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Journal articles on the topic 'COI DNA barcode'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Koroiva, Ricardo, Luís Reginaldo Ribeiro Rodrigues, and Diego José Santana. "DNA barcoding for identification of anuran species in the central region of South America." PeerJ 8 (October 21, 2020): e10189. http://dx.doi.org/10.7717/peerj.10189.

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The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences wer

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2

Epitashvili, Giorgi, Matthias Geiger, Jonas Astrin, Fabian Herder, Bella Japoshvili, and Levan Mumladze. "Towards retrieving the Promethean treasure: a first molecular assessment of the freshwater fish diversity of Georgia." Biodiversity Data Journal 8 (October 23, 2020): e57862. https://doi.org/10.3897/BDJ.8.e57862.

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In this study, we provide a first estimation of the molecular diversity of the freshwater fishes of Georgia. In addition to field collections, we integrated DNA barcode data obtained from recent works and public databases (BOLD and NCBI GenBank). Currently, the DNA barcode reference library for freshwater fishes of Georgia comprises 352 DNA barcodes for 50 species, 36 genera and 15 families (52% of total Georgian freshwater fish diversity), from which 162 DNA barcodes belonging to 41 species were newly generated as part of this study. A total of 22 species are reported from the Caspian Sea bas

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3

Yu, Hai-Jun, Xiao-Long Lin, Rui-Lei Zhang, Qian Wang, and Xin-Hua Wang. "Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes." ZooKeys 975 (October 12, 2020): 79–86. http://dx.doi.org/10.3897/zookeys.957.54668.

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The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear “barcode gap”. In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to sev

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Yu, Hai-Jun, Xiao-Long Lin, Rui-Lei Zhang, Qian Wang, and Xin-Hua Wang. "Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes." ZooKeys 975 (October 12, 2020): 79–86. https://doi.org/10.3897/zookeys.957.54668.

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The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear "barcode gap". In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to sev

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Estupiñán, Ruth A., Stephen F. Ferrari, Evonnildo. C. Gonçalves, Maria Silvanira R. Barbosa, Marcelo Vallinoto, and Schneider Maria Paula Cruz. "Evaluating the diversity of Neotropical anurans using DNA barcodes." ZooKeys 637 (December 2, 2016): 89–106. https://doi.org/10.3897/zookeys.637.8637.

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This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4–19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas lept

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Wang, Yujun, Xinjing Yao, Rui Liu, and Chang Liu. "DDQR (dynamic DNA QR coding): An efficient algorithm to represent DNA barcode sequences." PLOS ONE 18, no. 1 (2023): e0279994. http://dx.doi.org/10.1371/journal.pone.0279994.

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A DNA barcode is a short piece of standard DNA sequence used for species determination and discrimination. Representation of DNA barcodes is essential for DNA barcodes’ applications in the transportation and recognition of biological materials. Previously, we have compared different strategies for representing the DNA barcodes. In the present study, we have developed a compression algorithm based on binary coding or Huffman coding scheme, followed by converting the binary digits into Base64 digits. The combination of this compression algorithm and the QR representation leads to the dynamic DNA

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Laiho, Juha, and Gunilla Stahls. "DNA barcodes identify Central-Asian Colias butterflies (Lepidoptera, Pieridae)." ZooKeys 365 (December 30, 2013): 175–96. https://doi.org/10.3897/zookeys.365.5879.

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A majority of the known <i>Colias</i> species (Lepidoptera: Pieridae, Coliadinae) occur in the mountainous regions of Central-Asia, vast areas that are hard to access, rendering the knowledge of many species limited due to the lack of extensive sampling. Two gene regions, the mitochondrial COI ‘barcode’ region and the nuclear ribosomal protein RpS2 gene region were used for exploring the utility of these DNA markers for species identification. A comprehensive sampling of COI barcodes for Central-Asian <i>Colias</i> butterflies showed that the barcodes facilitated identification of most of the

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Zangaro, Francesco, Benedetta Saccomanno, Eftychia Tzafesta, Fabio Bozzeda, Valeria Specchia, and Maurizio Pinna. "Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA." NeoBiota 70 (December 14, 2021): 151–65. https://doi.org/10.3897/neobiota.70.71862.

