Barcode Of Life Data Research Articles

A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny.

Sparisoma species (parrotfish) comprise an important functional group contributing to coral-reef resilience. The morphological diagnostic characteristics for species identification are clearly described for adult forms but not for the early stages. Consequently, many taxonomical listings of Sparisoma larvae are restricted to the genus level. The aims of this study are to determine whether the morphological and molecular identification techniques are useful to assign the species taxonomic level to Sparisoma larvae occurring in the Gulf of Mexico and whether there is a set of diagnostic features that could be used to discriminate between species in larvae of different developmental stages. Morphological assignment of Sparisoma was performed based on morphological and meristic features for 30 larvae collected in the Gulf of Mexico from late August to mid-September 2015. To corroborate and complement the morphological assignments, molecular identification was carried out using DNA sequences from regions of two mitochondrial genes, mitochondrial cytochrome oxidase I (mtDNA COI) and mitochondrial 16S rRNA (mtDNA 16S rRNA). COI and 16S gene trees for Sparisoma and related fish taxa were constructed using sequences available in the NCBI (National Center for Biotechnology Information) GenBank and BOLD (Barcode of Life Data) databases. Two morphotypes were identified based on morphology, but no diagnostic characteristics for species discrimination were found. Molecular identification, in contrast, successfully discriminated four early development stages of Sparisoma atomarium, three stages of Sparisoma radians, and two stages of Sparisoma chrysopterum and Sparisoma aurofrenatum, therefore demonstrating the successful and necessary application of molecular taxonomic approaches for species-level identifications of Sparisoma larvae.

Unveiling South African insect diversity: DNA barcoding’s contribution to biodiversity data

Insects are one of the most species-rich groups on Earth. They comprise much of animal diversity and play vital roles in ecosystems, including pollination, pest control, and decomposition. However, only a fraction of this diversity has been formally described. South Africa is recognised as one of the most biologically diverse countries globally, with an estimated 44 000 insect species. Many crops rely on insect pollinators, including canola, apples, oranges, and sunflowers. A shortage of wild pollinators currently threatens crop yields, yet our knowledge of insect diversity within South Africa is sparse. There are few taxonomic specialists relative to South Africa’s biodiversity, and the methods used for insect identification can be time-consuming and expensive. DNA barcoding provides an important research tool to accelerate insect biodiversity research. In this review, we queried the public DNA barcoding BOLD (Barcode of Life Data System) database for records of “Insecta” within South Africa, and 416 211 published records assigned to 28 239 unique BINs (Barcode Index Numbers) were returned. We identified five taxonomic orders with more BINs than known species in southern Africa (Hymenoptera, Diptera, Thysanoptera, Plecoptera, and Strepsiptera). Most of the barcoded records were derived from Malaise trap sampling in Gauteng, Mpumalanga and Limpopo, while the rest of South Africa remains poorly sampled. We suggest that there is a need for a comprehensive national sampling effort alongside increased investment in taxonomic expertise to generate critical baseline data on insect biodiversity before species are lost to extinction.

Cryptic diversity of mudskipper genus Boleophthalmus (Gobiiformes: Oxudercidae) from the north coast of East Java, Indonesia

Abstract. Shabrina FN, Wibowo K, Arisuryanti T. 2024. Cryptic diversity of mudskipper genus Boleophthalmus (Gobiiformes: Oxudercidae) from the north coast of East Java, Indonesia. Biodiversitas 25: 412-420. Mudskippers of genus Boleophthalmus are commonly found in the Indo-Pacific area. This study aimed to examine the diversity of the genus Boleophthalmus from the north coast of East Java Province, Indonesia by employing the mitochondrial COI gene for DNA barcoding and morphological characterization. Ten individuals of this genus were analyzed. According to the similarity percentage evaluated using Basic Local Alignment Search Tool (BLAST) and Barcode of Life Data (BOLD) identification engines, all the individuals were identified as Boleophthalmus boddarti Pallas, 1770. However, phylogenetic analysis revealed that three of the individuals were identified as B. boddarti, and seven were identified as Boleophthalmus pectinirostris Linnaeus, 1758 originated from East Java, which is separated from the clade of B. pectinirostris from East Asia population. These results were supported by the genetic distance of 8.93%-13.81% and the morphological characteristics determined by principal component analysis (PCA). PCA revealed that B. boddarti and B. pectinirostris are primarily distinguished by the number of (longitudinal) scales (69-75 versus 113-123), length of second dorsal fin base (42.3-43.9 versus 38.1-49.0), and caudal fin length (18.1-22.4 versus 17.5-21.6). Further detailed studies are needed to clarify whether the seven individuals belonging to B. pectinirostris complex should be regarded as a new species or a new subspecies.

