DNA barcoding is a taxonomic method, that uses one or more standardized short genetic markers in an organism’s DNA to identify it as belonging to a particular species. Through this method unknown DNA samples are identified to registered species based on comparison to a reference library. DNA barcode databases are collections of DNA sequences that can be used to identify species and organisms based on their genetic code. DNA barcode databases provide a valuable resource for researchers, conservationists, educators, and the public to access and share information on biodiversity and taxonomy.
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Some of the most popular and widely used DNA barcode databases
The Barcode of Life Data System (BOLD) is the largest and most comprehensive DNA barcode database in the world. BOLD is a cloud-based data storage and analysis platform developed at the Centre for Biodiversity Genomics in Canada. It is freely available to anyone with interests in DNA barcoding, anywhere, anytime. BOLD consists of four main modules, a data portal, an educational portal, a registry of BINs (putative species), and a data collection and analysis workbench.
Data portal is a data retrieval interface that allows for searching over 9.7M public records in BOLD using multiple search criteria including, but not limited to, geography, taxonomy, and depository.
Education portal is a custom platform for educators and students to explore barcode data and contribute novel barcodes to the BOLD database.
BIN database is a searchable database of Barcode Index Numbers (BINs), sequence clusters that closely approximate species.
Workbench is a data collection and analysis environment that supports the assembly and validation of DNA barcodes and other sequences.
GenBank of the National Center for Biotechnology Information (NCBI), USA is the largest public repository of nucleotide sequences in the world. GenBank contains over 250 million sequences from more than 400,000 organisms, including many DNA barcodes. GenBank is integrated with other NCBI databases, such as the Nucleotide Database, the Protein Database, the Taxonomy Database, and the Sequence Read Archive (SRA). GenBank allows users to search, download, upload, and submit DNA sequence data, as well as to perform BLAST searches, multiple sequence alignments, phylogenetic analyses, and other bioinformatics tools.
The Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure funded by the world’s governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth. The data are provided by many institutions from around the world. GBIF aggregates data from various sources, such as museums, herbaria, research institutes, citizen science projects, and DNA barcode databases. Data available through the GBIF portal are primarily distribution data on plants, animals, fungi, and microbes for the world, and scientific names data. GBIF contains over 1.6 billion occurrence records from more than 1.4 million species, including many DNA barcodes. GBIF allows users to search, download, upload, and publish biodiversity data, as well as to explore and visualize data using maps, charts, graphs, and dashboards. GBIF’s information architecture makes these data accessible and searchable through a single portal.
Diat.barcode is a reference library dedicated to diatoms.
Phytool is a reference library dedicated to all microalgae.
The International Barcode of Life Consortium (iBOL) is working to establish baseline data.
There are some initiatives to collect DNA barcodes for certain life forms, e.g., FISH-BOL (Fish Barcode of Life) campaign for DNA barcoding all fish species. Available data are covered in BOLD.
Challenges and limitations of DNA barcoding
DNA barcoding is a powerful and useful technique for species identification and discovery, but it also has some challenges and limitations that need to be addressed.
Different groups of organisms may require different regions of DNA to be used as barcodes, depending on their evolutionary history and genetic diversity. Animals typically use a segment of the mitochondrial gene cytochrome c oxidase I (COI), while plants use a combination of two chloroplast genes: rbcL and matK. However, these regions may not be suitable for all taxa or situations and may need to be supplemented or replaced by other regions or markers.
The accuracy and reliability of DNA barcoding depend on the quality of the barcode data, which includes the sequence quality, the taxonomic annotation, and the geographic origin. Poor quality data can lead to errors or ambiguities in identification or classification.
Applications of DNA barcoding include identification of new species, safety assessment of food, identification and assessment of cryptic species, detection of alien species, identification of endangered and threatened species, linking egg and larval stages to adult species, securing intellectual property rights for bioresources, framing global management plans for conservation strategies, elucidate feeding niches, and forensic science. DNA barcode markers can be applied to address basic questions in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection.
Source: https://en.m.wikipedia.org/wiki/DNA_barcoding.