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The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference lib

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Pulgarín-R, Paulo, Martha Olivera-Angel, Luisa Ortíz, Duván Nanclares, Sara Velásquez-Restrepo, and Juan Díaz-Nieto. "DNA barcodes of birds from northern Colombia." Biodiversity Data Journal 9 (May 21, 2021): e64842. https://doi.org/10.3897/BDJ.9.e64842.

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DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood-sampled birds in a lowland tropical forest with various degrees of intervention using standard 3 × 12 m mist-nets. We extracted DNA and sequenced the COI barcode gen

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Ismailaj, Mariola, Francesco Zangaro, Valeria Specchia, et al. "Biodiversity Patterns and DNA Barcode Gap Analysis of COI in Coastal Lagoons of Albania." Biology 13, no. 11 (2024): 951. http://dx.doi.org/10.3390/biology13110951.

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Aquatic biodiversity includes a variety of unique species, their habitats, and their interactions with each other. Albania has a large hydrographic network including rivers, lakes, wetlands and coastal marine areas, contributing to a high level of aquatic biodiversity. Currently, evaluating aquatic biodiversity relies on morphological species identification methods, but DNA-based taxonomic identification could improve the monitoring and assessment of aquatic ecosystems. This study aims to evaluate the coverage of COI DNA barcodes in the reference libraries for the known aquatic animal species

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Xie, Xuena, Haoting Ye, Xuan Cai, et al. "DNA Mini-Barcodes, a Potential Weapon for Conservation and Combating Illegal Trade of Pangolin." Tropical Conservation Science 14 (January 2021): 194008292110173. http://dx.doi.org/10.1177/19400829211017361.

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Background Smuggling and illegal trade of pangolins and their scales has drastically reduced the wild population of pangolins. Accurate species identification is currently in urgent need as a powerful weapon for combating pangolin smuggling and trade and conserving the already endangered pangolin species. Aim of the study To develop an efficient method based on DNA mini-barcodes for accurate pangolin species identification and authentication of processed pangolin scales against the non-target species. Materials and methods The primers for amplifying the DNA mini-barcodes were designed based on

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Sonet, Gontran, Kurt Jordaens, Yves Braet, et al. "Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France." ZooKeys 365 (December 30, 2013): 307–28. https://doi.org/10.3897/zookeys.365.6027.

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Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available.We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome <i>c </i>oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two publ

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Guo, Hui-Fang, Bei Guan, Fu-Ming Shi, and Zhi-Jun Zhou. "DNA Barcoding of genus Hexacentrus in China reveals cryptic diversity within Hexacentrus japonicus (Orthoptera, Tettigoniidae)." ZooKeys 596 (June 7, 2016): 53–63. https://doi.org/10.3897/zookeys.596.8669.

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DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Hexacentrus species in China collections. In total, 83 specimens of five Hexacentrus species were barcoded using standard mitochondrial cytochrome c oxidase subunit I (COI) gene. Except for H. japonicus, barcode gaps were present in the remaining Hexacentrus species. Taxon ID tree generated seven BOLD's barcode index numbers (BINs), four of which were in agreement with the morphological spec

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Guo, Mali, Zhenzhen Peng, Xiaoting Zhang, et al. "Isolation and characterization of DNA barcodes from distinctive and rare terrestrial animals in China using universal COI and 16S primers." STEMedicine 2, no. 7 (2021): e95. http://dx.doi.org/10.37175/stemedicine.v2i7.95.

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Background: Accurate taxonomic identification is the cornerstone for monitoring, conservation and management of ecological resources. China has the highest biodiversities and the richest species assemblages in the world, but is lacking in sufficient assessment to the abundant genetic variability. DNA barcoding is a proven tool employing sequence information for rapid and unambiguous species delineation. However, the ability of barcodes to distinguish species that are archaic and distinctive evolutionary lines remains largely untested.Methods: In order to investigate the resources of terrestria

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15

Fahldieck, Moritz, Björn Rulik, Jana Thormann, and Ximo Mengual. "A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany." Biodiversity Data Journal 12 (September 24, 2024): e127190. https://doi.org/10.3897/BDJ.12.e127190.

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Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination.In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. O

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Zangaro, Francesco, Benedetta Saccomanno, Eftychia Tzafesta, Fabio Bozzeda, Valeria Specchia, and Maurizio Pinna. "Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA." NeoBiota 70 (December 14, 2021): 151–65. http://dx.doi.org/10.3897/neobiota.70.71862.