Mitochondrial genetic homogeneity of South American leafminer, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) in Tamil Nadu, India

The South American leafminer, Tuta absoluta is an exotic devastative pest on solanaceous vegetables, including tomatoes, which leads to a cent per cent economic loss in India. The molecular markers assist in assessing gene flow, migratory frequencies, and genetic variety, as well as helping to evaluate the genetic makeup and diversification of an exotic species population to indigenous ones. With this, the present study aimed to investigate the genetic divergence of T. absoluta in different districts of Tamil Nadu, India. The study depicted the examination of genetic divergence of T. absoluta by aiding amplified region of mitochondrial DNA encoding cytochrome oxidase I (COI) from the T. absoluta samples gathered from Coimbatore, Dharmapuri and Dindigul districts of Tamil Nadu. The findings showed that the phylogenetic tree constructed from all sequences of T. absoluta acquired from the NCBI (National Center for Biotechnology Information) and BOLD (The Barcode of Life Data System) databases exhibited 99 percent identity and aggregated together into a single clade. . 5Hence, the present study revealed the great genetic uniformity in T. absoluta populations in India and corroborates that most of the globe rely on the partial COI gene, evidenced by minimal nucleotide diversity.

Galls on galls: A hypergall-inducing midge and its parasitoid community.

The authors declare no conflicts of interest. Data for figures and tables (Baine, 2022) are archived on figshare at https://doi.org/10.6084/m9.figshare.21521211. The COI sequence accession numbers are archived in NCBI GenBank (OQ72748–OQ272753) and the Barcode of Life Data (BOLD) system (ACCOM001-22.COI-5P–ACCOM006-22.COI-5P). Appendix S1. Appendix S2. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

DNA Barcoding of Key Storage Pests Using Mitochondrial Cytochrome Oxidase I

Stored grain insect pests are of economic importance, and they spread rapidly through the grain trade. Hence, it is important to identify these pests accurately. Although several morphological methods exist, it is tedious and time-consuming. DNA barcoding using mitochondrial COI is an alternative approach that aids in precise species identification. In this study, 13 stored grain insect pests belonging to the order Coleoptera and Lepidoptera were collected from different storage structures in Coimbatore. A fragment of mt-COI was amplified and sequenced. Sequence analyses were carried out with BOLD (Barcode of Life Data System) and ABGD (Automatic Barcode Gap Discovery) tools. The barcoding gap analysis revealed that the inter-species genetic distance is greater than the intra-species genetic distance. The ABGD analysis for species delimitation partitioned the Coleopteran and Lepidopteran datasets into 9 and 4 putative species, respectively. The barcode gap was absent in more closely related species. However, analysis of their sequences revealed significant variations. Our results showed the ability of the mt-COI to discriminate between the species, thus provide a complementary technique for the diagnosis of stored grain insect pests.

