Barcode Of Life Data System Research Articles

The current state of DNA barcoding of macroalgae in the Mediterranean Sea: presently lacking but urgently required

AbstractThis review article explores the state of DNA barcoding of macroalgae in the Mediterranean Sea. Data from the Barcode of Life Data System (BOLD) were utilised in conjunction with a thorough bibliographic review. Our findings indicate that from around 1124 records of algae in the Mediterranean Sea, only 114 species have been barcoded. We thus conclude that there are insufficient macroalgal genetic data from the Mediterranean and that this area would greatly benefit from studies involving DNA barcoding. Such research would contribute to resolving numerous questions about macroalgal systematics in the area and address queries related to biogeography, especially those concerned with non-indigenous species. It could also possibly result in the development and application of better, cost-effective biodiversity monitoring programmes emanating from UN conventions and EU Directives. One possible way of achieving this is to construct DNA libraries via sequencing and barcoding, subsequently enabling better cost-effective biodiversity monitoring through environmental DNA metabarcoding.

BOLDigger – a Python package to identify and organise sequences with the Barcode of Life Data systems

DNA metabarcoding workflows produce hundreds to ten-thousands of Operational Taxonomic Units (OTUs) or Exact Sequence Variants (ESVs) per analysis. In most workflows, a taxonomic assignment to these generated sequences is needed. This is typically done using publicly available databases. Especially, yet not exclusively, for Eumetazoan metabarcoding, the Barcode of Life Data system (BOLD) is the most comprehensive and curated reference barcode database and, therefore, typically the first choice for taxonomic assignment. While an application programme interface (API) exists to query data in large batches, no information on the many and important unpublished data are obtained through the API. The alternative approach using the BOLD identification engine on the website provides full access, yet it is restricted to 100 sequences at once. We developed a small platform-independent and graphical user interface (GUI) software package, BOLDigger, which aims to solve this problem by automating the process of sending successive requests of up to 100 sequences without surpassing the capacities of BOLD. BOLDigger can be used to download the results of the identification engine, as well as metadata for the obtained hits. For the selection of the best fitting hit, three different methods are implemented. A new approach, combining a threshold-based approach with the metadata information, was implemented to make use of the metadata.

The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases.

Molecular identification methods, such as DNA barcoding, rely on centralized databases populated with morphologically identified individuals and their referential nucleotide sequence records. As molecular identification approaches have expanded in use to fields such as food fraud, environmental surveys, and border surveillance, there is a need for diverse international data sets. Although central data repositories, like the Barcode of Life Datasystems (BOLD), provided workarounds for formatting data for upload, these workarounds can be taxing on researchers with few resources and limited funding. To address these concerns, we present the Molecular Data Organization for Publication (MDOP) R package to assist researchers in uploading data to public databases. To illustrate the use of these scripts, we use the BOLD system as an example. The main intent of this writing is to assist in the movement of data, from academic, governmental, and other institutional computer systems, to public locations. The movement of these data can then better contribute to the global DNA barcoding initiative and other global molecular data efforts.

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.

The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01.

BackgroundThe InBIO Barcoding Initiative (IBI) Diptera 01 dataset contains records of 203 specimens of Diptera. All specimens have been morphologically identified to species level, and belong to 154 species in total. The species represented in this dataset correspond to about 10% of continental Portugal dipteran species diversity. All specimens were collected north of the Tagus river in Portugal. Sampling took place from 2014 to 2018, and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.New informationThis dataset contributes to the knowledge on the DNA barcodes and distribution of 154 species of Diptera from Portugal and is the first of the planned IBI database public releases, which will make available genetic and distribution data for a series of taxa. All specimens have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD) online database and the distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

Assessing the utility of DNA barcoding in wildlife forensic cases involving South African antelope

