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

2021 ◽  
Vol 4 ◽  
Author(s):  
Valentina Slavevska Stamenkovic ◽  
Jelena Hinic ◽  
Michal Grabowski ◽  
Tomasz Mamos ◽  
Leona Lovrenčić ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Morphological Characters ◽  
Freshwater Ecosystems ◽  
Aquatic Biota ◽  
Reference Library ◽  
Irreversible Loss ◽  
The Republic ◽  
Different Parts ◽  
Comprehensive Study

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

scholarly journals A DNA barcode reference library of the French Polynesian shore fishes

2019 ◽  
Author(s):  
Erwan Delrieu-Trottin ◽  
Jeffrey T. Williams ◽  
Diane Pitassy ◽  
Amy Driskell ◽  
Nicolas Hubert ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Biological Diversity ◽  
Dna Barcode ◽  
Reef Fishes ◽  
French Polynesia ◽  
Morphological Characters ◽  
Reference Library ◽  
Society Islands ◽  
Extensive Collection ◽  
I Gene

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

An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens

Zootaxa ◽  
2011 ◽  
Vol 3104 (1) ◽  
pp. 42 ◽  
Author(s):  
MICHELE CESARI ◽  
ILARIA GIOVANNINI ◽  
ROBERTO BERTOLANI ◽  
LORENA REBECCHI
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Intraspecific Variability ◽  
Original Description ◽  
Morphological Characters ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Type Locality ◽  
Moss Sample ◽  
Voucher Specimens

We have in recent papers revealed that an integrative taxonomy approach helps to solve taxonomic problems in tardigrades. However, whole tardigrades are required for DNA work, which leaves no hologenophore voucher specimens with adult morphology. Using a novel methodology for the Tardigrada, we introduce the practice of collecting high quality maximum magnification light microscopy images of recently thawed animals to act as hologenophore voucher specimens of animals later used for DNA barcode sequencing. Within the framework of a DNA barcoding project on tardigrades, we collected a moss sample from the type locality of Macrobiotus terminalis Bertolani & Rebecchi, 1993 (Castelsantangelo, Central Apennines, Italy), a species of the “Macrobiotus hufelandi group”. Within the moss sample we found several animals and eggs with a morphology that corresponded to the original description of M. terminalis, while others were attributable to Macrobiotus macrocalix Bertolani & Rebecchi, 1993. In this study, molecular (cox1 mtDNA) analyses demonstrated no intraspecific variability in M. terminalis from the type locality but very large interspecific differences when compared with M. macrocalix and GenBank data for other species within the M. “hufelandi group”. There was also a large difference between our M. terminalis sequences and the GenBank data of a specimen attributed to the same species. The GenBank sequence originated from a population in the Northern Apennines, whose morphology appeared to be like that of the specimens of the locus typicus. This confirmed the importance in utilising material from the type locality for linking molecular data to the species’ morphological characters. Our paper underlines the importance of an integrative taxonomy in species diagnoses and demonstrates a scenario where morphological observations alone are not always sufficient. Lastly, this work adds reliable information to the sequence reference library that provides a useful building block for further studies on similar and related tardigrade taxa.

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

Genome ◽  
2020 ◽  
pp. 1-11 ◽  
Author(s):  
Tomasz Rewicz ◽  
Arnold Móra ◽  
Grzegorz Tończyk ◽  
Ada Szymczak ◽  
Michal Grabowski ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Related Species ◽  
Dna Barcode ◽  
Taxonomic Status ◽  
Index Number ◽  
Reference Library ◽  
Nuclear Markers ◽  
Closely Related Species ◽  
Maltese Islands ◽  
Morphological Species

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

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

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

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

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

2019 ◽  
Author(s):  
Muhammad Tayyib Naseem ◽  
Muhammad Ashfaq ◽  
Arif Muhammad Khan ◽  
Akhtar Rasool ◽  
Muhammad Asif ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Insect Pests ◽  
Rhopalosiphum Padi ◽  
Aphis Gossypii ◽  
Dna Barcode ◽  
Reference Sequence ◽  
Neighbor Joining ◽  
Reference Library ◽  
Index Numbers ◽  
Intraspecific Divergence

