DNA barcoding for elasmobranch diversity assessment in Thailand: Its advantages and limitations

The assessment of elasmobranch biodiversity in Thailand benefits greatly from the application of DNA barcoding, which helps mitigate the challenge posed by a shortage of expert taxonomists. Fragments of COI and ND2 mitochondrial DNA were examined, and the strengths and weaknesses of these two markers were compared. In this study, DNA products from 153 elasmobranch samples were amplifiable and revealed a total of 28 shark species and 32 batoid species. Many species could be confidently identified as their morphological characteristics aligned with DNA barcodes. However, several exceptions were recognized. The absence of reference sequences for rare species presented a challenge for species verification, and the misidentification of reference sequences, as well as changes in species names due to taxonomic revisions, added complexity when comparing DNA barcoding sequences. Conflicts between morphology and genetics were also observed. While intraspecific genetic variation based on both DNA barcodes generally indicated 0-2% variation, this metric could not always be used for species delimitation. This was particularly true for species displaying low genetic variation among closely related species and species where cryptic diversity remained hidden and yet to be uncovered. In such cases, the morphological characteristics of the samples served as the primary means of species identification. Despite these challenges, DNA barcoding remains an invaluable tool for biodiversity assessment, especially in light of the shortage of skilled experts, and for identification of products made from vulnerable species. However, it is essential to exercise caution and be aware of these complexities in its application.

DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.

Identification of species based on DNA sequences (DNA barcodes) is an aid to a taxonomic classification using morphological characteristics. DNA barcoding uses standard short genomic regions that are universally present in target lineages and has sufficient sequence variation to identify species in the genus. A variety of loci has been suggested as DNA barcodes for plants, including genes and non-coding regions in the nuclear and plastid genomes such as psbA-trnH, matK, rbcL, and ITS. In this study, we evaluated five potential DNA barcodes including 18S, ITS, matK, psbA-trnH, and rbcL for their ability to distinguish between species across our samples in the genus Panax L. Multiple alignments with 41 GenBank sequences selected from 9 species showed that the 18S region had the highest level of average similarity (99.87 %), followed by rbcL, matK, psbA-trnH, and ITS regions with lower levels of average similarities (99.27 %, 98.66 %, 96.82 % and 96.50 %, respectively). The phylogenetic trees showed that four of eleven ginseng samples were Panax vietnamensis Ha et Grushv., and three samples were Panax stipuleanatus with bootstrap values of 100 %. However, sequences of all five screened loci in the last four samples, which were considered as Panax bipinnatifidus based on morphological characteristics, were highly similar to Panax stipuleanatus with the level of sequence similarity reached 99.81 % - 100 %. In addition, our results showed that of five investigated DNA regions, ITS, and psbA-trnH were the most promising barcodes that could identify P. vietnamensis Ha et Grushv. and P. stipuleanatus species within the genus Panax L.

Recently, the study about Marine fish identification is becoming a big challenge for us. Marine biodiversity is always to been underestimated for we can’t know how enormous it is. And because of the boundedness, the existing traditional taxonomic methods have not enough ability to detect the mystery of ocean and we must seek for a new way to research how many kinds of fishes in ocean and what kind of the fish is. What’s more, with the internationalization of market, not only taxonomy, but the seafood market chaos and plenty of issues about food safety also reflect the importance of Marine fish identification. In this context, a new identification tool -- --DNA barcodes has appeared. DNA barcodes is a Molecular identification methods which through sequencing the mitochondrial genes of Cytochrome c Oxidase subunit I(COI) sequence and being compared with DNA barcodes database to rapid identification of the sample. In this study, we will introduce the principle, advantages and limitations of DNA barcodes and summarize the application of DNA barcodes in the aspect of Marine fish and seafood identification. All kinds of application research show that DNA barcodes has high resolution and can easily identify fishes to species level. So we have reason to believe that the DNA barcodes can been made full use of in the field of Marine fish authenticity identification though the research of predecessors. What’s more, it benefits to enhance the effectiveness of food anti-counterfeit and can help to manage the seafood market more effectively.

