scholarly journals Gap analysis for DNA barcodes of aquatic macroinvertebrate species in the Southeast of Italy

2021 ◽  
Vol 4 ◽  
Author(s):  
Valeria Specchia ◽  
Francesco Zangaro ◽  
Eftychia Tzafesta ◽  
Maurizio Pinna
Keyword(s):  
Gap Analysis ◽  
Dna Barcode ◽  
Single Species ◽  
Regional Level ◽  
Dna Barcodes ◽  
Aquatic Macroinvertebrate ◽  
Apulia Region ◽  
Dna Metabarcoding ◽  
Taxonomic Groups ◽  
Macroinvertebrate Species

DNA metabarcoding for the identification of species and ecosystem biomonitoring is a promising innovative approach. The applicability of this tool is at first dependent on the coverage of the DNA sequence reference libraries. We performed a gap analysis of available DNA barcodes in the international databases using the aquatic macroinvertebrate species checklist of the Apulia region in southeast Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups in particular at local/regional level. The DNA-barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more extensive use of the DNA metabarcoding. We also highlighted the opportunity to develop combinations of primers useful at the regional level. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Aquatina di Frigole” in the Apulia region) which are richer in humic substances than other aquatic environments and in which DNA metabarcoding remains under explored.

scholarly journals Gap Analysis for DNA Barcode Reference Libraries for Aquatic Macroinvertebrate Species in the Apulia Region (Southeast of Italy)

2020 ◽  
Vol 8 (7) ◽  
pp. 538
Author(s):  
Valeria Specchia ◽  
Eftychia Tzafesta ◽  
Gabriele Marini ◽  
Salvatore Scarcella ◽  
Simona D’Attis ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Gap Analysis ◽  
Dna Barcode ◽  
Regional Level ◽  
New Combination ◽  
Dna Barcodes ◽  
Aquatic Macroinvertebrate ◽  
Apulia Region ◽  
Taxonomic Groups ◽  
Macroinvertebrate Species

The use of molecular tools (DNA barcoding and metabarcoding) for the identification of species and ecosystem biomonitoring is a promising innovative approach. The effectiveness of these tools is, however, highly dependent on the reliability and coverage of the DNA sequence reference libraries and it also depends on the identification of primer sets that work on the broadest range of taxa. In this study, a gap analysis of available DNA barcodes in the international libraries was conducted using the aquatic macroinvertebrate species checklist of the Apulia region in the southeast of Italy. Our analyses show that 42% of the 1546 examined species do not have representative DNA barcodes in the reference libraries, indicating the importance of working toward their completeness and addressing this effort toward specific taxonomic groups. We also analyzed the DNA barcode reference libraries for the primer set used to barcode species. Only for 52% of the examined barcoded species were the primers reported, indicating the importance of uploading this information in the databases for a more effective DNA barcode implementation effort and extensive use of the metabarcoding method. In this paper, a new combination of primers has revealed its experimental effectiveness at least on the species belonging to the three most represented taxa in the aquatic ecosystems of the Apulia region, highlighting the opportunity to develop combinations of primers useful at the regional level and the importance of studying DNA barcode gaps at the local/regional level. The DNA barcode coverage also varies among different taxonomic groups and aquatic ecosystem types in which a large number of species are rare. We tested the application of the DNA barcoding single species to a lagoon ecosystem (the lagoon named “Acquatina di Frigole” in the Apulia region) and we sampled two macroinvertebrate species lacking DNA barcodes from “Aquatina di Frigole” NATURA 2000 Site IT9150003, Fabulina fabula and Tritia nitida, generated two new CO1 barcodes and added them to a DNA barcode reference library.

scholarly journals DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

2019 ◽  
Author(s):  
Hannah Weigand ◽  
Arne J. Beermann ◽  
Fedor Čiampor ◽  
Filipe O. Costa ◽  
Zoltán Csabai ◽  
...  
Keyword(s):  
Gap Analysis ◽  
Dna Barcode ◽  
Aquatic Biota ◽  
Data Systems ◽  
Content Quality ◽  
Private Data ◽  
Dna Metabarcoding ◽  
Identification Of Species ◽  
Taxonomic Groups ◽  
Future Work

AbstractEffective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilization of metabarcoding in aquatic biomonitoring.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

scholarly journals Using DNA barcodes to assess identity and diversity of Dendropsophus minutus: Failure?