Evaluation of Arabian Vascular Plant Barcodes (rbcL and matK): Precision of Unsupervised and Supervised Learning Methods towards Accurate Identification

Arabia is the largest peninsula in the world, with >3000 species of vascular plants. Not much effort has been made to generate a multi-locus marker barcode library to identify and discriminate the recorded plant species. This study aimed to determine the reliability of the available Arabian plant barcodes (>1500; rbcL and matK) at the public repository (NCBI GenBank) using the unsupervised and supervised methods. Comparative analysis was carried out with the standard dataset (FINBOL) to assess the methods and markers’ reliability. Our analysis suggests that from the unsupervised method, TaxonDNA’s All Species Barcode criterion (ASB) exhibits the highest accuracy for rbcL barcodes, followed by the matK barcodes using the aligned dataset (FINBOL). However, for the Arabian plant barcode dataset (GBMA), the supervised method performed better than the unsupervised method, where the Random Forest and K-Nearest Neighbor (gappy kernel) classifiers were robust enough. These classifiers successfully recognized true species from both barcode markers belonging to the aligned and alignment-free datasets, respectively. The multi-class classifier showed high species resolution following the two classifiers, though its performance declined when employed to recognize true species. Similar results were observed for the FINBOL dataset through the supervised learning approach; overall, matK marker showed higher accuracy than rbcL. However, the lower rate of species identification in matK in GBMA data could be due to the higher evolutionary rate or gaps and missing data, as observed for the ASB criterion in the FINBOL dataset. Further, a lower number of sequences and singletons could also affect the rate of species resolution, as observed in the GBMA dataset. The GBMA dataset lacks sufficient species membership. We would encourage the taxonomists from the Arabian Peninsula to join our campaign on the Arabian Barcode of Life at the Barcode of Life Data (BOLD) systems. Our efforts together could help improve the rate of species identification for the Arabian Vascular plants.

DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians

The region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.

Knowledge Extraction from Specimen-Derived Data from GenBank to Enrich Biodiversity Information

DNA barcoding and environmental DNA (eDNA) are increasing the need for the utilization of gene sequences in the field of biodiversity. GBIF (Global Biodiversity Information Facility) and GGBN (Global Genome Biodiversity Network) are taking action on the treatment of gene sequences in the field of biodiversity (Finstad et al. 2020). Gene sequences have been collected and published by INSDC (International Nucleotide Sequence Database Collaboration) for over 30 years (Arita et al. 2020). Biodiversity information has been collected using standards such as Darwin Core (Wieczorek et al. 2012), but INSDC gene sequences are stored in their own format. In the field of bioinformatics, researchers are also organizing the BioHackathon series, notably the NBDC/DBCLS BioHackathon and the spin-off Biohackathon Europe, to standardize data through the Semantic Web (Garcia Castro et al. 2021, Vos et al. 2020), but the linkage with biodiversity information has just begun. In this study, as an example of linking gene sequence information with biodiversity information, I attempted to construct an infrastructure for knowledge extraction by utilising gene sequence entries derived from museum specimens from GenBank (Sayers et al. 2020). I have previously surveyed the BOLD (The Barcode of Life Data System) (Ratnasingham and Hebert 2007) IDs listed in GenBank (Nakazato 2020). I downloaded the fish and insect data from the GenBank FTP (file transfer protocol) site. Then I extracted the descriptions in the "specimen_voucher" field and obtained 749,627 (28% of the fish entries in GenBank) and 1,621,890 (13%) specimen IDs, respectively. I also extracted from the "note" field approximately 1000 entries describing the type of the specimen, such as "holotype", "lectotype", and "paratype". These extracts include descriptions written in natural language. NCBI (National Center for Biotechnology Information) publishes the BioCollections database (Sharma et al. 2019), and these data may be able to refine the description. In the future, I plan to map these extracted IDs to the collection IDs in the biodiversity information database. This will enable us to enrich the biodiversity information with GenBank descriptions, for example, by adding articles listed in GenBank as references to the specimen data.

