A complement to DNA barcoding reference library for identification of fish from the Northeast Pacific

Genome ◽  
2021 ◽  
Author(s):  
Sergei V Turanov ◽  
Yuri Ph. Kartavtsev
Keyword(s):  
Dna Barcoding ◽  
North Pacific Ocean ◽  
Molecular Genetic ◽  
Dna Barcode ◽  
Fish Fauna ◽  
Threshold Value ◽  
Published Data ◽  
Northeast Pacific ◽  
Barcoding Gap ◽  
The North

The seas of the North Pacific Ocean are characterized by a large variety of fish fauna, including endemic species. Molecular genetic methods, often based on DNA barcoding approaches, have been recently used to determine species boundaries and identify cryptic diversity within these species. This study complements the DNA barcode library of fish from the Northeast Pacific area. A library based on 154 sequences of the mitochondrial <i>COI</i> gene from 44 species was assembled and analyzed. It was found that 39 species (89%) can be unambiguously identified by the clear thresholds forming a barcoding gap. Deviations from the standard 2% threshold value resulted in detection of the species <i>Enophrys lucasi </i>in the sample, which is not typical for the eastern part of the Bering Sea. This barcoding gap also made it possible to identify naturally occurring low values of interspecific divergence of eulittoral taxa <i>Aspidophoroides</i> and the deep-sea genus <i>Coryphaenoides</i>. Synonymy of the genus <i>Albatrossia</i> in favor of the genus <i>Coryphaenoides</i> is suggested based on both the original and previously published data.

scholarly journals Filling gaps in the DNA barcode library - Aquatic insects (Ephemeroptera, Plecoptera, Trichoptera) from semi-mountainous and mountainous rivers of Ecoregion 6 (North Macedonia)

2021 ◽  
Vol 4 ◽  
Author(s):  
Biljana Rimcheska ◽  
Yanka Vidinova
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Aquatic Insects ◽  
Molecular Genetic ◽  
Dna Barcode ◽  
Balkan Peninsula ◽  
Molecular Genetic Data ◽  
Medium Quality ◽  
Total Dna ◽  
Data Library

This research provides pivotal molecular genetic data on the community structure of aquatic insects from semi-mountainous and mountainous rivers from the 6th Ecoregion that belongs to the territory of North Macedonia. The aim of this research is to fill the gaps for barcoding the aquatic macroinvertebrates from the Balkan Peninsula and check if the existing barcode library could provide improved identifications for the specimens that were not taxonomically determined to the lowest level possible. We analyzed 95 specimens from which total DNA was extracted and the COI barcode region amplified and sequenced. The taxa were selected from 20 different localities of the territory of western part of North Macedonia. The selected specimens were not determined to species-level in order to test the efficiency of the DNA barcoding methodology and what is missing in the DNA barcoding data library. From the result from one plate (95 specimens) we obtained: 16 samples without barodes, or failed and 10 samples did not have a match in the BOLD database. In the remining 69 samples, three were misidentified. In the total of 69 barcoded species new for the fauna of North Macedonia, 11 are mayflies: Baetis melanonyx, Ecdyonurus vitoshensis, E. macani; stonefly Isoperla vjose; and caddisflies: Agapetus delicatulus, Athripsodes bilineatus, Glossosoma klotho, Lepidostoma basale, Helicopsyche bacescui, Tinodes unicolor and Odontocerum hellenicum. We have also four rarely found species: Zwicknia bifrons, Drussus tenellus, Hydropsyche botosaneanui and Hydropsyche bulbifera, and one species without barcode available as Ecdyonurus sp. SK2 (potential new species). We found 83% efficiency of DNA barcoding, where some samples failed or were with low or medium quality for some specimens, as for the representatives from the genera Baetis, Oxietyra and Rhyacophila. In conclusion we can confirm that 10 of the selected vouchers need to be further identified by morphology and to be added in the BOLD barcode library, and maybe we'll have the possibility to describe a new species as well.

