BIOSCAN - Revealing Eukaryote Diversity, Dynamics, and Interactions

Between 2010 and 2015, the International Barcode of Life (iBOL) consortium successfully completed the BARCODE 500K project, a $125 million effort that delivered DNA barcode coverage for 500,000 species. BIOSCAN is a seven-year program (2019-2025) that builds on this foundation, expanding coverage of the barcode reference library to two million species and operationalising metabarcoding for eukaryote communities globally. BIOSCAN will scan species assemblages from at least 2,500 ecosystems and will codify species interactions for at least 2,500 sites. DNA barcoding is a well-established approach for rapid, cost-effective species diagnosis, with many applications in support of taxonomy, biosecurity, conservation, and monitoring. Uptake has been particularly significant in hyperdiverse invertebrate groups where morphological approaches to species identification are often limiting (because of the scale of diversity and the small number of expert taxonomists) or inapplicable (for example in associating individuals from different life stages). The barcode reference library maintained as BOLD Systems by the Centre for Biodiversity Genomics in Guelph, Ontario is a significant biodiversity informatics infrastructure for bridging genomics and classical taxonomy, collections research, and field surveys. Effort across multiple years in Canada has delivered a library of reference sequences for the COI mitochondrial barcode that covers most of the known insect fauna for the country, enabling a comprehensive assessment of Canadian arthropod diversity (Hebert et al. 2016, Langor and Sheffield 2019). The Global Malaise Trap Program is expanding lessons learned in Canada to support species inventories in new regions such as Kruger National Park in South Africa. As DNA barcode libraries approach completeness for any site, analysis can employ metabarcoding to lower costs significantly for monitoring programs that track changes in species composition. Data from this program, and from barcode-based exploration in other regions, will greatly expand the fraction of biodiversity that can be monitored and compared over time and space. GBIF has collected more than one billion species records, but around 60% of these are for birds, with another 25% for vascular plants. Metabarcoding offers the opportunity for a wider selection of taxa to be included in global data sets and in support of local conservation and planning. The BIOSCAN program, launched by iBOL in 2019, seeks to operationalise DNA barcoding at the global scale for development of species inventories and preliminary exploration of undescribed diversity, for surveying community composition across the world's ecosystems, and codifying species interactions (the symbiome). BIOSCAN will exploit the latest advances in sequencing platforms to lower costs, increase precision, and accelerate processing of samples, to speed the uptake of DNA barcoding for protecting life on Earth.

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A DNA barcode reference library of the French Polynesian shore fishes

10.1101/595793 ◽

2019 ◽

Author(s):

Erwan Delrieu-Trottin ◽

Jeffrey T. Williams ◽

Diane Pitassy ◽

Amy Driskell ◽

Nicolas Hubert ◽

...

Keyword(s):

Dna Barcoding ◽

Biological Diversity ◽

Dna Barcode ◽

Reef Fishes ◽

French Polynesia ◽

Morphological Characters ◽

Reference Library ◽

Society Islands ◽

Extensive Collection ◽

I Gene

AbstractThe emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

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Semi-Automated Library Preparation for High-Throughput DNA Sequencing Platforms

Journal of Biomedicine and Biotechnology ◽

10.1155/2010/617469 ◽

2010 ◽

Vol 2010 ◽

pp. 1-8 ◽

Cited By ~ 21

Author(s):

Eveline Farias-Hesson ◽

Jonathan Erikson ◽

Alexander Atkins ◽

Peidong Shen ◽

Ronald W. Davis ◽

...

Keyword(s):

Sample Preparation ◽

Dna Sequencing ◽

High Throughput ◽

Magnetic Beads ◽

Dna Barcode ◽

Cost Effective ◽

Dna Libraries ◽

Emulsion Pcr ◽

High Throughput Dna Sequencing ◽

Sequencing Platforms

Next-generation sequencing platforms are powerful technologies, providing gigabases of genetic information in a single run. An important prerequisite for high-throughput DNA sequencing is the development of robust and cost-effective preprocessing protocols for DNA sample library construction. Here we report the development of a semi-automated sample preparation protocol to produce adaptor-ligated fragment libraries. Using a liquid-handling robot in conjunction with Carboxy Terminated Magnetic Beads, we labeled each library sample using a unique 6 bp DNA barcode, which allowed multiplex sample processing and sequencing of 32 libraries in a single run using Applied Biosystems' SOLiD sequencer. We applied our semi-automated pipeline to targeted medical resequencing of nuclear candidate genes in individuals affected by mitochondrial disorders. This novel method is capable of preparing as much as 32 DNA libraries in 2.01 days (8-hour workday) for emulsion PCR/high throughput DNA sequencing, increasing sample preparation production by 8-fold.