Discovery of Eliozeta helluo (Diptera: Tachinidae: Phasiinae) in Korea, Japan and Mongolia with discussion of its systematic status based on morphology and DNA barcoding

• Eliozeta helluo is recorded for the first time in Korea, Japan and Mongolia. • Morphological variability and systematic status of E. helluo is discussed. • Three distinct lineages are detected within E. helluo clade by DNA barcodes. • East Asian and European samples are likely to be true E. helluo. • Non-monophyly of the genus Eliozeta is recognized. The genus Eliozeta Rondani, 1856 of the tribe Gymnosomatini includes two species that exhibit high intraspecific variability. One of these species, E. helluo (Fabricius, 1805), is reported here for the first time from Korea, Japan and Mongolia. Diagnoses and description are provided based on the examination of obtained specimens. Our study of E. helluo included 46 freshly frozen individuals having variable abdominal patterns and showing sexual dimorphism, allowing us to examine intraspecific variability and species status. We examined the morphological variations and analyzed the DNA barcode sequences of individuals, covering as many morphological variants as possible, to permit inferences about the number of biological species represented. A DNA barcoding analysis of six Korean plus two Mongolian E. helluo sequences and 112 gymnosomatine sequences retrieved from the Barcode of Life Data (BOLD) Systems revealed that E. helluo is a widely distributed and highly variable species. Furthermore, we discovered that the barcode sequences currently listed as E. helluo in BOLD Systems formed three distinct lineages within a single strong monophyletic clade. Although further study is needed, we believe that our samples plus most European samples represent the true E. helluo , but the other two lineages (Bulgarian and Middle Eastern samples) probably represent closely related and morphologically similar Eliozeta species. Our findings are also consistent with those of two previously published molecular studies on Eliozeta , in the non-monophyly of this genus.

Distribution of Culicoides biting midges (Diptera: Ceratopogonidae) in southern Australia and insight into the Culicoides victoriae morpho‐variants

AbstractCertain Culicoides species (biting midges) are important vectors globally of a range of viruses, protozoa and filarial parasites, imposing a significant economic and health burden. In a changing climate, understanding which Culicoides species occur in a region is important for biosecurity risk management. We examined the occurrence of predominant Culicoides species in south‐east Australia and provide insight into five Culicoides victoriae morpho‐variants. Culicoides were surveyed using Centre for Disease Control light traps and Yellow Sticky traps, with identification performed morphologically and molecularly. Two polymerase chain reaction – restriction fragment length polymorphism (PCR‐RFLP) assays based on mitochondrial cytochrome c oxidase subunit I were developed to differentiate morphologically similar C. victoriae, with a subset sequenced for nuclear carbomoylphosphate synthase. The structure of the five C. victoriae morpho‐variants was investigated through phylogenetic trees, haplotype networks and the Barcode Index Number system (BINs) in the Barcode of Life Data (BOLD) database. Twenty‐five different Culicoides species were identified in the sampled region with Culicoides austropalpalis, C. victoriae, C. marksi and C. molestus Gp sp No 2 being the most common. Two PCR‐RFLP assays were developed using either one or three enzymes, with a 90% or 99% success rate, respectively, of being able to differentiate the five C. victoriae morpho‐variants. Mitochondrial and nuclear sequence divergence supported by wing patterning allowed the recognition of multiple potentially new species of C. victoriae and identified species in uncharacterised regions.

The first step towards a DNA barcode reference database for mayflies (Ephemeroptera) of Slovakia