DNA barcoding is a tool for species identification and classification, overcoming traditional limitations; being fundamental for multiple studies and applications. This article will review the progress of the application of DNA barcoding for algal identification; as it presents advantages such as accuracy in species identification, its applicability to various stages and conditions for ecological studies and intraspecific genetic variability, which according to its approach will depend on several factors. DNA barcoding applications in microalgae, such as its molecular identification, is fundamental for diversity and ecology; expanding knowledge about microalgae; being useful in monitoring harmful algae (HABs) that are a danger to aquatic ecosystems; In addition, DNA barcoding of microalgae is used in biotechnology and food industries. In Peru, taxonomic research is of lesser incidence because there is no method that provides precise identification at the species level, among other reasons, but this DNA barcoding technique has proven to be an efficient tool for research in the conservation and management of organisms that are difficult to access or complex to differentiate, such as microalgae. To conclude, DNA barcoding represents an essential tool in modern microalgae research, which should be developed in Peru, as it has significant potential to advance our knowledge and management of these crucial organisms in Peruvian aquatic ecosystems

Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three large-scale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated. Key words: 18S rRNA; COI; DNA barcoding; ITS; rbcL; taxonomic databases

<abstract> <p>DNA barcoding is a crucial method for assessing and monitoring species diversity amidst escalating threats to global biodiversity. I explore DNA barcoding's potential as a robust and reliable tool for biodiversity assessment. It begins with a comprehensive review of existing literature, delving into the theoretical foundations, methodologies and applications of DNA barcoding. The suitability of various DNA regions, like the COI gene, as universal barcodes are extensively investigated. Additionally, the advantages and limitations of different DNA sequencing technologies and bioinformatics tools are evaluated within the context of DNA barcoding. To evaluate the efficacy of DNA barcoding, diverse ecosystems, including terrestrial, freshwater and marine habitats, are sampled. Extracted DNA from collected specimens undergoes amplification and sequencing of the target barcode region. Comparison of the obtained DNA sequences with reference databases allows for the identification and classification of the sampled organisms. Findings demonstrate that DNA barcoding accurately identifies species, even in cases where morphological identification proves challenging. Moreover, it sheds light on cryptic and endangered species, aiding conservation efforts. I also investigate patterns of genetic diversity and evolutionary relationships among different taxa through the analysis of genetic data. This research contributes to the growing knowledge on DNA barcoding and its applicability for biodiversity assessment. The advantages of this approach, such as speed, accuracy and cost-effectiveness, are highlighted, along with areas for improvement. By unlocking the genetic code, DNA barcoding enhances our understanding of biodiversity, supports conservation initiatives and informs evidence-based decision-making for the sustainable management of ecosystems.</p> </abstract>

Since the pre-historic era, humans have been using forests as a food, drugs and handcraft reservoir. Today, the use of botanical raw material to produce pharmaceuticals, herbal remedies, teas, spirits, cosmetics, sweets, dietary supplements, special industrial compounds and crude materials constitute an important global resource in terms of healthcare and economy. In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on a selected group of forest tree species with the aim of contributing to the identification, conservation and trade control of these valuable plant resources.The “core barcode” for land plants (rbcL, matK, and trnH-psbA) was tested on 68 tree specimens (24 taxa). Universality of the method, ease of data retrieval and correct species assignment using sequence character states, presence of DNA barcoding gaps and GenBank discrimination assessment were evaluated. The markers showed different prospects of reliable applicability. RbcL and trnH-psbA displayed 100% amplification and sequencing success, while matK did not amplify in some plant groups. The majority of species had a single haplotype. The trnH-psbA region showed the highest genetic variability, but in most cases the high intraspecific sequence divergence revealed the absence of a clear DNA barcoding gap. We also faced an important limitation because the taxonomic coverage of the public reference database is incomplete. Overall, species identification success was 66.7%.This work illustrates current limitations in the applicability of DNA barcoding to taxonomic forest surveys. These difficulties urge for an improvement of technical protocols and an increase of the number of sequences and taxa in public databases.

DNA barcode is a fragment of short DNA sequence from a standard part of the genome. DNA barcoding is an effective taxonomic method for species identification through analyzing the DNA barcodes. With the dramatic increasing of DNA barcode sequences, the analysis methods have developed rapidly, which promoted their applications in molecular identification for organisms. Since 2003, DNA barcoding has been widely used in species identification for animals, plants, fungi, etc. It has also robustly promoted the development of scientific disciplines, such as taxonomy, biodiversity science, and ecology. Based on review of DNA barcoding techniques, we summarized five main analysis methods on DNA barcodes, i.e. the genetic distance-, genetic similarity-, phylogenetic tree-, sequence characters-, and statistical classification-based methods. Moreover, we proposed a prospect for research and applications of DNA barcoding in the future.