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First records raise questions: DNA barcoding of Odonata in the middle of the Mediterranean

Genome ◽

10.1139/gen-2019-0226 ◽

2020 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Tomasz Rewicz ◽

Arnold Móra ◽

Grzegorz Tończyk ◽

Ada Szymczak ◽

Michal Grabowski ◽

...

Keyword(s):

Dna Barcoding ◽

Related Species ◽

Dna Barcode ◽

Taxonomic Status ◽

Index Number ◽

Reference Library ◽

Nuclear Markers ◽

Closely Related Species ◽

Maltese Islands ◽

Morphological Species

We present the results of the first-ever DNA barcoding study of odonates from the Maltese Islands. In total, 10 morphologically identified species were collected during a two-week long expedition in 2018. Eighty cytochrome c oxidase subunit I (COI) barcodes were obtained from the collected specimens. Intra- and interspecific distances ranged from 0.00% to 2.24% and 0.48% to 17.62%, respectively. Successful species identification based on ascribing a single morphological species to a single Barcode Index Number (BIN) was achieved for eight species (80%). In the case of two species, Ischnura genei and Anax parthenope, BINs were shared with other closely related species. The taxonomic status of I. genei is questionable and the phylogenetic relationship between A. imperator/parthenope is not clear. Further studies involving a series of adult specimens collected in a wide spatial range and nuclear markers are necessary to resolve these cases. Therefore, this dataset serves as an initial DNA barcode reference library for Maltese odonates, within a larger project: Aquatic Macroinvertebrates DNA Barcode Library of Malta.

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Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

BIO Web of Conferences ◽

10.1051/bioconf/20213800087 ◽

2021 ◽

Vol 38 ◽

pp. 00087

Author(s):

Elena Nikitina ◽

Abdurashid Rakhmatov

Keyword(s):

Dna Barcoding ◽

Large Scale ◽

Dna Barcode ◽

Dna Barcodes ◽

Biodiversity Monitoring ◽

Reference Library ◽

Accurate Identification ◽

Unknown Species ◽

Phylogenetic Status ◽

Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

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DNA Barcode for the Parthenogenetic Surinam Cockroach Pycnoscelus surinamensis (Linnaeus, 1758) (Blattodea: Blaberidae) from India

International Research Journal of Insect Sciences ◽

10.18488/irjis.v7i1.2895 ◽

2022 ◽

Vol 7 (1) ◽

pp. 1-7

Author(s):

A Shabnam ◽

K P Dinesh

Keyword(s):

Dna Barcoding ◽

Molecular Identification ◽

Western Ghats ◽

Dna Barcode ◽

Insect Fauna ◽

Mt Dna ◽

Faunal Diversity ◽

Southern Western Ghats

DNA Barcoding is one of the emerging tools in molecular identification of faunal diversity, specifically insect fauna. The Surinam cockroach, Pycnoscelus surinamensis is the only known roach to be obligatorily parthenogenetic, with reported haplotypes. P. surinamensis is well established in Indomalayan, tropical and subtropical regions and substantially documented from India with a phenetic approach. Herewith we report the first set of mt DNA barcode from a vouchered collection for the species from southern Western Ghats India. Discussions are made on the identity of two sequences each of Blatteria species and Pycnoscelus species reported from USA.

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BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae)

10.1101/705889 ◽

2019 ◽

Author(s):

Muhammad Tayyib Naseem ◽

Muhammad Ashfaq ◽

Arif Muhammad Khan ◽

Akhtar Rasool ◽

Muhammad Asif ◽

...

Keyword(s):

Dna Barcoding ◽

Insect Pests ◽

Rhopalosiphum Padi ◽

Aphis Gossypii ◽

Dna Barcode ◽

Reference Sequence ◽

Neighbor Joining ◽

Reference Library ◽

Index Numbers ◽

Intraspecific Divergence

AbstractDNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these taxa with conspecific taxa from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from 123 plant species at 87 sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. The 801 sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance; one species (Rhopalosiphum padi) was assigned to two BINs, while two others (Aphis affinis, Aphis gossypii) were assigned to the same BIN, while one species (Aphis astragalina) lacked a qualifying sequence. The 42 Linnaean species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced to 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 18 of 37 species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.