Mayflies (Ephemeroptera) represent a small but diverse order of amphibiotic insects, whose larvae contribute to several essential processes in freshwater habitats, such as bioturbation and bioirrigation, decomposition, nutrient cycling, and also serve as a primary source of nutrients for numerous organisms. Due to their cosmopolitan distribution and high-quality water requirements, they are also important indicators of ecosystem health and an integral part of biomonitoring protocols. Although the Slovak mayfly fauna is well researched, studies on genetic diversity, including DNA barcoding, are still lacking. The absence of the comprehensive DNA barcode reference libraries from various biogeographical regions and the presence of so-called cryptic lineages may prevent further efficient use and application of new approaches to aquatic ecosystem biomonitoring (Biomonitoring 2.0) based on eDNA analyses. Therefore, in the initial stage of our research, we bring the first insight into the genetic diversity of mayflies (based on mtDNA COI-5P barcoding fragment) from 47 localities of Slovakia mostly situated in the biogeographically significant Western Carpathians' territory. A total of 403 sequences of 42 morphologically determined species were added to the BOLD (Barcode of Life Data System) database, representing more than 1/3 of the mayfly fauna of Slovakia and covering 10 of 16 families. Sequences of these species were finally assigned to 62 BINs (Barcode Index Numbers) in BOLD (Fig. 1), whereby sequences of 12 species were divided into more than one BIN, indicating the presence of cryptic lineages. The largest number of BINs was represented by widely distributed species such as Baetis rhodani Pictet, 1843-1845 (6 BINs), Habroleptoides confusa Sartori & Jacob, 1986 (4 BINs) and Ecdyonurus venosus (Fabricius, 1775) (3 BINs). The sequences of the remaining nine species were split into two BINs. Maximum intraspecific variability (calculated by K2P) of some representatives was surprisingly high [e.g., E. venosus – 27.1 %; Baetis muticus (Linneaus, 1758) – 23.6 %; Caenis luctuosa (Burmeister, 1839) – 23.34 %, Baetis rhodani – 18.66 % and B. vernus Curtis, 1834 – 15.25 %] and far exceeded the level of intraspecific variability of the COI fragment based on the BOLD standards. The sequences of 23 individuals determined as Habroleptoides confusa, Baetis rhodani, B. buceratus Eaton, 1870, Caenis beskidensis Sowa, 1973 and Torleya major (Klapálek, 1905) created seven unique BINs, which represent the distant phylogenetic lineages of already existing BINs, that are currently unique to Slovakia. The coexistence of Baetis rhodani individuals of two different BINs was confirmed at five localities. Our study indicates clear importance of more detailed sampling and DNA barcoding due to the presence of unexpected intraspecific genetic diversity of mayflies captured in a relatively small area of the Western Carpathians.

Discovery of a highly variable bug killing fly species, Clytiomya continua (Diptera: Tachinidae: Phasiinae), in Korea with discussion on its systematic status

• Bug-killing fly species Clytiomya continua is recorded for the first time in Korea. • Unusually high morphological variability of C. continua is clarified. • Close relationship between the genera Clytiomya and Ectophasia is suggested. • Current concepts of the genera Clytiomya and Ectophasia are non-monophyletic. • Merging Clytiomya and Ectophasia into a single monophyletic genus is suggested. At present, the genus Clytiomya of the tribe Gymnosomatini includes four Palaearctic species, which exhibit high intraspecific variability. While studying Korean members of the bug-killing fly subfamily Phasiinae, we discovered C. continua for the first time in the Korean Peninsula . This is also the first record of Clytiomya from Korea. Our collection of C. continua includes over 150 freshly frozen individuals showing intraspecific variation as well as sexual dimorphism. This provided us an opportunity to examine their variability and species status. In fact, we initiated this study assuming the presence of multiple species. We examined the morphological variation, and analyzed the DNA barcode sequences of individuals, covering as many morphological variants as possible to distinguish any biological species. DNA barcoding analysis of 21 Korean C. continua sequences and over 180 phasiine sequences retrieved from the Barcode of Life Data (BOLD) Systems revealed that C. continua is a highly variable species with extreme sexual dimorphism. In both sexes, bright golden and dark dull individuals can be easily confused as two or more distinct species when there are only a few individuals available. Based on the examination of the Korean individuals, we provide taxonomic diagnosis and description. Moreover, DNA barcoding analysis demonstrated the close relationship between the genera Clytiomya and Ectophasia , although they both are not monophyletic. Further study is needed to clarify the species limits of the remaining three Clytiomya species.