Zootaxa ◽  
2008 ◽  
Vol 1691 (1) ◽  
pp. 67 ◽  
Author(s):  
M. ALEX SMITH
Keyword(s):  
Cytochrome C ◽  
Small Group ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Gene Region ◽  
Dna Barcodes ◽  
Taxonomic Groups

The 5' end (Folmer or Barcode region) of cytochrome c oxidase 1 (CO1) has been proposed as the gene region of choice for a standardized animal DNA barcode (Hebert et al. 2003). Concerns have been raised regarding the decision to utilize this particular mitochondrial gene region as a barcode. Nevertheless, widely divergent taxonomic groups have reported success using CO1 for both species identification and discovery. The utility of CO1 for barcoding amphibians was raised early on (Vences, et al. 2005) and concerns for this group were reported widely (Waugh 2007)—although some considered that the reporting of the concerns outstripped the data that had been analyzed at that point (Smith et al. 2008). Indeed, our analysis of CO1 for a small group of Holarctic amphibians was neither more difficult to generate nor to analyze than for other groups where we have utilized the technique.

scholarly journals Revision of the genus Megacraspedus Zeller, 1839, a challenging taxonomic tightrope of species delimitation (Lepidoptera, Gelechiidae)

ZooKeys ◽  
2018 ◽  
Vol 800 ◽  
pp. 1-278 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Dna Barcode ◽  
Single Species ◽  
Dna Barcodes ◽  
Female Adult ◽  
Phylogeographic History ◽  
Species Groups ◽  
Male Sex ◽  
Taxonomic Approach