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The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference lib

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17

Schmid-Egger, Christian, Stefan Schmidt, Paolo Rosa, and Oliver Niehuis. "DNA Barcoding of German Cuckoo Wasps (Hymenoptera: Chrysididae) Suggests Cryptic Species in Several Widely Distributed Species." Insects 15, no. 11 (2024): 850. http://dx.doi.org/10.3390/insects15110850.

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Germany is home to a rich cuckoo wasp fauna (Hymenoptera: Chrysididae) with about 108 species. However, several nomenclatural changes, the lack of identification keys, and the discovery of cryptic species difficult to identify based on external morphology have made the identification of several species a challenge. COI barcoding has been instrumental in the identification of some cuckoo wasp species and could help alleviate some of the above problems, but a reliable large reference database containing the cuckoo wasp barcodes is lacking. We present the COI barcodes of more than 800 specimens o

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Vineesh, N., C. Mohitha, K.K. Bineesh, Rahul G. Kumar, A. Gopalakrishnan, and V.S. Basheer. "DNA barcoding and taxonomic notes on the genus Macolor (Perciformes: Lutjanidae) from Indian waters." Journal of the Ocean Science Foundation 13 (November 12, 2014): 16–26. https://doi.org/10.5281/zenodo.1050491.

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The DNA “barcode”, the partial sequence of the mitochondrial gene cytochrome C oxidase subunit I (COI), was assessed for species identification within the genus Macolor. The Midnight Snapper, Macolor macularis Fowler 1931, is compared with its only congener, the Black and White Snapper, Macolor niger (Forsskål 1775), both collected from the south-west coast of India. The examination of fresh specimens of the two species showed diagnostic anatomical and coloration differences and the DNA barcoding showed a genetic divergence of 3.51% between the species. We provide a description and illustratio

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Mabragaña, Ezequiel, Valeria Gabbanelli, Florencia Matusevich, et al. "DNA Barcoding Southwestern Atlantic Skates: A 20-Year Effort in Building a Species Identification Library." Diversity 17, no. 5 (2025): 311. https://doi.org/10.3390/d17050311.

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The skate fauna in the Southwest Atlantic Ocean (SWA; 34–55° S) is represented by ~32 species, many of which share external features that have led to misidentifications and deficient fishery statistics. The use of DNA barcoding to discriminate SWA skate species was explored after 20 years of surveys. COI sequences were subjected to distance-based neighbor-joining (NJ), maximum likelihood (ML), barcode index number (BIN), automatic barcode gap discovery (ABGD), and nucleotide diagnostic character (NDC) analyses. For widely distributed species, a haplotype network was built. Overall, 187 specime

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Jafari, Samin, Björn Müller, Björn Rulik, Vera Rduch, and Peters Ralph S. "Another crack in the Dark Taxa wall: a custom DNA barcoding protocol for the species-rich and common Eurytomidae (Hymenoptera, Chalcidoidea)." Biodiversity Data Journal 11 (May 9, 2023): e101998. https://doi.org/10.3897/BDJ.11.e101998.

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DNA barcodes are a great tool for accelerated species identification and for complementing species delimitation. Furthermore, DNA barcode reference libraries are the decisive backbone feature for any metabarcoding study in biodiversity monitoring, conservation or ecology. However, in some taxa, DNA barcodes cannot be generated with published primers at a satisfying success rate and these groups will consequently be largely missing from any barcoding-based species list. Here, we provide a custom DNA barcoding forward primer for the Eurytomidae (Hymenoptera, Chalcidoidea), elevating the success

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Nugent, Cameron M., Tyler A. Elliott, Sujeevan Ratnasingham, and Sarah J. Adamowicz. "coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation." Genome 63, no. 6 (2020): 291–305. http://dx.doi.org/10.1139/gen-2019-0206.

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Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5′ region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of

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Wöger, Renate, Roland Wöger, and Matthias Nuss. "DNA barcodes for Aotearoa New Zealand Pyraloidea (Lepidoptera)." Biodiversity Data Journal 8 (November 27, 2020): e58841. https://doi.org/10.3897/BDJ.8.e58841.