Gap analysis of DNA barcoding in ERMS reference libraries for ascidians and cnidarians

BackgroundAll-inclusive DNA-barcoding libraries in the storage and analysis platform of the BOLD (Barcode of Life Data) system are essential for the study of the marine biodiversity and are pertinent for regulatory purposes, including ecosystem monitoring and assessment, such as in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). Here, we investigate knowledge gaps in the lists of DNA barcoded organisms within two inventories, Cnidaria (Anthozoa and Hydrozoa) and Ascidiacea from the reference libraries of the European Register of Marine Species (ERMS) dataset (402 ascidians and 1200 cnidarian species). ERMS records were checked species by species, against publicly available sequence information and other data stored in BOLD system. As the available COI barcode data adequately cover just a small fraction of the ERMS reference library, it is of importance to employ quality control on existing data, to close the knowledge gaps and purge errors off BOLD.ResultsResults revealed that just 22.9% and 29.2% of the listed ascidians and cnidarians species, respectively, are BOLD barcodes of which 58.4% and 52.3% of the seemingly barcoded species, respectively, were noted to have complete BOLD pages. Thus, only 11.44% of the tunicate and 17.07% of the cnidarian data in the ERMS lists are of high quality. Deep analyses revealed seven common types of gaps in the list of the barcoded species in addition to a wide range of discrepancies and misidentifications, discordances, and errors primarily in the GenBank mined data as with the BINs assignments, among others.ConclusionsGap knowledge in barcoding of important taxonomic marine groups exists, and in addition, quality management elements (quality assurance and quality control) were not employed when using the list for national monitoring projects, for regulatory compliance purposes and other purposes. Even though BOLD is the most trustable DNA-barcoding reference library, worldwide projects of DNA barcoding are needed to close these gaps of mistakes, verifications, missing data, and unreliable sequencing labs. Tight quality control and quality assurance are important to close the knowledge gaps of Barcoding of the European recommended ERMS reference library.

Revision of the birch-associated genus Massalongia (Diptera, Cecidomyiidae), with description of a new species from Japan and a taxonomic key to worldwide species.

Betula (Betulaceae), or birch, is a Holarctic genus of trees and shrubs whose species have ornamental, industrial, and medical importance. Gall midges of the genus Massalongia (Diptera: Cecidomyiidae: Cecidomyiidi) are exclusively associated with birches in the Palearctic region. In 2018, an undescribed Massalongia species was discovered forming leaf galls on the midveins of B. grossa on Mount Tara, Saga Prefecture, Kyushu, Japan. In this study the species is described as M. nakamuratetsui Elsayed & Tokuda, sp. nov., and a DNA barcode provided for it. The other known species of Massalongia are redescribed because the original descriptions are outdated and insufficient. A lectotype is designated for M. bachmaieri. In addition, the monotypic genus Apagodiplosis, containing A. papyriferae associated with B. papyrifera in the Nearctic region, is synonymized here under Massalongia, resulting in M. papyriferaecomb. nov., rendering Massalongia a Holarctic genus with six species. Comparing the sequence data of M. nakamuratetsui with all sequences available in The Barcode of Life Data (BOLD) system supports the occurrence of Massalongia in the Nearctic region and suggest that more species could be discovered there. Massalongia species form leaf or bud galls, and their mature larvae drop to the ground in autumn and overwinter in characteristic waterproof bottle-like cocoons, which is possibly a protective adaptation for pupation in wet and snowy lands. A taxonomic key to all Massalongia species is provided.

Sixteen Years of DNA Barcoding in China: What Has Been Done? What Can Be Done?

