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Journal articles on the topic 'DNA barcoding'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 March 2023

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1

Wulansari, Nuring, Mala Nurilmala, and N. Nurjanah. "Detection Tuna and Processed Products Based Protein and DNA Barcoding." Jurnal Pengolahan Hasil Perikanan Indonesia 18, no. 2 (August 25, 2015): 119–27. http://dx.doi.org/10.17844/jphpi.2015.18.2.119.

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Shadrin, D. M. "DNA Barcoding: Applications." Russian Journal of Genetics 57, no. 4 (April 2021): 489–97. http://dx.doi.org/10.1134/s102279542104013x.

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3

Mitchell, Andrew. "DNA barcoding demystified." Australian Journal of Entomology 47, no. 3 (August 2008): 169–73. http://dx.doi.org/10.1111/j.1440-6055.2008.00645.x.

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Zuo, Yunjuan, Zhongjian Chen, Katsuhiko Kondo, Tsuneo Funamoto, Jun Wen, and Shiliang Zhou. "DNA Barcoding ofPanaxSpecies." Planta Medica 77, no. 02 (August 27, 2010): 182–87. http://dx.doi.org/10.1055/s-0030-1250166.

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5

Xu, Jianping. "Fungal DNA barcoding." Genome 59, no. 11 (November 2016): 913–32. http://dx.doi.org/10.1139/gen-2016-0046.

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Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.

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ŠLAPETA, JAN. "DNA barcoding ofCryptosporidium." Parasitology 145, no. 5 (November 8, 2017): 574–84. http://dx.doi.org/10.1017/s0031182017001809.

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SUMMARYCryptosporidiumspp. (Apicomplexa) causing cryptosporidiosis are of medical and veterinary significance. The genusCryptosporidiumhas benefited from the application of what is considered a DNA-barcoding approach, even before the term ‘DNA barcoding’ was formally coined. Here, the objective to define the DNA barcode diversity ofCryptosporidiuminfecting mammals is reviewed and considered to be accomplished. Within theCryptosporidiumliterature, the distinction between DNA barcoding and DNA taxonomy is indistinct. DNA barcoding and DNA taxonomy are examined using the latest additions to the growing spectrum of namedCryptosporidiumspecies and within-species and between-species identity is revisited. Ease and availability of whole-genome DNA sequencing of the relatively smallCryptosporidiumgenome offer an initial perspective on the intra-host diversity. The opportunity emerges to apply a metagenomic approach to purified field/clinicalCryptosporidumisolates. The outstanding question remains a reliable definition ofCryptosporidiumphenotype. The complementary experimental infections and metagenome approach will need to be applied simultaneously to addressCryptosporidiumphenotype with carefully chosen clinical evaluations enabling identification of virulence factors.

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Carvalho, C. B. V. "DNA Barcoding in Forensic Vertebrate Species Identification." Brazilian Journal of Forensic Sciences, Medical Law and Bioethics 4, no. 1 (2014): 12–23. http://dx.doi.org/10.17063/bjfs4(1)y201412.

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8

Munch, Kasper, Wouter Boomsma, Eske Willerslev, and Rasmus Nielsen. "Fast phylogenetic DNA barcoding." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1512 (October 7, 2008): 3997–4002. http://dx.doi.org/10.1098/rstb.2008.0169.

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We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria for determining the taxonomic level at which a particular DNA sequence can be assigned.

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Scicluna, Stephanie M., Blessing Tawari, and C. Graham Clark. "DNA Barcoding of Blastocystis." Protist 157, no. 1 (February 2006): 77–85. http://dx.doi.org/10.1016/j.protis.2005.12.001.

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Durand, J. D., N. Hubert, K. N. Shen, and P. Borsa. "DNA barcoding grey mullets." Reviews in Fish Biology and Fisheries 27, no. 1 (November 11, 2016): 233–43. http://dx.doi.org/10.1007/s11160-016-9457-7.

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Valentini, Alice, François Pompanon, and Pierre Taberlet. "DNA barcoding for ecologists." Trends in Ecology & Evolution 24, no. 2 (February 2009): 110–17. http://dx.doi.org/10.1016/j.tree.2008.09.011.

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Hanner, Robert, Robin Floyd, Andrea Bernard, Bruce B. Collette, and Mahmood Shivji. "DNA barcoding of billfishes." Mitochondrial DNA 22, sup1 (October 2011): 27–36. http://dx.doi.org/10.3109/19401736.2011.596833.

