Species-specific fish larvae drift in anthropogenically constructed riparian zones on the Vienna impoundment of the River Danube, Austria: Species occurrence, frequencies, and seasonal patterns based on DNA barcoding

In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.

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Temporal Detection Limits of Remnant Larval Bloodmeals in Nymphal Ixodes scapularis (Say, Ixodida: Ixodidae) Using Two Next-Generation Sequencing DNA Barcoding Assays

Journal of Medical Entomology ◽

10.1093/jme/tjaa192 ◽

2020 ◽

Author(s):

Genevieve A M Lumsden ◽

Evgeny V Zakharov ◽

Sarah Dolynskyj ◽

J Scott Weese ◽

L Robbin Lindsay ◽

...

Keyword(s):

Next Generation Sequencing ◽

Dna Barcoding ◽

Ixodes Scapularis ◽

Life Stage ◽

Next Generation ◽

Host Detection ◽

Host Identification ◽

Species Specific ◽

Generation Sequencing ◽

Assay Detection

Abstract Using next-generation sequencing DNA barcoding, we aimed to determine: 1) if the larval bloodmeal can be detected in Ixodes scapularis nymphs and 2) the post-moult temporal window for detection of the larval bloodmeal. Subsets of 30 nymphs fed on a domestic rabbit (Oryctolagus cuniculus Linnaeus, Lagomorphia: Leporidae) as larvae were reared and frozen at 11 time points post-moult, up to 150 d. Vertebrate DNA was amplified using novel universal (UP) and species-specific primers (SSP) and sequenced for comparison against cytochrome c oxidase subunit I barcodes to infer host identification. Detectable bloodmeals decreased as time since moult increased for both assays. For the SSP assay, detection of bloodmeals decreased from 96.7% (n = 29/30) in day 0 nymphs to 3.3% (n = 1/30) and 6.7% (n = 2/30) at 4- and 5-mo post-moult, respectively. A shorter temporal detection period was achieved with the UP assay, declining from 16.7% (n = 5/30) in day 0 nymphs to 0/30 in 3-d-old nymphs. Bloodmeal detection was nonexistent for the remaining cohorts, with the exception of 1/30 nymphs at 2-mo post-moult. Host detection was significantly more likely using the SSP assay compared to the UP assay in the first three time cohorts (day 0: χ 2 = 39.1, P < 0.005; day 2: χ 2 = 19.2, P < 0.005; day 3: χ 2 = 23.3, P < 0.005). Regardless of the primer set used, the next-generation sequencing DNA barcoding assay was able to detect host DNA from a larval bloodmeal in the nymphal life stage; however, a short window with a high proportion of detection post-moult was achieved.

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Duplex DNA barcoding allows accurate species determination of morphologically similar limpets (Patella spp.) from non-destructive sampling

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315416000813 ◽

2016 ◽

Vol 97 (7) ◽

pp. 1479-1482 ◽

Cited By ~ 1

Author(s):

Thomas J. Ashton ◽

Meriem Kayoueche-Reeve ◽

Andrew J. Blight ◽

Jon Moore ◽

David M. Paterson

Keyword(s):

Dna Barcoding ◽

Species Abundance ◽

Microscopic Analysis ◽

Cost Effective ◽

Field Studies ◽

Similar Species ◽

Species Determination ◽

Destructive Sampling ◽

Species Specific ◽

Non Destructive

Accurate discrimination of two morphologically similar species of Patella limpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.

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Interactions multispécifiques: répartition spatio-temporelle des larves de capelan (Mallotus villosus), d'éperlan (Osmerus mordax) et de hareng de l'Atlantique (Clupea harengus harengus) an sein de la communauté planctonique de l'estuaire moyen du Saint-Laurent

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f82-154 ◽

1982 ◽

Vol 39 (8) ◽

pp. 1164-1174 ◽

Cited By ~ 13

Author(s):

R. Courtois ◽

M. Simoneau ◽

J. J. Dodson

Keyword(s):

Fish Larvae ◽

Clupea Harengus ◽

Temporal Organization ◽

Physical Factors ◽

Osmerus Mordax ◽

Mallotus Villosus ◽

Saint Lawrence River ◽

Capelin Mallotus Villosus ◽

Clupea Harengus Harengus ◽

Species Specific

The study of the spatial and temporal organization of the planktonic community of the middle estuary of the Saint Lawrence River revealed that fish larvae were distributed in such a way as to minimize interactions between species. Smelt (Osmerus mordax) larvae were distributed upstream whereas capelin (Mallotus villosus) and Atlantic herring (Clupea harengus harengus) larvae were found downstream in June 1979. Capelin larvae were more abundant at the surface (0–20 m) whereas herring larvae were concentrated in deeper waters (20–60 m). The ecological separation observed was maintained by multiple physical factors and appeared to be the consequence of species-specific reproductive strategies. The abundance of chaetognaths, euphausiids, and amphipods in deeper waters suggests that these forms could be important predators of fish larvae. Herring larvae may be particularly vulnerable because of their distribution in deep water. Capelin larvae which are very abundant in June could also be vulnerable to predation during the diurnal migrations of the macroplankton. Smelt larvae appear to be little affected by predation from these forms as a result of their distribution in fresher waters.