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An overview of molecular identification of insect fauna with special emphasis on chalcid wasps (Hymenoptera: Chalcidoidea) of India

Acta agriculturae Slovenica ◽

10.14720/aas.2018.111.1.22 ◽

2018 ◽

Vol 111 (1) ◽

pp. 229

Author(s):

Ajaz RASOOL ◽

Tariq AHMAD ◽

Bashir Ahmad GANAI ◽

Shaziya GULL

Keyword(s):

Dna Barcoding ◽

Dna Sequences ◽

Biological Diversity ◽

Global Climate ◽

Biological Effects ◽

Dna Barcode ◽

Habitat Destruction ◽

Insect Fauna ◽

Processed Material ◽

The Face

Identifying organisms has grown in importance as we monitor the biological effects of global climate change and attempt to preserve species diversity in the face of accelerating habitat destruction. Classical taxonomy falls short in this race to catalogue biological diversity before it disappears. Differentiating subtle anatomical differences between closely related species requires the subjective judgment of highly trained specialists – and few are being trained in institutes today. DNA barcodes allow non-experts to objectively identify species – from small, damaged, or even industrially processed material. The aim of DNA barcoding is to establish a shared community resource of DNA sequences commonly used for identification, discrimination or taxonomic classification of organisms. It is a method that uses a short genetic marker in an organism's DNA to identify and distinguish its belonging from particular species, varieties or inter varieties. This simple technique has attracted attention from taxonomists, ecologists, conservation biologists, agriculturists, plant-quarantine officers and studies using the DNA barcode has rapidly increased. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made them a major target of DNA barcoding. In this review, we present an overview of DNA barcoding of insects with emphasis on Chalcid wasps of India.

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Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding

Scientific Reports ◽

10.1038/s41598-021-95610-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yuchi Chen ◽

Xiaocheng Zhu ◽

Panayiotis Loukopoulos ◽

Leslie A. Weston ◽

David E. Albrecht ◽

...

Keyword(s):

Dna Barcoding ◽

Native Species ◽

Management Strategies ◽

Dna Barcode ◽

Cost Effective ◽

Species Level ◽

Morphological Examination ◽

South Wales ◽

Interspecific Distance ◽

Genotypic Identification

AbstractAustralia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.

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DNA barcoding of marine fish species from Rongcheng Bay, China

PeerJ ◽

10.7717/peerj.5013 ◽

2018 ◽

Vol 6 ◽

pp. e5013 ◽

Cited By ~ 7

Author(s):

Lijuan Wang ◽

Zhihao Wu ◽

Mengxia Liu ◽

Wei Liu ◽

Wenxi Zhao ◽

...

Keyword(s):

Dna Barcoding ◽

Fish Species ◽

Dna Barcode ◽

Gc Content ◽

Genetic Distances ◽

Dna Barcodes ◽

Reference Library ◽

Fish Species Identification ◽

Northern Yellow Sea ◽

Coastal Bay

Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.

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Establishing the first DNA barcode reference library for freshwater decapod species (Crustacea: Decapoda) in Republic of North Macedonia

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65138 ◽

2021 ◽

Vol 4 ◽

Author(s):

Valentina Slavevska Stamenkovic ◽

Jelena Hinic ◽

Michal Grabowski ◽

Tomasz Mamos ◽

Leona Lovrenčić ◽

...

Keyword(s):

Dna Barcoding ◽

Dna Barcode ◽

Morphological Characters ◽

Freshwater Ecosystems ◽

Aquatic Biota ◽

Reference Library ◽

Irreversible Loss ◽

The Republic ◽

Different Parts ◽

Comprehensive Study

The freshwater ecosystems in the Republic of North Macedonia are considered as biodiversity hotspot on the European level since they provide diverse habitats that correspond with the complex of ecological preferences that many species require. This specially applies to the freshwater crustaceans that, unfortunately, have never been in the focus of a continuous research. In R. North Macedonia, freshwater crustaceans usually inhabit ecosystems exposed to negative anthropogenic impact. Thus, some species may become extinct presenting an irreversible loss for the Macedonian natural heritage. Although DNA barcoding, as a highly effective tool for fast species detection, is already a routine protocol in many taxonomical studies all over the world, there is still no official national DNA barcoding initiative in Republic of North Macedonia. This study employs DNA barcoding based on the ca. 650-bp long standard fragment of the mt COI gene of Astacus astacus, Austropotamobius torrentium, Potamon fluviatile and Potamon ibericum previously identified based on morphological characters, collected from different parts in R. North Macedonia. The ability of the DNA barcoding to rapidly identify all species has been proven. Our research presents the first comprehensive study that employs DNA barcoding as a molecular tool in decapod taxonomy in Republic of North Macedonia, giving the first attempt to establish DNA barcode reference library for freshwater decapod species in the country. We hope that further application of this approach will lead to the construction of DNA barcode reference library for different aquatic biota in the country. Such a library will find purpose in effective and modern bioassessment protocols as well as in phylogenetic research detecting interpopulation genetic variability.

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