Poaching of South African wildlife is considered a threat to biodiversity. In the absence of diagnostic morphometric traits, DNA barcoding is considered as a method of choice for species identification. Here, we report on forensic case work involving the illegal hunting of antelope species. Three forensic cases which included confiscated material were submitted between 2018 and 2019 and for species identification. Laboratory procedures including DNA extraction and sequencing of cytochrome c oxidase 1 (COI) and cytochrome b (cytb) were conducted following forensic procedures to determine species identification. Generated sequences matched to reference sequences on the National Centre for Biotechnology Information (NCBI) and the Barcode of Life Data Systems (BOLD) to impala (Aepyceros melampus, 99.4–99.7 % homology), eland (Tragelaphus oryx, 99.8–100 % homology) and kudu (T. strepsiceros, 99.6–99.7 % homology). Phylogenetic analysis and intra- and interspecies distance further confirmed species identification with high bootstrap support (96–100 %). Average intraspecies sequence divergence was 0–1.15% and pairwise comparisons between taxa satisfied the 10-fold genetic distance. Thus both COI and cytb barcoding genes are suitable methodologies for forensic identification of species in the cases presented here. However, analysis of the reference samples identified species where barcoding may potentially fail. These include taxa that have undergone recent, rapid radiations resulting in high intraspecies distance or species that can hybridize. We thus recommend in these cases a reference database that includes geographically widespread samples is required and analysis with additional mitochondrial and/or nuclear markers.

DNA barcoding reveals incorrect labelling of insects sold as food in the UK.

BackgroundInsects form an established part of the diet in many parts of the world and insect food products are emerging into the European and North American marketplaces. Consumer confidence in product is key in developing this market, and accurate labelling of content identity is an important component of this. We used DNA barcoding to assess the accuracy of insect food products sold in the UK.MethodsWe purchased insects sold for human consumption from online retailers in the UK and compared the identity of the material ascertained from DNA barcoding to that stated on the product packaging. To this end, the COI sequence of mitochondrial DNA was amplified and sequenced, and compared the sequences produced to reference sequences in NCBI and the Barcode of Life Data System (BOLD).ResultsThe barcode identity of all insects that were farmed was consistent with the packaging label. In contrast, disparity between barcode identity and package contents was revealed in two cases of foraged material (mopane worm and winged termites). One case of very broad family-level description was also highlighted, where material described as grasshopper was identified as Locusta migratoria from DNA barcode.ConclusionOverall these data indicate the need to establish tight protocols to validate product identity in this developing market. Maintaining biosafety and consumer confidence rely on accurate and consistent product labelling that provides a clear chain of information from producer to consumer.

Comparative Evaluation of Web Page and Label Presentation for Imported Seafood Products Sold on Chinese E-Commerce Platform and Molecular Identification Using DNA Barcoding

With the expansion of e-commerce, an increasing number of Chinese consumers are turning to online markets to purchase foreign seafood. When buying seafood online, customers cannot physically evaluate the product, and the market Web page instead of the seafood label conveys all of the product information. However, specific regulations concerning the information presented on the Web page have not been created, which may foster seafood fraud and misdescription. Because mislabeling of seafood has become a widely reported issue in the Chinese offline market, the online scenario must be investigated comprehensively. This study focused on various seafood products that originated from 20 countries and were sold by one of the largest e-commerce companies in China. For each country, only the product with the greatest overall monthly transaction volume was selected, and 5 samples were purchased per product for a total of 100 samples. The Web page description (including the heading of the Web page and the description of the commodity) and the label of the received products were compared to evaluate the description consistency. DNA barcoding technology was used for seafood species identification, and the scientific names retrieved from the sequence analysis after consulting the Barcode of Life Data systems and GenBank were compared with the expected species, genus, and family to determine the description authenticity. Only 25% of the samples had consistent descriptions on the Web page and on the label of the received product. Most of the inconsistency originated from the geographical origin, and only four products (G10, G50, G19, and G69) had inconsistent species, genus, and family descriptions. Molecular analysis revealed that in 65% of samples the species was correctly described. The online seafood market presents challenges regarding seafood fraud and opportunities for seafood species substitution.

A re-examination of the taxonomic status of Prostoma jenningsi-a Freshwater Nemertean.