scholarly journals DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns

2021 ◽  
Vol 9 ◽  
Author(s):  
Parvin Aghayeva ◽  
Salvatore Cozzolino ◽  
Donata Cafasso ◽  
Valida Ali-zade ◽  
Silvia Fineschi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Species Level ◽  
Floristic Survey ◽  
Barcoding Gap ◽  
Plant Groups ◽  
History Of ◽  
Nuclear Its ◽  
Species Assignment ◽  
Assignment Success

DNA barcoding has rapidly become a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here, we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) for correct species assignment in a floristic survey on the Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups, we tested whether our selection of barcode markers allows identification of the “barcoding gap” in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that the rate of species-level resolution amongst selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower than the nuclear ITS marker. The latter confirmed, in orchids, both the existence of a barcoding gap and that all accessions of the same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal.The ITS marker resulted in its being the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS were revealed as the most promising plant barcode marker, we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.

scholarly journals A database of net zooplankton of the Far East seas and adjacent Pacific Ocean waters

2021 ◽  
Author(s):  
Igor V. Volvenko
Keyword(s):  
Pacific Ocean ◽  
North Pacific ◽  
North Pacific Ocean ◽  
World Ocean ◽  
Operating Experience ◽  
Time Of Day ◽  
Anthropogenic Factors ◽  
Published Data ◽  
The North ◽  
The North Pacific

Abstract. This article describes the unique database of zooplankton collected by the large Juday net in 1984–2013 in the Chukchi, Bering, Okhotsk, Japan seas and the North Pacific Ocean: the sources and extent of the information contained therein, its benefits and drawbacks, the first operating experience and prospects. The information in this database has already been used to quantify the inventory of marine biological resources and appraise the waters of the North Pacific. In particular, in 2016, five tabular reference books were created and printed containing the species composition, occurrence and abundance of zooplankton in the surveyed area. The data is aggregated by species, developmental stages, size fractions, regions, vertical layers of water, light and dark time of day, four seasons of the year and perennial periods. This information has recently been verified, corrected, translated into English and from text to digital format to increase its availability to the scientific community worldwide (Volvenko, 2021 https://doi.org/10.5281/zenodo.4448646). The substantial volume and high quality of the collated data, along with the information presented in reference books and previously published data on macrofauna and the nutrition of common fish and squid, will enable the next important steps to be taken to understand the Far Eastern seas and the Pacific – one of the most productive and economically important regions of the world ocean. The scope of application of this data is fundamental to the management of marine resources, aquaculture development, nature conservation, and assessment of the damage of various anthropogenic factors on nature.

A reliable DNA barcode reference library for the identification of the North European shelf fish fauna

2014 ◽  
pp. n/a-n/a ◽  
Author(s):  
Thomas Knebelsberger ◽  
Monica Landi ◽  
Hermann Neumann ◽  
Matthias Kloppmann ◽  
Anne F. Sell ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Fish Fauna ◽  
Reference Library ◽  
The North ◽  
European Shelf

scholarly journals DNA Barcoding Subtropical Aphids and Implications for Population Differentiation

Insects ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 11 ◽  
Author(s):  
Qiang Li ◽  
Jun Deng ◽  
Cui Chen ◽  
Linda Zeng ◽  
Xiaolan Lin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Population Differentiation ◽  
Dna Barcode ◽  
Threshold Value ◽  
Aphid Species ◽  
Sampling Effort ◽  
Pest Species ◽  
Aphis Spiraecola ◽  
Geographical Regions ◽  
Taxonomic Groups

DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.

scholarly journals Are there widespread peracarid species in the deep sea (Crustacea: Malacostraca)?