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Spatial and seasonal patterns in fish larvae distribution in the Banda Sea (Indonesia)

Netherlands Journal of Sea Research ◽

10.1016/0077-7579(90)90081-q ◽

1990 ◽

Vol 25 (4) ◽

pp. 591-600 ◽

Cited By ~ 5

Author(s):

Soewito ◽

P.H. Schalk

Keyword(s):

Fish Larvae ◽

Seasonal Patterns

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The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata

PeerJ ◽

10.7717/peerj.8755 ◽

2020 ◽

Vol 8 ◽

pp. e8755

Author(s):

Adrian Kannan ◽

Suganiya Rama Rao ◽

Shyamala Ratnayeke ◽

Yoon-Yen Yow

Keyword(s):

16S Rdna ◽

Dna Barcoding ◽

Peninsular Malaysia ◽

Coi Gene ◽

Diagnostic Tools ◽

Species Discrimination ◽

Pomacea Canaliculata ◽

Agricultural Wetlands ◽

Barcoding Gap ◽

Species Specific

Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.

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DNA barcoding of Aristolochia plants and development of species-specific multiplex PCR to aid HPTLC in ascertainment of Aristolochia herbal materials

PLoS ONE ◽

10.1371/journal.pone.0202625 ◽

2018 ◽

Vol 13 (8) ◽

pp. e0202625 ◽

Cited By ~ 5

Author(s):

Piroonrat Dechbumroong ◽

Surattana Aumnouypol ◽

Jessada Denduangboripant ◽

Suchada Sukrong

Keyword(s):

Multiplex Pcr ◽

Dna Barcoding ◽

Species Specific

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Mass appearance of the Ponto-Caspian invader Pontogammarus robustoides in the River Tisza catchment: bypass in the southern invasion corridor?

Knowledge and Management of Aquatic Ecosystems ◽

10.1051/kmae/2020003 ◽

2020 ◽

pp. 9 ◽

Cited By ~ 1

Author(s):

Zoltán Csabai ◽

Péter Borza ◽

Tomasz Rewicz ◽

Bálint Pernecker ◽

Balázs J. Berta ◽

...

Keyword(s):

Dna Barcoding ◽

Western Europe ◽

Main Channel ◽

Fish Stocking ◽

Ship Traffic ◽

Dispersal Barrier ◽

River Danube ◽

Pontogammarus Robustoides ◽

First Time ◽

Invasion Corridor

The river Danube is the backbone of the ‘southern invasion corridor’, one of the most important passages for the spread of Ponto-Caspian invaders in Europe. However, not all of these species used the passive or active upstream movement in the main channel to reach the upper sections and tributaries, some found detours. Mass occurrences of the Ponto-Caspian peracarid, Pontogammarus robustoides (Sars, 1894) were recorded at 17 sites along the entire Hungarian section of the River Maros, for the first time in the River Tisza catchment and also in Hungary. Those populations are found ca. 707 km upstream from the closest known and confirmed locality in the lower Danube section. We confirmed their identity by DNA barcoding and showed that all individuals fit in with the lower Danube population, thus identifying the source of this introduction. The most likely vector allowing the jump dispersal of the species is fish stocking in the Romanian section of the River Maros, which − combined with downstream drift to the Serbian Danube section and the relatively busy ship traffic between Belgrade and Vienna − might provide the opportunity to bypass the dispersal barrier represented by the unregulated Middle Danube and open the way towards Western Europe.

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DNA barcoding of fish larvae reveals uncharacterised biodiversity in tropical peat swamps of New Guinea, Indonesia

Marine and Freshwater Research ◽

10.1071/mf16078 ◽

2017 ◽

Vol 68 (6) ◽

pp. 1079 ◽

Cited By ~ 3

Author(s):

Arif Wibowo ◽

Niklas Wahlberg ◽

Anti Vasemägi

Keyword(s):

Dna Barcoding ◽

Fish Larvae ◽

Juvenile Fish ◽

Significant Proportion ◽

New Guinea ◽

Spatial And Temporal Variability ◽

Species Identity ◽

Additional Species ◽

Tropical Peat ◽

Peat Swamp

The Indonesian archipelago, Borneo, Sumatra and West New Guinea (Papua), hosts half of the world’s known tropical peat swamps, which support a significant proportion of the estimated biodiversity on Earth. However, several species groups that inhabit peat swamp environments remain poorly characterised and their biology, particularly during early life stages, is not well understood. In the present study we characterised larval and juvenile fish biodiversity, as well as spatial and temporal variability, in a pristine peat swamp environment of the River Kumbe in West New Guinea, Indonesia, based on analysis of the mitochondrial cytochrome-c oxidase subunit 1 (COI) sequence (501bp). Altogether, 10 fish species were detected in the peat swamp habitat during the larval and juvenile stages, whereas 13 additional species were caught at older stages. Twelve species were detected only in a single site, whereas some species, such as the Western archerfish (Toxotes oligolepis) and Lorentz’s grunter (Pingalla lorentzi), were observed in all sampling sites. The occurrence of fish larvae also varied temporally for several species. In contrast with many earlier DNA barcoding studies in fish, we were not able to determine the species identity for a large proportion of sequenced larvae (68%) because of the lack of corresponding COI sequences in the reference dataset. Unidentified sequences clustered into five separate monophyletic clades. Based on genetic divergences, the putative taxonomic origin for the five morphotypes are Atherinidae, Osteoglossidae, Terapontidae and Gobiidae.

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