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13

SMITH, M. ALEX, NIKOLAI A. POYARKOV, and PAUL D. N. HEBERT. "DNA BARCODING: CO1 DNA barcoding amphibians: take the chance, meet the challenge." Molecular Ecology Resources 8, no. 2 (June 28, 2008): 235–46. http://dx.doi.org/10.1111/j.1471-8286.2007.01964.x.

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14

Hikam, Agus Mohammad, Nurul Jadid Mubarakati, Muhammad Dailami, and Abdul Hamid A. Toha. "DNA barcoding pada invertebrata laut." Jurnal Biologi Udayana 25, no. 1 (June 25, 2021): 46. http://dx.doi.org/10.24843/jbiounud.2021.v25.i01.p06.

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Banyaknya spesies invertebrata laut yang memiliki kemiripan morfologi menyebabkan kesalahan identifikasi sangat mungkin terjadi. Identifikasi spesies secara molekuler sangat diperlukan dalam mempelajari taksonomi yang akurat. Penelitian ini bertujuan untuk menentukan identitas invertebrata laut dari Perairan Papua dengan teknik DNA barcoding menggunakan marka gen COI (Cytochrome c oxidase I). Penelitian mengidentifikasi 29 individu invertebrata laut, yang terdiri dari teripang (6 sampel), lobster (6 sampel), gurita (6 sampel), chiton (5 sampel), dan bulu babi (6 sampel). Metode identifikasi molekuler terdiri dari isolasi DNA, PCR fragmen gen COI, sekuensing, dan analisis sekuens DNA menggunakan software bioinformatika.Hasil penelitian ini menunjukkan bahwa teripang merupakan spesies Bohadschia marmorata, lobser merupakan spesies Panulirus versicolor, gurita merupakan spesies Octopus cyanea, chiton merupakan spesies Ischnochiton australis, dan bulu babi merupakan spesies Tripneustes gratilla, berdasarkan analisis BLAST dan Boldsystem. Dengan tingkat kemiripan sampel dan rujukan dalam kisaran 84.58 sampai 100.00%. Indeks disparitas, jarak genetik dan pohon filogenetik mendukung hasil ini.

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Wangiyana, I. Gde Adi Suryawan. "DNA BARCODING LIBRARY DATABASE OF AQUILARIA MEMBER AND GYRINOPS MEMBER." Jurnal Silva Samalas 3, no. 2 (December 29, 2020): 68. http://dx.doi.org/10.33394/jss.v3i2.3693.

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Aquilaria and Gyrinops are the primary agarwood producer on international trade. For authentication and standardization purposes, it is essential to carry DNA barcoding studies of these genera. DNA barcoding studies on plants need a database of several regions on the plant genome that could act as a barcoding marker. These DNA barcoding markers could be divided into Chloroplasts barcoding and Nuclear barcoding. Several markers have been used for DNA barcoding study of agarwood producer species, including trnL-trnF, matK, rbcL, rpoC1, ycf1 (Chloroplast barcoding), and ITS (Nuclear barcoding). This review breakdown the availability of those DNA barcoding markers on the online genebank database for Aquilaria and Gyrinops. Aquilaria genus has 12 species members, while Gyrinops genus has six species members. The sequence of region trnL-trnF is the only barcoding marker covering all 12 species members of Aquilaria and six species members of Gyrinops. Both ITS and matK have covered nine species among 12 total species members of Aquilaria. The rbcL, rpoC1, and ycf1, respectively, have covered eight, five, and four species members of Aquilaria. Most of the barcoding markers have covered three species members of Gyrinops except for ITS (5 species) and rpoC1 (1 species). However, Gyrinops members have no ycf1 sequence on genebank database. Based on sequence availability on the genebank database, it could be concluded that the trnL-trnF region is the most promising DNA barcoding marker for the Aquilaria and Gyrinops members especially for the phylogenetic analysis purpose.

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16

Cahyaningsih, Ria, Lindsey Jane Compton, Sri Rahayu, Joana Magos Brehm, and Nigel Maxted. "DNA Barcoding Medicinal Plant Species from Indonesia." Plants 11, no. 10 (May 21, 2022): 1375. http://dx.doi.org/10.3390/plants11101375.

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Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use.

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17

DasGupta, B., K. M. Konwar, I. I. Mandoiu, and A. A. Shvartsman. "DNA-BAR: distinguisher selection for DNA barcoding." Bioinformatics 21, no. 16 (June 16, 2005): 3424–26. http://dx.doi.org/10.1093/bioinformatics/bti547.