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Identification of pyraloid species is often hampered by highly similar external morphology requiring microscopic dissection of genitalia. This becomes especially obvious when mass samples from ecological studies or insect monitoring have to be analysed. DNA barcode sequences could accelerate identification, but are not available for most pyraloid species from New Zealand. Hence, we are presenting a first DNA-barcode library for this group, providing 440 COI barcodes (cytochrome C oxidase I sequences) for 73 morphologically-identified species, which is 29% of Pyraloidea known from New Zealand.

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Liu, Kehan, Ranran Xing, Ruixue Sun, Yiqiang Ge, and Ying Chen. "An Accurate and Rapid Way for Identifying Food Geographical Origin and Authenticity: Editable DNA-Traceable Barcode." Foods 12, no. 1 (2022): 17. http://dx.doi.org/10.3390/foods12010017.

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DNA offers significant advantages in information density, durability, and replication efficiency compared with information labeling solutions using electronic, magnetic, or optical devices. Synthetic DNA containing specific information via gene editing techniques is a promising identifying approach. We developed a new traceability approach to convert traditional digitized information into DNA sequence information. We used encapsulation to make it stable for storage and to enable reading and detection by DNA sequencing and PCR-capillary electrophoresis (PCR-CE). The synthesized fragment consist

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Melo, Martim, Rita Covas, Ricardo Lima, et al. "DNA Barcode library of the endemic-rich avifauna of the oceanic islands of the Gulf of Guinea." Biodiversity Data Journal 11 (October 23, 2023): e110428. https://doi.org/10.3897/BDJ.11.e110428.

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The BioSTP: DNA Barcoding of endemic birds from oceanic islands of the Gulf of Guinea dataset contains records of 155 bird specimens belonging to 56 species in 23 families, representing over 80% of the diversity of the breeding landbird community. All specimens were collected on Príncipe, São Tomé and Annobón Islands between 2002 and 2021 and morphologically identified to species or subspecies level by qualified ornithologists. The dataset includes all endemic species and 3/4 of the extant endemic subspecies of the islands. This dataset is the second release by BioSTP and it greatly increases

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Nugent, Cameron M., and Sarah J. Adamowicz. "Alignment-free classification of COI DNA barcode data with the Python package Alfie." Metabarcoding and Metagenomics 4 (September 10, 2020): e55815. https://doi.org/10.3897/mbmg.4.55815.

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Characterization of biodiversity from environmental DNA samples and bulk metabarcoding data is hampered by off-target sequences that can confound conclusions about a taxonomic group of interest. Existing methods for isolation of target sequences rely on alignment to existing reference barcodes, but this can bias results against novel genetic variants. Effectively parsing targeted DNA barcode data from off-target noise improves the quality of biodiversity estimates and biological conclusions by limiting subsequent analyses to a relevant subset of available data. Here, we present Alfie, a Python

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Wang, Lijuan, Zhihao Wu, Mengxia Liu, et al. "DNA barcoding of marine fish species from Rongcheng Bay, China." PeerJ 6 (June 25, 2018): e5013. http://dx.doi.org/10.7717/peerj.5013.

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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%,

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Jennings, W. Bryan, Piero A. Ruschi, Gustavo Ferraro, et al. "Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails." Genome 62, no. 2 (2019): 77–83. http://dx.doi.org/10.1139/gen-2018-0145.

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Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ∼6000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e., mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders—Characiformes, Cichliformes, Cyprinodontiform

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Tzafesta, Eftychia, Benedetta Saccomanno, Francesco Zangaro, Maria Rosaria Vadrucci, Valeria Specchia, and Maurizio Pinna. "DNA Barcode Gap Analysis for Multiple Marker Genes for Phytoplankton Species Biodiversity in Mediterranean Aquatic Ecosystems." Biology 11, no. 9 (2022): 1277. http://dx.doi.org/10.3390/biology11091277.

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The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered by the substantial lack of reference sequences. The main objective of this study was to analyze the current coverage of DNA barcode reference libraries for phytoplankton species of the aquatic Mediterranean ecoregion in the southeast of Italy (Apulia Region) in order to assess the applicabi

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Vasquez, Adrian A., Brittany L. Bonnici, Safia Haniya Yusuf, Janiel I. Cruz, Patrick L. Hudson, and Jeffrey L. Ram. "Improved Chironomid Barcode Database Enhances Identification of Water Mite Dietary Content." Diversity 14, no. 2 (2022): 65. http://dx.doi.org/10.3390/d14020065.

