Comment on "Identifying spiders through DNA barcodes"

2005 ◽  
Vol 83 (3) ◽  
pp. 498-504 ◽  
Author(s):  
Lorenzo Prendini
Keyword(s):  
Mitochondrial Gene ◽  
Cost Effective ◽  
Identification System ◽  
Morphological Identification ◽  
Life Stages ◽  
Dna Barcodes ◽  
Cytochrome C Oxidase I ◽  
Taxonomic Impediment ◽  
Gene Coding ◽  
Global Identification

R.D.H. Barrett and P.D.N Hebert have demonstrated that it is possible to identify members of a mostly local spider fauna using a short fragment of the mitochondrial gene coding for cytochrome c oxidase I. There are instances where DNA-based identification may be very useful, e.g., in identifying juvenile life stages of groups in which adults are required for morphological identification, or matching morphologically different sexes or life stages when those associations are unknown. DNA-based identification may be the easiest and most cost-effective way, or even the only feasible way, to address some of these questions. However, these are also the least challenging problems in taxonomy, and their solution is unlikely to relieve the "taxonomic impediment". Furthermore, to promote the utility of DNA barcoding as a global identification system, these authors must demonstrate that their approach works for distinguishing all the members of a speciose clade, wherever in the world they occur. Much of diversity occurs allopatrically and neither the study by R.D.H. Barrett and P.D.N. Hebert, nor any other presented to date, even begins to address the feasibility of DNA-based identification at this level of detail.

Identifying spiders through DNA barcodes

2005 ◽  
Vol 83 (3) ◽  
pp. 481-491 ◽  
Author(s):  
Rowan D.H Barrett ◽  
Paul D.N Hebert
Keyword(s):  
Mating Systems ◽  
Mitochondrial Gene ◽  
Model Systems ◽  
Dna Barcodes ◽  
Cytochrome C Oxidase I ◽  
Accurate Identification ◽  
Spider Species ◽  
Taxonomic Impediment ◽  
Gene Coding ◽  
Identification Tool

With almost 40 000 species, the spiders provide important model systems for studies of sociality, mating systems, and sexual dimorphism. However, work on this group is regularly constrained by difficulties in species identification. DNA-based identification systems represent a promising approach to resolve this taxonomic impediment, but their efficacy has only been tested in a few groups. In this study, we demonstrate that sequence diversity in a standard segment of the mitochondrial gene coding for cytochrome c oxidase I (COI) is highly effective in discriminating spider species. A COI profile containing 168 spider species and 35 other arachnid species correctly assigned 100% of subsequently analyzed specimens to the appropriate species. In addition, we found no overlap between mean nucleotide divergences at the intra- and inter-specific levels. Our results establish the potential of COI as a rapid and accurate identification tool for biodiversity surveys of spiders.

DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae)

2006 ◽  
Vol 36 (2) ◽  
pp. 337-350 ◽  
Author(s):  
Shelley L Ball ◽  
Karen F Armstrong
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Insect Pest ◽  
Reference Sequence ◽  
Identification System ◽  
Pest Species ◽  
Dna Barcodes ◽  
Data Set

Reliable and rapid identification of exotic pest species is critical to biosecurity. However, identification of morphologically indistinct specimens, such as immature life stages, that are frequently intercepted at borders is often impossible. Several DNA-based methods have been used for species identification; however, a more universal and anticipatory identification system is needed. Consequently, we tested the ability of DNA "barcodes" to identify species of tussock moths (Lymantriidae), a family containing several important pest species. We sequenced a 617 base pair fragment of the mitochondrial gene cytochrome c oxidase 1 for 20 lymantriid species. We used these, together with other Noctuoidea species sequences from GenBank and the Barcoding of Life Database to create a "profile" or reference sequence data set. We then tested the ability of this profile to provide correct species identifications for 93 additional lymantriid specimens from a data set of mock unknowns. Of the unknowns, 100% were correctly identified by the cytochrome c oxidase 1 profile. Mean interspecific sequence (Kimura 2-parameter) divergence was an order of magnitude greater (14%) than mean intraspecific divergence (<1%). Four species showed deeper genetic divergences among populations. We conclude that DNA barcodes provide a highly accurate means of identifying lymantriid species and show considerable promise as a universal approach to DNA-based identification of pest insects.

scholarly journals A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1138
Author(s):  
Shamila Weerakoon Abeynayake ◽  
Sonia Fiorito ◽  
Adrian Dinsdale ◽  
Mark Whattam ◽  
Bill Crowe ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Pcr Amplification ◽  
Cost Effective ◽  
Diagnostic Methods ◽  
Coi Gene ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Accurate Identification ◽  
Invertebrate Pests ◽  
Barcode Sequencing

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 identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.