2012 ◽  
Vol 33 (2) ◽  
pp. 139-162 ◽  
Author(s):  
Angelika Brandt ◽  
Magdalena Błażewicz-Paszkowycz ◽  
Roger Bamber ◽  
Ute Mühlenhardt-Siegel ◽  
Marina Malyutina ◽  
...  
Keyword(s):  
Deep Sea ◽  
Molecular Genetic ◽  
Wide Distribution ◽  
Published Data ◽  
Genetic Studies ◽  
Widespread Species ◽  
Cosmopolitan Species ◽  
The North ◽  
Large Databases

Are there widespread peracarid species in the deep sea (Crustacea: Malacostraca)?The global zoogeographic distribution of the most widespread peracarid species occurring in three or more ocean basins below 2000 m is analysed. Basing on the published data we investigated 45 peracarid species, which have a most widespread distribution and most likely are cosmopolitan. Thirty-three species have a wide distribution in the Northern Hemisphere. Most species occur in the North Atlantic, however, 16 of these species occur also in the North Pacific, a more limited number of species occurs in the South Atlantic or South Pacific The Southern Ocean displays some special zoogeographic features and 22 widespread species occur there below 2000 m, including highly eurybathic ones. In total, 11 of the analysed species occur in all oceans.Eucopia australis(Lophogastrida),Munneurycope murrayi(Isopoda) andEurythenes gryllus(Amphipoda) are the species with the widest distributions. Other peracarids occurring in all oceans are: the isopodsParamunnopsis oceanicaandEurycope sarsi, the mysidCaesaromysis hispidathe lophogastridEucopia unguiculata, the amphipodMesopleustes abyssorumand the tanaidsExspina typica, Paranarthura insignisandPseudotanais nordenskioldi. No cumacean species has been reported with an ocean-wide distribution butCampylaspis glabraoccurs in the Atlantic, Indian and Pacific oceans. Among plenty of rare species in each order there are only few species with wide distribution records. There is evidence from molecular genetic studies that some of the widespread peracarids represent several cryptic species, however, some,e.g. Eucopia australis, seem to be truly cosmopolitan species. Geography of sampling is biasing our view of biogeography. The history and quality of taxonomic work as well as the reliability of geo- graphic records (quality control of large databases) limits our investigations of widespread or cosmopolitan species as much as the limited knowledge of variation within most species causes difficulties in defining morpho-species with certainty.

scholarly journals Affirmation of dna barcoding as a powerful tool in cataloguing medicinal and aromatic plants in mediterranean forests

2013 ◽  
Author(s):  
Αγγελική Λαΐου
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Mediterranean Forests ◽  
Aromatic Plants ◽  
Medicinal And Aromatic Plants ◽  
Barcoding Gap