Prostoma jenningsi was first recorded at the Clay 'Ole pond in Lancashire, UK, in 1969 and was distinguished histologically from other Prostoma by the presence of 11 proboscidial nerves (with all other Prostoma species thought to have 9-10). P. jenningsi was considered to be the only species endemic to Lancashire and listed in the British Red Data Book as 'Insufficiently Known' as well as a 'Species of Principal Importance' under the UK Natural Environment and Rural Communities Act (2006). A limited number of Prostoma spp were recovered from the Clay 'Ole in 2011 (the first confirmation of the presence of Prostoma spp. since 1999). In 2015, further sampling was undertaken and expanded to other ponds in Lancashire resulting in the discovery of Prostoma spp. at a further 3 locations. Thereafter, DNA sequencing of nuclear 18S ribosomal RNA and mitochondrial Cytochrome Oxidase I (COI) genes were undertaken and phylogenetic analyses performed to establish the taxonomic status of recovered specimens. All available Prostoma sequences (Prostoma eilhardi and Prostoma graecense) were downloaded from GenBank® and Barcode of Life Data System (BOLD) databases for comparison. All 18S sequences from samples in Lancashire were identical to each other and to all downloaded Prostoma sequences, allowing no further analyses. With COI, 50 individuals were collected from 4 locations across Lancashire and sequenced, comparing a total of 480 base pairs. Average uncorrected p-distances between UK and European samples were low, although some more geographically distant samples from California, USA, displayed higher uncorrected p-distance values. Results suggest that the Prostoma recovered from the Clay 'Ole (and all other sampled locations in Lancashire) are not distinct from P. eilhardi and P. graecense (as downloaded from GenBank® and BOLD) suggesting that there is a strong case for the species status of P. jenningsi to be revoked. Further regional and national sampling is required to obtain a clearer evaluation of the distribution of Prostoma and the levels of genetic diversity present in the UK. In addition, results from this study indicate that thorough taxonomical re-evaluation of species within the Prostoma genus is required.

Vietnamellidae (Insecta, Ephemeroptera) of Thailand.

The genus Vietnamella Tshernova, 1972 is investigated in detail for the first time in Thailand. As a consequence, four species are recognized, namely Vietnamella maculosasp. nov., Vietnamella thani Tshernova, 1972, Vietnamella sp. B and Vietnamella sp. C. Herein, larvae and eggs of V. maculosasp. nov. are described and reported from Chiang Rai Province. The larva of Vietnamella sp. B from Tak Province is also described, but not named due to insufficient material, and the imaginal stages and eggs of V. thani Tshernova, 1972 are described and presented for the first time. Our morphological evidence is supported with COI data. The phylogeny showed that four different lineages of the genus Vietnamella occur in Thailand, one of them, viz., Vietnamella sp. C, only known from a couple of COI sequences retrieved from the Barcode of Life Data System (BOLD). Diagnoses for all known Oriental species are also presented.

HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves.

Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5–10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

Delimiting species of water mites of the genus Hydrodroma (Acari: Hydrachnidiae: Hydrodromidae) from North America and Europe: Integrative evidence of species status from COI sequences and morphology

Water mites of the genus Hydrodroma are common and frequently abundant in freshwater habitats on all continents other than Antarctica. Despite the broad geographic distribution, morphological differences between named species are minor and refer usually to one or two traits. DNA diagnostics may therefore prove useful for species delimitation in addition to morphological analyses. In this study, we use multiple statistical approaches, including Automatic Barcode Gap Discovery (ABGD), K2P distances, Neighbor-Joining (NJ) clustering and statistical parsimony (SP) based on mitochondrial cytochrome c oxidase subunit I (COI), and morphology to explore diversity among Hydrodroma species from North America and Europe. The results of ABGD confirmed species status of Hydrodroma despiciens (Müller, 1776), Hydrodroma pilosa Besseling, 1940, Hydrodroma torrenticola (Walter, 1908) from Europe and identified three species-level taxa from Canada, here provisionally called Hydrodroma sp. A, Hydrodroma sp. B and Hydrodroma sp. C. This outcome is congruent with NJ analysis that yielded a tree in which individuals clearly clustered into well-supported groups that matched described and putative species. The genetic distances between named and putative species ranged from 12.79% to 22.15%. Moreover, ABGD and NJ analyses based on COI sequences from our study and additional sequences available in GenBank and BOLD (Barcode of Life Datasystem) revealed five more clusters among North American Hydrodroma that likely also represent undescribed species. The results imply that future studies of Hydrodroma from other geographical locations and different habitat types are likely to reveal many more species of the genus. Moreover, this study highlights the potential utility of DNA barcoding in estimating true species diversity of the water mites, which is of fundamental importance in freshwater ecological studies and biodiversity surveys.