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18

Fahmi, Melta Rini, Ruby Vidia Kusumah, Idil Ardi, Shofihar Sinansari, and Eni Kusrini. "DNA BARCODING IKAN HIAS INTRODUKSI." Jurnal Riset Akuakultur 12, no. 1 (May 30, 2017): 29. http://dx.doi.org/10.15578/jra.12.1.2017.29-40.

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Identifikasi spesies menjadi tantangan dalam pengelolaan ikan hias introduksi baik untuk tujuan budidaya maupun konservasi. Penelitian ini bertujuan untuk melakukan identifikasi molekuler ikan hias introduksi yang beredar di pembudidaya dan pasar ikan hias Indonesia dengan menggunakan barcode DNA gen COI. Sampel ikan diperoleh dari pembudidaya dan importir ikan hias di kawasan Bandung dan Jakarta. Total DNA diekstraksi dari jaringan sirip ekor dengan menggunakan metode kolom. Amplifikasi gen target dilakukan dengan menggunakan primer FishF1, FishF2, FishR1, dan FishR2. Hasil pembacaan untai DNA disejajarkan dengan sekuen yang terdapat pada genbank melalui program BLAST. Identifikasi dilakukan melalui kekerabatan pohon filogenetik dan presentasi indeks kesamaan dengan sekuen genbank. Hasil identifikasi menunjukkan sampel yang diuji terbagi menjadi lima grup, yaitu: Synodontis terdiri atas lima spesies, Corydoras: empat spesies, Phseudoplatystoma: tiga spesies, Botia: tiga spesies, dan Leporinus: tiga spesies dengan nilai boostrap 99-100. Indeks kesamaan sekuen menunjukkan sebanyak 11 spesies memiliki indeks kesamaan 99%-100% dengan data genbank yaitu Synodontis decorus, Synodontis eupterus, Synodontis greshoffi, Botia kubotai, Botia lohachata, Rasbora erythromicron, Corydoras aeneus, Gyrinocheilus aymonieri, Eigenmannia virescens, Leporinus affinis, Phractocephalus hemioliopterus. Dua spesies teridentifikasi sebagai hasil hibridisasi (kawin silang) yaitu Leopard catfish (100% identik dengan Pseudoplatystoma faciatum) dan Synodontis leopard (100% identik dengan Synodontis notatus). Hasil analisis nukleotida penciri diperoleh tujuh nukleotida untuk Synodontis decora, 10 nukleotida untuk Synodontis tanganyicae, 13 nukleotida untuk Synodontis euterus, empat nukleotida untuk Synodontis notatus, dan 14 untuk Synodontis grashoffi. Kejelasan identifikasi spesies ikan menjadi kunci utama dalam budidaya, perdagangan, manajemen, konservasi, dan pengembangan ilmu pengetahuan.Species identification becomes a new challenge in the management of ornamental fish either for cultivation, or for conservation proposes. The objective of this study was to identify currently existing introduced ornamental fish in Indonesian farmers and markets using DNA barcodes COI gene. Fish samples were collected from farmers and importers of ornamental fish in Bandung and Jakarta. Total genome was extracted from caudal fin tissue using the column method. Amplification of the target gene was done by using FishF1, FishF2, FishR1, and FishR2 primers. DNA sequence was aligned with the sequences from genbank by BLAST program. Species identification was decided through the phylogenetic tree and similarity index with genbank sequences. The results showed that all of tested samples fall into five groups; Synodontis consisted of five species, Corydoras four species, Phseudoplatystoma four species, Botia three species, and Leporinus three species with 99-100 boostrap value. Sequence similarity index showed around 11 species have 99%-100% similarity index with sequence data on genbank which are Synodontis decorus, Synodontis eupterus, Synodontis greshoffi, Botia kubotai, Botia lohachata, Rasbora erythromicron, Corydoras aeneus, Gyrinocheilus aymonieri, Eigenmannia virescens, Leporinus affinis, Phractocephalus hemioliopterus. Two species were identified as hybridization product (interbreeding) including leopard catfish (100% identical with Pseudoplatystoma faciatum) and the leopard Synodontis (100% identical with Synodontis notatus). Analysis of nucleotide diagnostic showed Synodontis decora has seven nucleotides diagnostic, Synodontis tanganyicae 10 nucleotides, Synodontis euterus 13 nucleotides, Synodontis notatus four nucleotides, and Synodontis grashoffi 14 nucleotides. The correct identification of fish species is a useful tool for aquaculture, global marketing, management or conservation, and academic/scientific purpose.