Potential Use of DNA Barcodes in Regulatory Science: Applications of the Regulatory Fish Encyclopedia

2008 ◽  
Vol 71 (1) ◽  
pp. 210-217 ◽  
Author(s):  
HAILE F. YANCY ◽  
TYLER S. ZEMLAK ◽  
JACQULINE A. MASON ◽  
JEWELL D. WASHINGTON ◽  
BRADLEY J. TENGE ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Fish Muscle ◽  
The United States ◽  
Identification System ◽  
Dna Barcodes ◽  
Potential Applications ◽  
Species Specific ◽  
Product Forms

The use of a DNA-based identification system (DNA barcoding) founded on the mitochondrial gene cytochrome c oxidase subunit I (COI) was investigated for updating the U.S. Food and Drug Administration Regulatory Fish Encyclopedia (RFE; http://www.cfsan.fda.gov/~frf/rfe0.html). The RFE is a compilation of data used to identify fish species. It was compiled to help regulators identify species substitution that could result in potential adverse health consequences or could be a source of economic fraud. For each of many aquatic species commonly sold in the United States, the RFE includes high-resolution photographs of whole fish and their marketed product forms and species-specific biochemical patterns for authenticated fish species. These patterns currently include data from isoelectric focusing studies. In this article, we describe the generation of DNA barcodes for 172 individual authenticated fish representing 72 species from 27 families contained in the RFE. These barcode sequences can be used as an additional identification resource. In a blind study, 60 unknown fish muscle samples were barcoded, and the results were compared with the RFE barcode reference library. All 60 samples were correctly identified to species based on the barcoding data. Our study indicates that DNA barcoding can be a powerful tool for species identification and has broad potential applications.

Species delimitation in the leaf beetle genus Macroplea (Coleoptera, Chrysomelidae) based on mitochondrial DNA, and phylogeographic considerations

2006 ◽  
Vol 37 (4) ◽  
pp. 467-479 ◽  
Author(s):  
Gregor Kölsch ◽  
Bo Vest Pedersen ◽  
Olof Biström
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Species Delimitation ◽  
Mitochondrial Gene ◽  
Leaf Beetle ◽  
Genetic Distances ◽  
Amino Acid Substitutions ◽  
Species Status ◽  
Leaf Beetles ◽  
Gene Coding

AbstractThe genus Macroplea Samouelle, 1819 is a group of highly specialized aquatic leaf beetles occurring in the Palaearctic. Since the members of this genus are morphologically very similar, we addressed the question of species identification and delimitation by analysing the second half of the mitochondrial gene coding for the cytochrome oxidase I (COI) subunit. Species limits are inferred from the multimodal frequency distribution of genetic distances between specimens: low genetic distances within a species are clearly set apart from distances between species. The species status of the hitherto controversial species M. japana (Jacoby, 1885) is confirmed. The pattern of nucleotide and amino acid substitutions is discussed in the light of functional domains of the COI molecule. Although the data are preliminary, the results provide new data on the distribution of the species. Together with the phylogenetic analysis they allow for a discussion of the phylogeography of the genus.

scholarly journals The dynamics of mitochondrial-linked gene expression among tissues and life stages in two contrasting strains of laying hens

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262613
Author(s):  
Clara Dreyling ◽  
Martin Hasselmann
Keyword(s):  
Gene Expression ◽  
Energy Metabolism ◽  
Life Span ◽  
Laying Hens ◽  
Mitochondrial Gene ◽  
Model Organisms ◽  
Life Stages ◽  
Mitochondrial Gene Expression ◽  
Cellular Energy ◽  
Cellular Energy Metabolism

The cellular energy metabolism is one of the most conserved processes, as it is present in all living organisms. Mitochondria are providing the eukaryotic cell with energy and thus their genome and gene expression has been of broad interest for a long time. Mitochondrial gene expression changes under different conditions and is regulated by genes encoded in the nucleus of the cell. In this context, little is known about non-model organisms and we provide the first large-scaled gene expression analysis of mitochondrial-linked genes in laying hens. We analysed 28 mitochondrial and nuclear genes in 100 individuals in the context of five life-stages and strain differences among five tissues. Our study showed that mitochondrial gene expression increases during the productive life span, and reacts tissue and strain specific. In addition, the strains react different to potential increased oxidative stress, resulting from the increase in mitochondrial gene expression. The results suggest that the cellular energy metabolism as part of a complex regulatory system is strongly affected by the productive life span in laying hens and thus partly comparable to model organisms. This study provides a starting point for further analyses in this field on non-model organisms, especially in laying-hens.

scholarly journals DNA barcode identification of commercial fish sold in Mexican markets