Aspidimorpha (Megaspidomorpha) angolensis Weise (Coleoptera: Chrysomelidae: Cassidinae): a potential new pest of sweet potato (Ipomoea batatas) in South Africa

Six tortoise beetle species from the genus Aspidimorpha have been recorded feeding on sweet potato (Ipomoea batatas) in South Africa. All these species are reported to have little impact on the crop and have a low pest status. However, another species has recently been observed, causing over 90% leaf damage to crops in Limpopo Province, South Africa. The objective of the study was to use morphological and molecular techniques to identify this new tortoise beetle. All life stages of the beetle were collected, and examination of these specimens revealed that the adults and larvae corresponded with the morphological descriptions of Aspidimorpha (Megaspidomorpha) angolensis Weise. The mitochondrial cytochrome c oxidase subunit I gene was used for possible molecular identification. No matching nucleotide sequences were found for A. (M.) angolensis in the databases of either the National Centre for Biotechnology Information (NCBI) or the barcode of life data systems; hence, they could not be used in the characterisation of the beetle. The nucleotide sequences produced were deposited at NCBI for future use. Existing information suggests that A. (M.) angolensis is a new pest of sweet potato and its aggressive feeding warrants the speedy development of management strategies. These should include investigations into biological control options, e.g. natural enemies, as well as the efficacy of insecticides for possible future registration.

<strong>Undergraduate teaching of scientific concepts using DNA barcoding of Trichoptera</strong>

Student instruction is often segregated into specific subjects, giving the impression that different areas of study are largely unrelated. Teaching in “silos” inhibits the formation of connections among subjects. An academic curriculum that integrates DNA barcoding can expose students to a wide variety of scientific concepts, technical skills, problem solving, and fieldwork. In an approach that emphasizes conceptual interconnections, students are instructed in methods of caddisfly collection, specimen vouchering, DNA extraction, PCR amplification and sequencing of the COI barcode fragment, data curation in the Barcode of Life Data Systems (BOLD), and phylogenetic analysis. Accompanying development of these technical skills are learning objectives which include recognizing that DNA comes from real organisms and consists of molecules that are a physical part of those organisms, rather than being an obtuse symbolic abstraction. Students learn to logically pull together concepts from multiple scientific fields, use them in a practical setting, and experience science more broadly as a unified and interconnected discipline.

New faunistic and taxonomic insights on little known Crambidae from forested habitats of Italian Peninsula (Lepidoptera: Pyraloidea)

We provided new distribution data and taxonomic notes concerning eleven Crambidae species new or little known for the Italian fauna. Most records were collected in Calabria, the southernmost region of peninsular Italy, where forested habitats were surveyed during last years. Some accessory data were mined from Barcode of Life Data System (BOLD) and were used to refine the distribution of treated species. In detail, we found three species new for Italian fauna: Evergestis subfuscalis (Staudinger, 1870), Udea languidalis (Eversmann, 1842), and Hyperlais siccalis (Guenée, 1854). Three species not recorded in peninsular Italy so far: Cynaeda gigantea (Wocke, 1871), Evergestis dumerlei Leraut, 2003, and Catoptria staudingeri (Zeller, 1863). Four species not recorded in southern Italy so far, Evergestis infirmalis (Staudinger, 1870), Cynaeda dentalis ([Denis & Schiffermüller], 1775), Paratalanta pandalis (Hübner, 1796), Hodebertia testalis (Fabricius, 1794). Evergestis sophialis (Fabricius, 1787) was for the first time recorded in Calabria. Barcoding analysis allowed us to confirm the status of Evergestis subfuscalis as bona species, eastern vicariant of E. mundalis. Furthermore, we underlined the needs of a revision of the Udea fimbriatralis species group as barcodes of western and eastern European specimens appear to be intermingled, suggesting the presence of one unique variable species. In conclusion, the importance of the Italian peninsula as a bridge between western and eastern European faunas was remarked.

Phylogeographic Study of Freshwater Fish Channa striata (Bloch) and Channa punctata (Bloch) Construed Using DNA Barcodes Between Three Rivers in Southern Tamil Nadu Region, India

Channa striata and Channa punctata are freshwater fishes with good nutritional and economic importance. The genus Channa had been reported as a species complex till date and hence, the phylogeographic study based on DNA barcodes for two Channa sp. was initiated to substantiate the genetic diversity with respect to their geographic location. In this study, fish samples of C. striata and C. punctata collected from selected sites in three major rivers (Cauvery, Vaigai and Thamirabarani) flowing through Southern Tamil Nadu region, India. Morphometric and meristic characteristics were recorded. PCR amplification of Cytochrome Oxidase I gene from fishes in each location was sequenced and submitted to Barcode of Life Data System. Three Barcode Index Numbers (BIN’s) were obtained, C. punctata from all sites shared a common BIN AAE8814, C. striata from Cauvery had a different BIN ACB7973 whereas C. striata from Thamirabarani and Vaigai shared an identical BIN AAB2498. The phylogeographic analysis based on Mantel’s test for C. striata yielded a positive correlation between the genetic divergence and geographical distance but for C. punctata it showed negative correlation.

Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials.

Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown “barcode” sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.

Big Data Knowledge of Major Lineages of Life and Priorities for Genomic Research

Genomic science is revolutionizing and accelerating biodiversity research. For collections-based institutions to continue to lead and support biodiversity research, they must adapt to this new reality. Simultaneously, “big data” is accumulating so rapidly that we have unprecedented capacity to plan strategically to use genomics to advance basic and applied science on multiple fronts. For example, seven “big data” sources have the following numbers of records (2018 data): Global Biodiversity Information Facility (GBIF), ~1B; Biodiversity Heritage Library (BHL), ~3.6M; National Center for Biotechnology Information (NCBI), ~220M; Open Tree of Life (OToL), 1.9M; Barcode of Life Data System (BOLD), ~6.3M; Encyclopedia of Life (EOL), ~99K; Global Genome Biodiversity Network (GGBN), ~2M. Collectively, they offer more than 1.2B records on biodiversity. At the scale of species (~2M described, multiple millions undescribed), these data are still too sparse to permit comprehensive conclusions. At the scale of families (i.e. deeper clades of life), the situation is far more promising: about 9,911 families are known, and relatively few are discovered each year. This suggests that at the family rank (and above), our knowledge of life on Earth is reasonably complete. Approximately 160,000 valid and accepted genera exist, but certainly many new genera await discovery and description. Genomics is the fastest way to group species into more inclusive lineages such as genera and families, and is certainly faster than traditional alpha taxonomy. Synergistically, these “big data” answer four important questions at deeper clade levels: What is it? Where is it? What do we know about it? What do we know about its genome? Approximately 4,500 eukaryotic genomes have been sequenced. The converse of what we know is what we do not know, another meaning of “dark taxa.” We can use the distribution and density of big data at deeper clade levels (families, genera) to quantitatively analyze “dark taxa” and therefore to strategically optimize knowledge and preservation of biodiversity at a global scale. Technicalities of the quantitative prioritization scheme are debatable, but some initial, simple scoring systems can help to prioritize lineages for collection and genetic research so as to most efficiently illuminate regions in the tree of life that that are neither preserved, imaged, geo-located, studied, nor known genomically. This analysis presents criteria and goals for collaborating to build a global genomic collection to maximize efficient acquisition of biodiversity genomic knowledge, and identifies the most valuable and highest priority taxa for genomic research.

Towards Linked Open Molecular Data: Recommendations for researchers, collections, infrastructures and publishers

The variety of molecular methods used to analyze biosamples is continuously increasing, as is the need for the standardized deposition, documentation and citation of both the samples as well as the methods applied to them. Global initiatives such as the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), Barcode of Life Data System (BOLD, http://www.boldsystems.org), the Global Biodiversity Information Facility (GBIF, http://www.gbif.org) and the Global Genome Biodiversity Network (GGBN, http://www.ggbn.org), in addition to many others, have been working towards standardized access to biological data for many years. Collectively, these biodiversity data management platforms provide a considerable and indispensable infrastructure to the research community. However, cross-linking the massive amounts of protein and DNA sequence data submitted to these databases every year with standardized records of the underlying biological material remains challenging. Best practices for standardized data submissions and data citations are urgently needed. In the long run, two goals should be achieved above all else: all sequence data should be linked to natural history collections, and biological material that was used for molecular research, especially DNA sequencing, should be deposited and, thus, made accessible in public, well curated collections. all sequence data should be linked to natural history collections, and biological material that was used for molecular research, especially DNA sequencing, should be deposited and, thus, made accessible in public, well curated collections. Here we will provide recommendations both for researchers and collections how to cite underlying biological material at INSDC and in publications in a standardized way towards Linked Open Data. We will also address how the global infrastructures and publishers can improve their interoperability.