Over the past 16 years, more than half (59.68%) of research papers in China on DNA barcoding have been published in Chinese rather than English. Using the records in BOLD (Barcode of Life Data) system, we found Chinese scientists have contributed nearly 120 thousand DNA barcodes for more than 16 thousand species as of September, 2019, with barcoded species distributed throughout China. Based on 2,624 articles and 494 dissertations published during the last 16 years, we reviewed the basic statistics of these studies, including the type of articles contributed by Chinese scientists, the preference of taxonomic groups, the characteristic of barcoding studies in China, the current limitations, and potential future directions as well. We found that most barcode data pertain primarily to plants and animals. Most work in China has focused on verification of the authenticity of species used in traditional Chinese medicine, while other applications paid more attention to food safety, inspection and quarantine, and control of pests and invasive species. In methodology and technology, a number of new DNA barcoding methods were developed by Chinese scientists. However, there are several severe limitations of research on DNA barcoding in China in general, such as the lack of leadership in pioneering international projects, the absence of an open bioinformatics infrastructure, and the fact that some Chinese journals do not clearly require data transparency and availability for DNA barcodes, impeding the further development of barcode libraries and research in China. In the future, Chinese scientists should build authoritative online libraries, while aiming for theoretical innovations for both concepts and methodology of DNA barcoding.

Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry.

Interception of potential invasive species at ports-of-entry is essential for effective biosecurity and biosurveillance programs. However, taxonomic assessment of the immature stages of most arthropods is challenging; characters for identification are often dependent on adult morphology and reproductive structures. This study aims to strengthen the identification of such specimens through DNA barcoding, with a focus on microlepidoptera. A sample of 241 primarily immature microlepidoptera specimens intercepted at U.S. ports-of-entry from 2007 to 2011 were selected for analysis. From this sample, 201 COI-5P sequences were generated and analyzed for concordance between morphology-based and DNA-based identifications. The retrospective analysis of the data over 10 years (2009 to 2019) using the Barcode of Life Data (BOLD) system demonstrates the importance of establishing and growing DNA barcode reference libraries for use in specimen identification. Additionally, analysis of specimen identification using public data (43.3% specimens identified) vs. non-public data (78.6% specimens identified) highlights the need to encourage researchers to make data publicly accessible. DNA barcoding surpassed morphological identification with 42.3% (public) and 66.7% (non-public) of the sampled specimens achieving a species-level identification, compared to 38.3% species-level identification by morphology. Whilst DNA barcoding was not able to identify all specimens in our dataset, its incorporation into border security programs as an adjunct to morphological identification can provide secondary lines of evidence and lower taxonomic resolution in many cases. Furthermore, with increased globalization, database records need to be clearly annotated for suspected specimen origin versus interception location.

MBRAVE: The Multiplex Barcode Research And Visualization Environment

Widespread interest in the study of metabarcoding has resulted in data proliferation and the development of a multitude of powerful computational tools. Yet consistent and reproducible interpretation of the data remains challenging. The integration of different data types, software tools, and analytical parameters pose a barrier to scaling research. Further, though the majority of the necessary tools for performing these analyses are already implemented, there is limited support for high throughput analysis due to the requirement for heavy computational capacity. As a result of these complexities, many researchers lack the time, training, or infrastructure to work with larger datasets. mBRAVE, the Multiplex Barcode Research And Visualization Environment, is a cloud-based data storage and analytics platform with standardized pipelines and a sophisticated web interface for transforming raw high-throughput sequencing (HTS) data into biological insights. mBRAVE integrates common analytical methods and links to the Barcode of Life Data (BOLD) System for reference datasets, presenting users with the ability to analyze large volumes of data, without requiring special technical training. mBRAVE's cloud architecture provides centralized and automated storage and compute capacity, thereby reducing the burden on individual researchers. The mBRAVE platform seeks to alleviate the main informatic challenges faced by the metabarcoding research community: the storage and consistent interpretation of HTS data. It is now available for researcher use at www.mbrave.net.

Current situation of DNA Barcoding data in biodiversity and genomics databases and data integration for museomics