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

scholarly journals BIOSCAN - Revealing Eukaryote Diversity, Dynamics, and Interactions

2019 ◽  
Vol 3 ◽  
Author(s):  
Donald Hobern ◽  
Paul Hebert
Keyword(s):  
Dna Barcoding ◽  
Species Interactions ◽  
Dna Barcode ◽  
Cost Effective ◽  
Global Scale ◽  
Lessons Learned ◽  
Reference Library ◽  
Local Conservation ◽  
Insect Fauna ◽  
Sequencing Platforms

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

scholarly journals Morphological features of larvae of Drusus osogovicus Kumanski, 1980 (Insecta, Trichoptera) from the Republic of North Macedonia, DNA barcoding of the species and notes on its ecology and distribution

2021 ◽  
Vol 4 ◽  
Author(s):  
Jelena Hinic ◽  
Valentina Slavevska Stamenkovic ◽  
Halil Ibrahimi ◽  
Mladen Kučinić ◽  
Julijana Arsovska ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Larval Stage ◽  
Morphological Characters ◽  
Morphological Features ◽  
Diagnostic Characters ◽  
Ecological Preferences ◽  
The Republic

The Balkan endemic caddisfly species Drusus osogovicus Kumanski, 1980 that was previously known only from Bulgaria was recently reported from the Republic of North Macedonia as well. However, all data on the presence of the species included only adult specimens as the larval stage remained unknown. In the following study we present the first description of the larval stage of Drusus osogovicus based on morphological characters. In order to prove the conspecificity between the larvae and the adults, DNA barcoding of the specimens was also conducted. Furthermore, lists of the crucial diagnostic characters present only in D. osogovicus larvae as well as information on the distribution and ecological preferences of the species are also provided.

Pathology associated with three new Clinostomum metacercariae from Argentina with morphological and DNA barcode identification

2020 ◽  
Vol 94 ◽  
Author(s):  
M.M. Montes ◽  
S.E. Plaul ◽  
Y. Croci ◽  
M. Waldbillig ◽  
W. Ferrari ◽  
...  
Keyword(s):  
South America ◽  
Inflammatory Response ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Inflammatory Cells ◽  
Morphological Characters ◽  
Pathological Analysis ◽  
Vascular Congestion ◽  
Morphological Approach ◽  
Parasitological Study

Abstract In the Laboratory of Parasites of Fishes, Crustaceans and Mollusks (CEPAVE), we undertook a parasitological study on three species of fish from the Espinal and Esteros del Iberá ecoregions of Argentina. Clinostomid metacercariae were found parasitizing Characidium rachovii, Crenicichla vittata and Gymnogeophagus balzanii. In this study, we analysed the damage that these parasites inflict on their hosts through the evaluation of histological sections. In addition, Clinostomum metacercariae were identified using morphological characters and DNA barcoding. In the pathological analysis, we observed that muscle tissue was the most affected. The inflammatory response showed vascular congestion areas and infiltration of numerous inflammatory cells, mainly lymphocytes. The molecular and morphological approach supports the presence of three new lineages of clinostomid metacercariae in Argentina. This could lead to the discovery of a high number of lineages or species of Clinostomum from South America.

scholarly journals DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11424
Author(s):  
Lukas Zangl ◽  
Elisabeth Glatzhofer ◽  
Raphael Schmid ◽  
Susanne Randolf ◽  
Stephan Koblmüller
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Dna Barcode ◽  
Morphological Diversity ◽  
Morphological Characters ◽  
Coi Gene ◽  
Phylogeographic Structure ◽  
Geographic Scale ◽  
Study Region ◽  
Statistical Parsimony

Background Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region. Methods Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites. Results Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and especially in B. westwoodi.

scholarly journals DNA barcoding of marine fish species from Rongcheng Bay, China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5013 ◽  
Author(s):  
Lijuan Wang ◽  
Zhihao Wu ◽  
Mengxia Liu ◽  
Wei Liu ◽  
Wenxi Zhao ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Dna Barcode ◽  
Gc Content ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Reference Library ◽  
Fish Species Identification ◽  
Northern Yellow Sea ◽  
Coastal Bay

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

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