Genome ◽  
2018 ◽  
Vol 61 (6) ◽  
pp. 457-466 ◽  
Author(s):  
Stephanie Sarmiento-Camacho ◽  
Martha Valdez-Moreno
Keyword(s):  
Conservation Status ◽  
Dna Barcode ◽  
Common Species ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Commercial Fish ◽  
Sphyrna Lewini ◽  
Pangasianodon Hypophthalmus ◽  
Makaira Nigricans ◽  
The Status

The substitution of high-value fish species for those of lower value is common practice. Although numerous studies have addressed this issue, few have been conducted in Mexico. In this study, we sought to identify fresh fillets of fish, sharks, and rays using DNA barcodes. We analyzed material from “La Viga” in Mexico City, and other markets located on the Gulf and Caribbean coasts of Mexico. From 134 samples, we obtained sequences from 129, identified to 9 orders, 28 families, 38 genera, and 44 species. The most common species were Seriola dumerili, Pangasianodon hypophthalmus, Carcharhinus falciformis, Carcharhinus brevipinna, and Hypanus americanus. Pangasianodon hypophthalmus was most commonly used as a substitute for higher-value species. The substitution rate was 18% of the total. A review of the conservation status of the specimens identified against the IUNC list enabled us to establish that some species marketed in Mexico are threatened: Makaira nigricans, Lachnolaimus maximus, Hyporthodus flavolimbatus, and Isurus oxyrinchus are classified as vulnerable; Lopholatilus chamaeleonticeps and Sphyrna lewini are endangered; and the status of Hyporthodus nigritus is critical. These results will demonstrate to the Mexican authorities that DNA barcoding is a reliable tool for species identification, even when morphological identification is difficult or impossible.

scholarly journals PCR-based detection of cow’s milk in goat and sheep cheeses marketed in the Czech Republic

2011 ◽  
Vol 24 (No. 3) ◽  
pp. 127-132 ◽  
Author(s):  
E. Mašková ◽  
I. Paulíčková
Keyword(s):  
Mitochondrial Gene ◽  
Retail Trade ◽  
Animal Origin ◽  
The Czech Republic ◽  
Goat Cheese ◽  
Gene Coding ◽  
Reverse Primer ◽  
Pcr Method ◽  
Italian Origin ◽  
Species Specific

A method based on the polymerase chain reaction (PCR) principle was validated for detecting cow&rsquo;s milk in goat and sheep cheeses. DNA was isolated from the cheeses using the isolation kit Invisorb Spin Food I by Invitek Co., designed for the samples of animal origin. The PCR method applied utilizes the sequence of the mitochondrial gene coding cytochrome b which is specific for mammals. It uses the common forward primer and the reverse primer species-specific. After electrophoresis, cow DNA was characterised by the fragment of the size of 274 bp, goat DNA by the fragment of 157 bp, and sheep DNA by the fragment of 331 bp. The detection limit of the PCR method described (1%) was determined with model samples made from pure goat cheese with a defined addition of cheese made from cow&rsquo;s milk. The method validated was applied in the analysis of 17 goat cheeses and 7 sheep cheeses obtained from retail trade. Products of Czech, Slovak, French, Dutch, and Italian origin were examined. The presence of undeclared cow&rsquo;s milk was detected in three kinds of goat cheese and in one of sheep cheese. &nbsp;

scholarly journals Exploring unknown life stages of Arctic Tanytarsini (Diptera: Chironomidae) with DNA barcoding

Zootaxa ◽  
2011 ◽  
Vol 2743 (1) ◽  
pp. 27 ◽  
Author(s):  
ELISABETH STUR ◽  
TORBJØRN EKREM
Keyword(s):  
Dna Barcoding ◽  
Coi Gene ◽  
Morphological Identification ◽  
Life Stages ◽  
Larval Morphology ◽  
Gene Sequences ◽  
Larval Stages ◽  
Identification Keys ◽  
Close Resemblance ◽  
First Results

We present the first results from a project on Spitsbergen and Bear Island where the ultimate goal is to provide genetic and morphological identification keys to all species. Five Tanytarsini species have been recorded from Svalbard. By sequencing partial COI gene sequences, we have associated larvae of all of these, and describe the hitherto undescribed larval stages of Microspectra insignilobus Kieffer, M. radialis Goetghebuer and Tanytarsus heliomesonyctios Langton. We also present keys to larva, pupa and imagines of all Tanytarsini species found on Svalbard and discuss larval morphology in relationship to characters preserved in subfossil material. Of particular interest is the mandible and mentum of T. heliomsonyctios which show close resemblance to the tentatively associated larvae of Corynocera oliveri Lindeberg. An overview over Tanytarsus species with “lugens-type” larvae is given and the phylogenetic value of mandibular accessory teeth is briefly discussed.

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