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Chironomids are one of the most biodiverse and abundant members of freshwater ecosystems. They are a food source for many organisms, including fish and water mites. The accurate identification of chironomids is essential for many applications in ecological research, including determining which chironomid species are present in the diets of diverse predators. Larval and adult chironomids from diverse habitats, including lakes, rivers, inland gardens, coastal vegetation, and nearshore habitats of the Great Lakes, were collected from 2012 to 2019. After morphological identification of chironomids

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Letsiou, Stavroula, Panagiotis Madesis, Efstathios Vasdekis, et al. "DNA Barcoding as a Plant Identification Method." Applied Sciences 14, no. 4 (2024): 1415. http://dx.doi.org/10.3390/app14041415.

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In the last two decades, plant taxonomy has bloomed, following the development of a novel technique, namely, DNA barcoding. DNA barcodes are standardized sequences, ideally unique, coding or non-coding, either from the genome of the organism or from its organelles, that are used to identify/classify an organismal group; in short, the method includes amplification of the DNA barcode, sequencing and comparison with a reference database containing the relevant sequences from different species. In plants, the use a universal DNA barcode, such as COI, which is used in animals, has not been achieved

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Yang, Guangju, Wenjing Wang, Yuwei Tong, and Zhijun Zhou. "Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera)." ZooKeys 1229 (February 24, 2025): 25–42. https://doi.org/10.3897/zookeys.1229.129123.

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DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5' end of the mitochondrial cytochrome <i>c</i> oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Un

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Slater-Baker, Mollie-Rosae, Michelle Guzik, Juanita Rodriguez, et al. "Three new species of Australian miracine parasitoid wasps collected by regional schools as part of the Insect Investigators citizen science project (Hymenoptera, Braconidae, Miracinae)." Journal of Hymenoptera Research 98 (January 24, 2025): 19–45. https://doi.org/10.3897/jhr.98.137806.

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Miracinae is a poorly known and rarely collected subfamily of parasitoid wasps belonging to the family Braconidae. Here, three new species are described from material collected by Australian regional schools as part of the <i>Insect Investigators</i> citizen science project and named in collaboration with students: <i>Mirax supremus</i> Slater-Baker, sp. nov., <i>Mirax ceduna</i> Slater-Baker, sp. nov. and <i>Mirax kaatijan</i> Slater-Baker, sp. nov. The barcoding region of the cytochrome c oxidase subunit I (<i>COI</i>) gene was obtained for each new species and analysed alongside all publicl

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Silva, Fabio Laurindo da, Torbjørn Ekrem, and Alaide Aparecida Fonseca-Gessner. "DNA barcodes for species delimitation in Chironomidae (Diptera): a case study on the genusLabrundinia." Canadian Entomologist 145, no. 6 (2013): 589–602. http://dx.doi.org/10.4039/tce.2013.44.

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AbstractIn this study, we analysed the applicability of DNA barcodes for delimitation of 79 specimens of 13 species of nonbiting midges in the subfamily Tanypodinae (Diptera: Chironomidae) from São Paulo State, Brazil. Our results support DNA barcoding as an excellent tool for species identification and for solving taxonomic conflicts in genusLabrundinia.Molecular analysis of cytochrome c oxidase subunit I (COI) gene sequences yielded taxon identification trees, supporting 13 cohesive species clusters, of which three similar groups were subsequently linked to morphological variation at the lar

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Abeynayake, Shamila Weerakoon, Sonia Fiorito, Adrian Dinsdale, et al. "A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes." Genes 12, no. 8 (2021): 1138. http://dx.doi.org/10.3390/genes12081138.

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The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based i

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35

Raupach, Michael J., Björn Rulik, and Jörg Spelda. "Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)." ZooKeys 1082 (January 20, 2022): 103–25. http://dx.doi.org/10.3897/zookeys.1082.69851.

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DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Br

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36

Raupach, Michael J., Björn Rulik, and Jörg Spelda. "Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)." ZooKeys 1082 (January 20, 2022): 103–25. https://doi.org/10.3897/zookeys.1082.69851.