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19

Valentini, Alice, Christian Miquel, and Pierre Taberlet. "DNA Barcoding for Honey Biodiversity." Diversity 2, no. 4 (April 19, 2010): 610–17. http://dx.doi.org/10.3390/d2040610.

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20

K. Lim, Burton. "Editorial - DNA Barcoding of Mammals." Open Zoology Journal 5, no. 1 (January 26, 2012): 1. http://dx.doi.org/10.2174/1874336601205010001.

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21

Aliabadian, Mansour, Kevin Beentjes, Kees (C S. ). Roselaar, Hans van Brandwijk, Vincent Nijman, and Ronald Vonk. "DNA barcoding of Dutch birds." ZooKeys 365 (December 30, 2013): 25–48. http://dx.doi.org/10.3897/zookeys.365.6287.

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22

EBACH, MALTE C., and CRAIG HOLDREGE. "More Taxonomy, Not DNA Barcoding." BioScience 55, no. 10 (2005): 823. http://dx.doi.org/10.1641/0006-3568(2005)055[0823:mtndb]2.0.co;2.

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23

Ramesh, Madhulika, Aparajita Sen, Meenakshi Vachher, and Arti Nigam. "Delineating Bacteria Using DNA Barcoding." Molecular Genetics, Microbiology and Virology 36, S1 (December 2021): S65—S73. http://dx.doi.org/10.3103/s0891416821050128.

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Hussein, Y. A., M. M. Youssef, A. M. Hereba, S. S. Al-Shokair, and M. M. Waheed. "DNA Barcoding of Mammalian Spermatozoa." Journal of Camel Practice and Research 28, no. 3 (2021): 283–90. http://dx.doi.org/10.5958/2277-8934.2021.00044.8.

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Lakra, Wazir Singh, M. Singh, Mukunda Goswami, A. Gopalakrishnan, K. K. Lal, V. Mohindra, U. K. Sarkar, et al. "DNA barcoding Indian freshwater fishes." Mitochondrial DNA Part A 27, no. 6 (December 24, 2015): 4510–17. http://dx.doi.org/10.3109/19401736.2015.1101540.

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Larson, Brendon MH. "DNA barcoding: the social frontier." Frontiers in Ecology and the Environment preprint, no. 2007 (2007): 1. http://dx.doi.org/10.1890/060128.

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Larson, Brendon MH. "DNA barcoding: the social frontier." Frontiers in Ecology and the Environment 5, no. 8 (October 2007): 437–42. http://dx.doi.org/10.1890/060128.1.

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Larson, Brendon MH. "DNA barcoding: the social frontier." Frontiers in Ecology and the Environment 5, no. 8 (2007): 437. http://dx.doi.org/10.1890/1540-9295(2007)5[437:dbtsf]2.0.co;2.

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Shekhovtsov, S. V., I. N. Shekhovtsova, and S. E. Peltek. "DNA Barcoding: Methods and Approaches." Biology Bulletin Reviews 9, no. 6 (November 2019): 475–83. http://dx.doi.org/10.1134/s2079086419060057.

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Jackson, Miranda, and Br Albert S. Gahr. "DNA Barcoding & Macroinvertebrate Identification." American Biology Teacher 81, no. 3 (March 1, 2019): 162–67. http://dx.doi.org/10.1525/abt.2019.81.3.162.

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Macroinvertebrates are readily available at the undergraduate level and provide an indicator of stream quality. DNA barcoding is the use of a sequence comparison of a specific region of the DNA that allows for classification of the organism. In most undergraduate courses, the discussion of genetic identification and stream quality assessment remain separated concepts. However, joining these lectures into a three-part laboratory learning module could bridge this gap and prepare students for a real-world application. During the first week of the proposed activity, students perform taxonomic identification. The following week, they perform a DNA isolation. In the last week, they use polymerase chain reaction and electrophoresis, possibly with a lecture examining a barcode for an example of the final outcome. In our research, we have determined effective methods that will allow all three sections to be completed in three three-hour undergraduate lab sessions, with minor modifications. Furthermore, the data we collected showed 54% efficiency. The methods we outline introduce new techniques and skills that prepare students for next-level education or employment and attempt to integrate ecological or environmental analysis with genetic analysis and DNA extraction techniques, making this lab series worth exploring at the undergraduate level.

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Li, Dezhu, and Chunxia Zeng. "Prospects for plant DNA barcoding." Biodiversity Science 23, no. 3 (2015): 297–98. http://dx.doi.org/10.17520/biods.2015135.