The museomics activity regards museum-preserved specimens as rich resources for DNA studies by extracting and analyzing DNA from these specimens in conjunction with their biodiversity information. Also in biodiversity field, DNA sequence data such as DNA barcoding has become essential as evidence for species identification and phylogenetic analysis as well as occurrence and morphological information. To accelerate biodiversity informatics, it is important to utilize both biodiversity occurrence and morphology data, and bioinformatics sequencing data. There are many databases for biodiversity domain such as GBIF (The Global Biodiversity Information Facility) for species occurrence records, EoL (The Encyclopedia of Life) as a knowledge base of all species, and BOLD (The Barcode of Life Data) for DNA barcoding data. In genomics science, molecular data involving DNA and protein sequences have been captured by the DNA Data Bank in Japan (DDBJ), the European Bioinformatics Institute (EBI, UK), and the National Center for Biotechnology Information (NCBI, US) under the International Nucleotide Sequence Database Collaboration (INSDC) for more than 30 years. Recently, NCBI launched a new database called BioCollections, including 7,930 culture collections, museums, herbaria, and other natural history collections. In addition, we can submit biodiversity information such as specimen voucher IDs, BOLD IDs, and latitude/longitude with DNA sequences. To find out the current situation, I downloaded GenBank (Nucleotide) files (updated at 22 Feb 2019) from the NCBI FTP (file transfer protocol) site and extracted biodiversity features including specimen voucher IDs and BOLD IDs. For Insecta, there are 2,427,343 sequence entries with specimen voucher ID and 1,766,142 entries with BOLD ID of 3,389,495 total entries. The most abundant species with voucher IDs is “Cecidomyiidae sp. BOLD−2016” (Diptera) (35,861 sequence entries). The most frequently referred voucher ID is “USNMENT00921257” (1510 sequence entries), indicating Stenamma megamanni (Hymenoptera, Formicidae, Myrmicinae). For flowering plants (Magnoliophyta), of 3,094,140 total entries, 1,109,420 sequence entries are assigned with voucher IDs and 73,409 entries with BOLD IDs. Additionally, 79,891 matK entries and 63,821 rbcL entries are submitted with voucher IDs, without BOLD IDs. I also retrieved BOLD data for Insecta and flowering plants. The 2,368,801 GenBank entries are referred from 4,176,481 BOLD total entries for Insecta, and the 259,245 GenBank entries from 345,706 BOLD entries for flowering plants. Some DNA barcoding data exist redundantly in BOLD database because BOLD imports sequences from NCBI submitted as DNA barcoding data in BOLD. These entries have different BOLD IDs but same BIN_URL is assigned. Recently, high-throughput sequencing technology, also called next-generation sequencing technology (NGS), has made a great impact in genomic science. Biodiversity researchers became to perform not only DNA barcoding but also RNA-Seq with NGS. NGS also accelerates museomics activity. NGS data are archived to the Sequence Read Archive (SRA) database, and sample information is described in BioSample database in INSDC. To utilize NGS data for biodiversity field, we will need to integrate such databases and other biodiversity databases. We, Database Center for Life Science, tackle to integrate life science data with Semantic Web technology. We held annual meetings to integrate life science data, called BioHackathons, in which researchers from all over the world participated. We began to RDFize BioSample data, but we should import existing schemes used in the biodiversity field including Darwin Core.

Larva, pupa and DNA barcodes of the Neotropical geometrid moth Glena mielkei (Lepidoptera: Geometridae: Ennominae: Boarmiini)

Glena mielkei Vargas, 2010 (Lepidoptera: Geometridae: Ennominae: Boarmiini) is a Neotropical geometrid moth native to the Atacama Desert of northern Chile whose larvae are folivorous on the shrub Trixis cacalioides (Asteraecae). The last instar and pupa are described and illustrated, and DNA barcode sequences are provided for the first time for G. mielkei. Descriptions are made based on larvae collected in the type locality. Comparisons with the available descriptions of congeneric species suggest that the chaetotaxy of the SV group of the abdominal segment and the morphology of the cremaster could be useful tools to species identification based on last instar and pupa, respectively. A search in BOLD (Barcode of Life Data System) showed that the only DNA barcode haplotype found in the two specimens sequenced was closest to Physocleora Warren, 1897 than Glena Hulst, 1896. These results coincide with the morphological peculiarities of the genitalia highlighted in the original description of G. mielkei, suggesting that a definitive assessment of the generic status of this geometrid moth deserves further integrative studies.