Από την προϊστορική εποχή, ο άνθρωπος χρησιμοποιεί τα φυτά ως φάρμακα ενώ τα τελευταία χρόνια τα φαρμακευτικά και αρωματικά φυτά (MAPs) που συλλέγονται φυσικά από το περιβάλλον διακατέχουν πρωταγωνιστικό ρόλο. Τα ΦΑΦ (MAPs - medicinal and aromatic plants) Φαρμακευτικά και Αρωματικά Φυτά κατέχουν πρωταγωνιστικό ρόλο στη σύγχρονη θεραπευτική αποτελώντας παράλληλα έναν σημαντικό οικονομικό πόρο. Κατά συνέπεια, τα ΦΑΦ αποτελούν ιδανική περίπτωση για την ανάπτυξη της γενετικής μεθόδου κωδικοποίησης DNA. Στην παρούσα διδακτορική διατριβή, περισσότερα από 100 δείγματα συλλέχθηκαν από διαφορετικές βιογεωγραφικές περιοχές της Ιταλίας και της Ελλάδας (για κάθε είδος, τρεις προελεύσεις δειγμάτων από την Ιταλία και μία από την Ελλάδα) συμπεριλαμβανομένων επίσης ορισμένων εκπροσώπων ειδών από άλλες χώρες για γενετική σύγκριση. Ως εκ τούτου, συλλεχθηκαν και αναλύθηκαν 38 φαρμακευτικά και αρωματικά φυτικά είδη, που προέρχονται από 22 γένη, με συνολικό αριθμό 30 διαφορετικών προελεύσεων που ανήκουν σε 17 οικογένειες φυτών. Χρησιμοποιήθηκε "πυρήνας barcode" για τα φυτά της ξηράς rbcL και matK, ενώ δοκιμάστηκε ο trnH-psbA ως πρόσθετος δείκτης.Ο RbcL παρουσίασε 100% επιτυχία πολλαπλασιασμού, ακολουθούμενος από τον trnH-psbA 98%, ενώ ο matK δεν ήταν σε θέση να πολλαπλασιάσει ορισμένες συγκεκριμένες ομάδες φυτών (συνολική επιτυχία ενίσχυσης 91). Η επιτυχία διάκρισης των ειδών επιχειρήθηκε με τη χρήση διαδοχικών αλληλουχιών με τη χρήση Blastclust, την παρουσία του barcoding-gap (μη διορθωμένες p-αποστάσεις), εξετάστηκε η μονοφιλία των ειδών μέσω της απεικόνισης του δενδρογράμματος RAxML ελέγχοντας τις γενετικές αποστάσεις των ειδών ενώ τέλος λήφθηκε υπόψη η διάκριση των ειδών μέσω της αξιολόγησης του GenBank. Οι παραπάνω προσεγγίσεις αποδίδουν παρόμοια αποτελέσματα σε επίπεδο διακρίσεων των ειδών χρησιμοποιώντας όλους τους συνδυασμένους δείκτες. Η περιοχή trnH-psbA συγκέντρωσε τις υψηλότερες τιμές γενετικής μεταβλητότητας. Ωστόσο, αυτή η απόκλιση δεν επέτρεψε αξιόπιστη ευθυγράμμιση όλων των αλληλουχιών και, κατά συνέπεια, συνέβαλε στην απουσία του barcoding gap. Όσον αφορά τα αποτελέσματα που ανακτήθηκαν από τις καταχωρήσεις των αλληλουχιών στην πλατφόρμα Genbank, το χαμηλότερο ποσοστό μοριακών δεδομένων ανακτήθηκε από την MatK (το 37% των ειδών στη GenBank), ακόμη και αν θεωρείται ένας από τους πιο διαδεδομένους και προτεινόμενους βασικούς κώδικες με τη μεγαλύτερη διακριτική ισχύ. Η πλειονότητα των δεδομένων που καταχωρήθηκαν για την περιοχή trnH-psbA (65% των ειδών στη GenBank) αποδείχθηκε ικανοποιητική με αρκετά καλή κάλυψη, τονίζοντας ότι αυτός ο δείκτης, συνίσταται ως η πιο ευρέως χρησιμοποιούμενη πλαστιδική περιοχή. Γενικά, πρέπει να δοθεί ιδιαίτερη προσοχή στη διατήρηση της βιοποικιλότητας των φαρμακευτικών και αρωματικών φυτών, μέσω της ανάπτυξης μίας πλήρους, ολοκληρωμένης βάσης δεδομένων DNA. Ένας σημαντικός περιορισμός για την ανάπτυξη της μεθόδου του DNA barcoding σε πιθανούς δυνητικούς χρήστες συσχετίζεται άμεσα με την ελλιπή λίστα αναφοράς της βάσης δεδομένων, καθώς και η άμεση ανάπτυξη περισσότερο εξελιγμένων μεθόδων ομοιότητας με μικρότερη πιθανότητα σφαλμάτων. Επιπλέον, η χρήση τέταρτου δείκτη θα μπορούσε να είναι αναγκαία για την απόκτηση επαρκούς κάλυψης αναγνώρισης και διαχωρισμού των ειδών. Εν κατακλείδι, η παρούσα διδακτορική διατριβή υπογραμμίζει τη χρησιμότητα του DNA barcode ως ένα ελπιδοφόρο εργαλείο για την παροχή πρακτικής και τυποποιημένης αναγνώρισης των φαρμακευτικών και αρωματικών φυτών συμβάλλοντας έτσι στη διατήρηση και τον έλεγχο του εμπορίου αυτών των πολύτιμων φυτικών πόρων.

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