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DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Br

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37

Venera-Pontón, Dagoberto, Amy Driskell, Grave Sammy De, Darryl Felder, Justin Scioli, and Rachel Collin. "Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy." Biodiversity Data Journal 8 (January 7, 2020): e47333. https://doi.org/10.3897/BDJ.8.e47333.

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DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of <i>cytochrome c oxidase</i> subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least

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Linh, Nguyen Manh, Pham The Thu, Nguyen Van Quan, et al. "DNA BARCODING APPLICATION OF MITOCHONDRIAL COI GENE TO IDENTIFY SOME FISH SPECIES OF FAMILY GOBIIDAE IN VIETNAM." Tạp chí Khoa học và Công nghệ biển 18, no. 4 (2019): 443–51. http://dx.doi.org/10.15625/1859-3097/18/4/13662.

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The family Gobiidae is a relatively high abundance family of coastal fish with about 2000 species in 210 genera described. In Vietnam, the study on Gobiidae is very complex due to the large number of species, small size and high morphological variation which makes difficulties in identification and classification. In this study, the DNA barcoding technique has been used through mitochondrial cytochrome oxidase I (COI) gene to classify 30 specimens of Gobiidae from three coastal areas (North, Central and South) in Vietnam to evaluate the effectiveness compared to the morphological classificatio

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Thu, Pham The, Nguyen Manh Linh, Nguyen Van Quan, Pham Van Chien, Dao Huong Ly, and Le Ba Hoang Hiep. "DNA barcoding for identification of some fish species (Carangidae) in Vietnam coastal area." Tạp chí Khoa học và Công nghệ biển 19, no. 4 (2020): 527–36. http://dx.doi.org/10.15625/1859-3097/19/4/14909.

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Carangidae family has got about 148 species belonging to 32 genera. In Vietnam, Carangidae is of high commercial value and playing an important role in the ecosystem. In the context Vietnam has received yellow card for seafood since Nov. 2017 by the EU, in which one of the main reasons was related to the restriction of traceability. In this study, DNA barcoding technique of mitochondrial cytochrome oxidase I (COI) gene was used to classify 56 specimens of Carangidae from three coastal areas (Northern, Central and Southern) in Vietnam to evaluate the effectiveness compared to the morphological

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Huemer, Peter, Ole Karsholt, Leif Aarvik, et al. "DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity." ZooKeys 921 (March 24, 2020): 141–57. http://dx.doi.org/10.3897/zookeys.921.49199.

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For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but

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Huemer, Peter, Ole Karsholt, Leif Aarvik, et al. "DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity." ZooKeys 921 (March 24, 2020): 141–57. https://doi.org/10.3897/zookeys.921.49199.

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For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but

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Yang, Guangju, Wenjing Wang, Yuwei Tong, and Zhijun Zhou. "Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera)." ZooKeys 1229 (February 24, 2025): 25–42. https://doi.org/10.3897/zookeys.1229.129123.

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DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5’ end of the mitochondrial cytochrome c oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Units (MO

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Kasalo, Niko, Josip Skejo, and Martin Husemann. "DNA Barcoding of Pygmy Hoppers—The First Comprehensive Overview of the BOLD Systems’ Data Shows Promise for Species Identification." Diversity 15, no. 6 (2023): 696. http://dx.doi.org/10.3390/d15060696.

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The COI gene is widely used as a DNA barcode in animals that can assist in the identification of species. One of the widely used aggregators of DNA barcodes is the Barcode of Life Data System (BOLD Systems), which contains around 2500 sequences of Tetrigidae, an understudied orthopteran family with unresolved taxonomy and species that are difficult to identify. In this paper, we provide a summary of the metadata provided with the COI sequences and present a phylogenetic analysis of photographically vouchered sequences using Maximum Likelihood and Bayesian analysis. We found that (1) the subfam

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Mohammed-Geba, Khaled, Ahmad Hamed Obuid-Allah, Naser Abdellatif El-Shimy, Mohamed Abd El-Moez Mahbob, Rouwaida Saadawy Ali, and Shimaa Mohamed Said. "DNA Barcoding for Scorpion Species from New Valley Governorate in Egypt Reveals Different Degrees of Cryptic Speciation and Species Misnaming." Conservation 1, no. 3 (2021): 228–40. http://dx.doi.org/10.3390/conservation1030018.