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KELLY, RYAN P., INDRA NEIL SARKAR, DOUGLAS J. EERNISSE, and ROB DESALLE. "DNA barcoding using chitons (genusMopalia)." Molecular Ecology Notes 7, no. 2 (January 12, 2007): 177–83. http://dx.doi.org/10.1111/j.1471-8286.2006.01641.x.

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Moritz, Craig, and Carla Cicero. "DNA Barcoding: Promise and Pitfalls." PLoS Biology 2, no. 10 (September 28, 2004): e354. http://dx.doi.org/10.1371/journal.pbio.0020354.

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Nielsen, Rasmus, and Mikhail Matz. "Statistical Approaches for DNA Barcoding." Systematic Biology 55, no. 1 (February 1, 2006): 162–69. http://dx.doi.org/10.1080/10635150500431239.

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WARD, ROBERT D., BRONWYN H. HOLMES, and TIM D. O’HARA. "DNA barcoding discriminates echinoderm species." Molecular Ecology Resources 8, no. 6 (November 2008): 1202–11. http://dx.doi.org/10.1111/j.1755-0998.2008.02332.x.

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LAKRA, W. S., M. S. VERMA, M. GOSWAMI, K. K. LAL, V. MOHINDRA, P. PUNIA, A. GOPALAKRISHNAN, K. V. SINGH, R. D. WARD, and P. HEBERT. "DNA barcoding Indian marine fishes." Molecular Ecology Resources 11, no. 1 (December 13, 2010): 60–71. http://dx.doi.org/10.1111/j.1755-0998.2010.02894.x.

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COULSON, M. W., D. DENTI, L. VAN GUELPEN, C. MIRI, E. KENCHINGTON, and P. BENTZEN. "DNA barcoding of Canada’s skates." Molecular Ecology Resources 11, no. 6 (June 9, 2011): 968–78. http://dx.doi.org/10.1111/j.1755-0998.2011.03034.x.

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Austin, Andrew, and Andrew Mitchell. "Preface to 'DNA Barcoding Invertebrates'." Invertebrate Systematics 26, no. 6 (2012): iii. http://dx.doi.org/10.1071/isv26n6_pr.

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Bucklin, Ann, Dirk Steinke, and Leocadio Blanco-Bercial. "DNA Barcoding of Marine Metazoa." Annual Review of Marine Science 3, no. 1 (January 15, 2011): 471–508. http://dx.doi.org/10.1146/annurev-marine-120308-080950.

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Galinskaya, Tatiana V., Nadezhda Yu Oyun, Anastasia A. Teterina, and Anatole I. Shatalkin. "DNA barcoding of Nothybidae (Diptera)." Oriental Insects 50, no. 2 (April 2, 2016): 69–83. http://dx.doi.org/10.1080/00305316.2016.1174747.

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Chao, Zhi, Weiping Zeng, Jing Liao, Li Liu, Zhenbiao Liang, and Xiaolei Li. "DNA barcoding Chinese medicinal Bupleurum." Phytomedicine 21, no. 13 (November 2014): 1767–73. http://dx.doi.org/10.1016/j.phymed.2014.09.001.

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WOOD, JAMIE R. "DNA barcoding of ancient parasites." Parasitology 145, no. 5 (March 20, 2018): 646–55. http://dx.doi.org/10.1017/s0031182018000380.

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SUMMARYAncient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in ‘real-time’ processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts. The application of DNA metabarcoding and high-throughput sequencing to ancient specimens has so far been limited, but in future promises great potential for gaining empirical data on poorly understood processes such as parasite co-extinction.

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Weigand, Alexander. "ABCD: „Barcoding“ jenseits der DNA." Im Focus Onkologie 17, no. 4 (April 2014): 3. http://dx.doi.org/10.1007/s15015-014-0989-1.

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Taufan Harisam, R., Asrul Sahri Siregar, Norman Arie Prayogo, Purnama Sukardi, and Nguyen The Hung. "DNA Barcoding for mangrove identification." IOP Conference Series: Earth and Environmental Science 406 (December 29, 2019): 012018. http://dx.doi.org/10.1088/1755-1315/406/1/012018.

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LI, De-Zhu, Jian-Quan LIU, Zhi-Duan CHEN, Hong WANG, Xue-Jun GE, Shi-Liang ZHOU, Lian-Ming GAO, Cheng-Xin FU, and Shi-Lin CHEN. "Plant DNA barcoding in China." Journal of Systematics and Evolution 49, no. 3 (May 2011): 165–68. http://dx.doi.org/10.1111/j.1759-6831.2011.00137.x.

