Methods: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties. Results: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine–cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers. Conclusions: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera. Full article