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(1) Background: Scorpions (Arthropoda: Arachnida) represent a diverse group of invertebrates, accounting for a significant proportion of earth’s predators and ecosystems’ modulators. Surviving mostly in hardly reachable nests, and representing key hazards to human health, they attracted major interest for characterizing their eco-, morpho-, and genotypes. (2) Methods: Four scorpion species were collected from the New Valley governorate in Upper Egypt, where a high level of scorpionism and related neurological symptoms are found, that were Leiurus quinquestriatus, Androctonus amoreuxi, Orthochi

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Zhao, Yizheng, Hui Wang, Huimin Huang, and Zhijun Zhou. "A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China." ZooKeys 1123 (October 5, 2022): 147–71. http://dx.doi.org/10.3897/zookeys.1123.86704.

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Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa.

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46

Zhao, Yizheng, Hui Wang, Huimin Huang, and Zhijun Zhou. "A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China." ZooKeys 1123 (October 5, 2022): 147–71. https://doi.org/10.3897/zookeys.1123.86704.

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Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa.

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Valdez-Moreno, Martha, Manuel Mendoza-Carranza, Eduardo Rendón-Hernández, Erika Alarcón-Chavira, and Manuel Elías-Gutiérrez. "DNA Barcodes Applied to a Rapid Baseline Construction in Biodiversity Monitoring for the Conservation of Aquatic Ecosystems in the Sian Ka’an Reserve (Mexico) and Adjacent Areas." Diversity 13, no. 7 (2021): 292. http://dx.doi.org/10.3390/d13070292.

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This study is focused on the aquatic environments of the Sian Ka’an reserve, a World Heritage Site. We applied recently developed protocols for the rapid assessment of most animal taxa inhabiting any freshwater system using light traps and DNA barcodes, represented by the mitochondrial gene Cytochrome Oxidase I (COI). We DNA barcoded 1037 specimens comprising mites, crustaceans, insects, and fish larvae from 13 aquatic environments close or inside the reserve, with a success rate of 99.8%. In total, 167 barcode index numbers (BINs) were detected. From them, we identified 43 species. All others

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Ortega-Morales, Aldo I., Luis M. Hernández-Triana, Rahuel J. Chan-Chable, et al. "DNA Barcoding of Mosquitoes from the Pantanos de Centla Biosphere Reserve, Southeastern Mexico." Journal of the American Mosquito Control Association 37, no. 4 (2021): 198–207. http://dx.doi.org/10.2987/21-6967.

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ABSTRACT Accurate identification of mosquito species is essential to support programs that involve the study of distribution and mosquito control. Numerous mosquito species are difficult to identify based only on morphological characteristics, due to the morphological similarities in different life stages and large numbers of some species that are members of morphologically similar species complexes. In the present study, the mosquitoes collected in the Pantanos de Centla Biosphere Reserve, southeastern Mexico, were evaluated using a combination of morphological and molecular approaches (mitoc

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Bikashvili, Ani, Nino Kachlishvili, Bella Japoshvili, and Levan Mumladze. "Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus." Biodiversity Data Journal 10 (September 13, 2022): e84887. https://doi.org/10.3897/BDJ.10.e84887.

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This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total, 289 COI barcode sequences were obtained from 33 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analysed by means of the Barcode Index Number (BIN) and the other tools available in BOLD Systems. Results showed that the knowledge of freshwater molluscs dive

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Camacho-Sánchez, Fátima Yedith, A. Alonso Aguirre, José Alberto Narváez-Zapata, et al. "DNA barcode analysis of the endangered green turtle (Chelonia mydas) in Mexico1." Genome 64, no. 9 (2021): 879–91. http://dx.doi.org/10.1139/gen-2019-0213.

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Technological and analytical advances to study evolutionary biology, ecology, and conservation of green turtles (Chelonia mydas) are realized through molecular approaches including DNA barcoding. We characterized the usefulness of COI DNA barcodes in green turtles in Mexico to better understand genetic divergence and other genetic parameters of this species. We analyzed 63 sequences, including 25 from green turtle field specimens collected from the Gulf of Mexico and from the Mexican Pacific and 38 already present in the Barcode of Life Data Systems (BOLD). A total of 13 haplotypes were identi

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