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Perl, R. G. Bina, Zoltán T. Nagy, Gontran Sonet, Frank Glaw, Katharina C. Wollenberg, and Miguel Vences. "DNA barcoding Madagascar’s amphibian fauna." Amphibia-Reptilia 35, no. 2 (2014): 197–206. http://dx.doi.org/10.1163/15685381-00002942.

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We provide a DNA barcoding survey of Malagasy amphibians, including 251 of the 292 nominal species known to date, by complementing previous data with 280 newly determined barcoding sequence fragments of the mitochondrial cytochrome oxidase subunit I (COI) gene. Amplification success for the newly determined sequences was highest (94%) with one set of universal COI primers (dgLCO1490-dgHCO2198) while other primer sets had distinctly lower success rates. By and large, we observed relatively high average interspecific genetic distances of 25-27% within the Mantellidae and Microhylidae, and genetic distances of 13-21% within the Hyperoliidae. Lower values of 6-7% were observed between some sister species in all families, with extreme lows of 0.2-0.3% between a few sister species pairs in microhylids and mantellids for which we postulate mitochondrial introgression or yet unsettled taxonomy. Within-species divergences were relatively high especially in mantellids where they averaged 5.3%, due to the inclusion of numerous deep conspecific lineages (by definition with high divergences to other specimens) in our study. Above this, the degree of polymorphism was difficult to establish owing to limited sampling per population in our assessment. Compared to a previous assessment from 2009 based on 16S rDNA sequences, we identify 14 additional undescribed candidate species and raise the maximum estimate of species in the island’s batrachofauna to well over 500.

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Ward, Robert D., Tyler S. Zemlak, Bronwyn H. Innes, Peter R. Last, and Paul D. N. Hebert. "DNA barcoding Australia's fish species." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (September 15, 2005): 1847–57. http://dx.doi.org/10.1098/rstb.2005.1716.

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Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene ( cox1 ). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus , flatheads of the family Platycephalidae, and tunas of the genus Thunnus —were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.

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Apriliyanti, Margaretha Sandra, Sutanti Sutanti, and Deny Sapto Chondro Utomo. "IDENTIFIKASI PLANKTON DI KAWASAN BUDIDAYA RUMPUT LAUT KABUPATEN BANTAENG, SULAWESI SELATAN DENGAN METODE DNA BARCODING." Jurnal Teknologi Perikanan dan Kelautan 9, no. 1 (January 16, 2019): 65–72. http://dx.doi.org/10.24319/jtpk.9.65-72.

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DNA barcoding merupakan metode yang dapat digunakan untuk mengidentifikasi plankton dengan melihat materi genetiknya. DNA barcoding dilakukan dengan beberapa tahapan, yaitu ekstraksi, amplifikasi, purifikasi, dan sekuensing. Sampel yang digunakan adalah diambil pada bulan Juli 2017 dan Desember 2017 dari kawasan budidaya rumput laut Kabupaten Bantaeng, Sulawesi Selatan. Penelitian ini bertujuan untuk mengidentifikasi plankton dari kawasan budidaya rumput laut di Kabupaten Bantaeng, Sulawesi Selatan dengan metode DNA barcoding menggunakan primer 18S rDNA. Hasil penelitian menunjukkan bahwa plankton yang teridentifikasi adalah zooplankton, yaitu Pegurus bernhardus, Canthocalanus pauper, Calanus finmarchicus, dan Copepoda pada stasiun B, Acartia longiremis dan Subeucalanus pileatus pada stasiun C, dan Oithona sp. pada stasiun D dan E.

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EBACH, MALTE C. "Taxonomy and the DNA Barcoding Enterprise." Zootaxa 2742, no. 1 (January 17, 2011): 67. http://dx.doi.org/10.11646/zootaxa.2742.1.5.

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DNA Barcoding is elusive to many taxonomists. Like the numbers in a barcode, barcoding attempts to link a type specimen with a part of its DNA, most commonly from the mitochondrial Cytochrome c Oxidase subunit I (COI) gene.

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Geary, Janis, Emma Camicioli, and Tania Bubela. "DNA barcoding in the media: does coverage of cool science reflect its social context?" Genome 59, no. 9 (September 2016): 738–50. http://dx.doi.org/10.1139/gen-2015-0210.

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Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.

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