ABSTRACTHorticultural collections of ornamental plants are vital elements in our efforts to conserve threatened plants, such as species of the staghorn fern genus Platycerium. Accurate species identification in these collections is often challenging but crucial to ensure the objectives of ex situ conservation. Here, we promote the establishment of reference DNA barcode libraries as an effective approach to take on the challenge to detect mislabeled accessions. To achieve this goal, a reference dataset was assembled employing a total of 287 accessions that were mainly obtained from the staghorn fern collections cultivated at the Xishuangbanna Tropical Botanical Garden, Yunnan, China. Five chloroplast genome loci were assessed as DNA barcodes reflecting their wide utilization in plant systematics. The results confirmed not only the utility of commonly used chloroplast DNA fragments as DNA barcodes for these ferns but most importantly found no obvious evidence for frequent misidentification of staghorn fern accessions maintained in botanical gardens, although some mislabeling was detected. The established reference dataset enabled us to secure the species identity of staghorn fern accessions handled in conservation practices or commercial trade. In turn, the application of DNA barcoding was confirmed as an effective tool to secure the species identity of accessions used in ex situ conservation collections of staghorn ferns by enabling reliable identification of all individuals, especially immature individuals that lack the morphological characteristics of adult plants utilized in expert identification keys. In conclusion, assembled DNA barcoding reference datasets are promoted as a practical approach to be applied in horticultural collection management but also for regulating the plant trade.

Over 90% of global commercial trade occurs between seaports, which are initial points-of-entry for nonnative, potentially invasive propagules. As such, there is a need to develop means to both rapidly intercept and identify propagules as they arrive. Here, we focus on plant propagules that are assumed to be non-native, in seed form. Because standard morphological techniques alone are laborious and require taxonomic expertise, we sought to address if identification through barcoding of the plastid DNA (rbcL + matK genes) of plant seeds could improve current processes in the early detection and rapid response to prevent entry/establishment of nonnative plant species. This research conducted a preliminary foray to evaluate the utility of widely accepted plant plastid DNA barcodes to identify plant propagules (seeds, hereafter) collected from the air-intake grilles of refrigerated shipping containers of a single agricultural commodity arriving at the Port of Savannah, Georgia, USA. We ask four questions: (1) Can DNA barcoding be used to detect seeds collected from shipping containers at the port? (2) What is the genetic composition of propagules entering the port? (3) How do morphological identifications compare to those based on genetic analysis? (4) Are nonnative invasive plant species present on shipping containers entering the Port of Savannah? This research collected 11,044 seeds from 628 refrigerated shipping containers between 2015 and 2017. Seeds were then morphologically sorted into Seed Types. Barcoding of the matK and rbcL gene regions of the plastid genomes directly isolated from seeds resulted in poor amplification. This is likely due to a host of potential confounding factors. Therefore, we germinated seeds and utilized leaf-tissues for sequencing of these two gene regions. From BLASTn analyses, results returned top hits for a variety of species, with up to 22 possible nonnative plant species and one definite Federal Noxious Weed. This work investigates the interception application of DNA barcoding to improve agro- and bio-security issues posed by nonnative and invasive species. Though this study required the germination of the seeds to obtain leaf-tissue suitable for our DNA barcoding method, we effectively demonstrated seed viability. Our seed identification process was lengthy and understandably not feasible for real-time application. Therefore, we seek to improve our methods for future applications by testing other approaches that may better complement morphological identification. Next reasonable steps include improved extraction protocols, metabarcoding to generate DNA barcode sequences directly from groups of seeds harvested from shipping containers and implementing other next-generation sequencing techniques.

Application of DNA barcoding to the entire traditional Chinese medicine industrial chain: A case study of Rhei Radix et Rhizoma

With increasing international food trade, food quality and safety are high priority worldwide. The consumption of contaminated and adulterated food can cause serious health problems such as infectious diseases and allergies. Therefore, the authentication and traceability systems are needed to improve food safety. The mitochondrial DNA can be used for species authentication of food and food products. Effective DNA barcode markers have been developed to correctly identify species. The US FDA approved to the use of DNA barcoding for various food products. The DNA barcoding technology can be used as a regulatory tool for identification and authenticity. The application of DNA barcoding can reduce the microbiological and toxicological risks associated with the consumption of food and food products. DNA barcoding can be a gold-standard method in food authenticity and fraud detection. This review describes the DNA barcoding method for preventing food fraud and adulteration in meat, fish, and medicinal plants.

During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.