The taxonomy of the Palearctic genusMegacraspedusZeller, 1839 (Lepidoptera, Gelechiidae) is revised, based on external morphology, genitalia and DNA barcodes. An integrative taxonomic approach supports the existence of 85 species which are arranged in 24 species groups (disputed taxa from other faunal regions are discussed). Morphology of all species is described and figured in detail. For 35 species both sexes are described; for 46 species only the male sex is reported, in one species the male is unknown, whereas in three species the female adult and/or genitalia morphology could not be analysed due to lack of material.DNA barcode sequences of the COI barcode fragment with > 500 bp were obtained from 264 specimens representing 62 species or about three-quarters of the species. Species delimitation is particularly difficult in a few widely distributed species with high and allegedly intraspecific DNA barcode divergence of nearly 14%, and with up to 23 BINs in a single species. Deep intraspecific or geographical splits in DNA barcode are frequently not supported by morphology, thus indicating a complex phylogeographic history or other unresolved molecular problems.The following 44 new species (22 of them from Europe) are described:Megacraspedusbengtssonisp. n.(Spain),M.junnilainenisp. n.(Turkey),M.similellussp. n.(Bulgaria, Romania, Turkey),M.golestanicussp. n.(Iran),M.tokarisp. n.(Croatia),M.nelisp. n.(France, Italy),M.faunierensissp. n.(Italy),M.gredosensissp. n.(Spain),M.bidentatussp. n.(Spain),M.fuscussp. n.(Spain),M.trineaesp. n.(Portugal, Spain),M.skouisp. n.(Spain),M.spinophallussp. n.(Spain),M.occidentellussp. n.(Portugal),M.granadensissp. n.(Spain),M.heckfordisp. n.(Spain),M.tenuiuncussp. n.(France, Spain),M.devoratorsp. n.(Bulgaria, Romania),M.brachypterissp. n.(Albania, Greece, Macedonia, Montenegro),M.barcodiellussp. n.(Macedonia),M.sumpichisp. n.(Spain),M.tabellisp. n.(Morocco),M.gallicussp. n.(France, Spain),M.libycussp. n.(Libya, Morocco),M.latiuncussp. n.(Kazahkstan),M.kazakhstanicussp. n.(Kazahkstan),M.knudlarsenisp. n.(Spain),M.tenuignathossp. n.(Morocco),M.glaberipalpussp. n.(Morocco),M.nupponenisp. n.(Russia),M.pototskiisp. n.(Kyrgyzstan),M.feminensissp. n.(Kazakhstan),M.kirgizicussp. n.(Afghanistan, Kazakhstan, Kyrgyzstan),M.ibericussp. n.(Portugal, Spain),M.steinerisp. n.(Morocco),M.gibeauxisp. n.(Algeria, Tunisia),M.multipunctellussp. n.(Turkey),M.teriolensissp. n.(Croatia, Greece, Italy, Slovenia),M.korabicussp. n.(Macedonia),M.skuleisp. n.(Spain),M.longivalvellussp. n.(Morocco),M.peslierisp. n.(France, Spain),M.pacificussp. n.(Afghanistan), andM.armatophallussp. n.(Afghanistan).NevadiaCaradja, 1920,syn. n.(homonym),CauloecistaDumont, 1928,syn. n.,ReichardtiellaFilipjev, 1931,syn. n., andVadeniaCaradja, 1933,syn. n.are treated as junior synonyms ofMegacraspedus. Furthermore the following species are synonymised:M.subdolellusStaudinger, 1859,syn. n.,M.tuttiWalsingham, 1897,syn. n., andM.grossisquammellusChrétien, 1925,syn. n. ofM.lanceolellus(Zeller, 1850);M.culminicolaLe Cerf, 1932,syn. n.ofM.homochroaLe Cerf, 1932;M.separatellus(Fischer von Röslerstamm, 1843),syn. n.andM.incertellusRebel, 1930,syn. n.ofM.dolosellus(Zeller, 1839);M.mareotidellusTurati, 1924,syn. n.ofM.numidellus(Chrétien, 1915);M.litovalvellusJunnilainen, 2010,syn. n.ofM.imparellus(Fischer von Röslerstamm, 1843);M.kaszabianusPovolný, 1982,syn. n.ofM.leuca(Filipjev, 1929);M.chretienella(Dumont, 1928),syn. n.,M.halfella(Dumont, 1928),syn. n., andM.arnaldi(Turati & Krüger, 1936),syn. n.ofM.violacellum(Chrétien, 1915);M.escalerellusSchmidt, 1941,syn. n.ofM.squalidaMeyrick, 1926.Megacraspedusribbeella(Caradja, 1920),comb. n.,M.numidellus(Chrétien, 1915),comb. n.,M.albella(Amsel, 1935),comb. n.,M.violacellum(Chrétien, 1915),comb. n., andM.grisea(Filipjev, 1931),comb. n.are newly combined inMegacraspedus.

scholarly journals Unravelling the plant diversity of the Amazonian canga through DNA barcoding

2021 ◽  
Author(s):  
Santelmo Vasconcelos ◽  
Gisele Nunes ◽  
Mariana Dias ◽  
Jamily Lorena ◽  
Renato Oliveira ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Plant Diversity ◽  
Vascular Plants ◽  
Dna Barcode ◽  
Brazilian Amazon ◽  
Dna Barcodes ◽  
Dna Metabarcoding ◽  
Industrial Mining ◽  
First Time ◽  
Species Being

The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harbouring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera and 115 families of vascular plants, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.

scholarly journals Mind the gap-analysis! – How complete are DNA barcode reference libraries for monitoring-relevant aquatic species in Europe?

2021 ◽  
Vol 4 ◽  
Author(s):  
Hannah Weigand
Keyword(s):  
Gap Analysis ◽  
General Pattern ◽  
Dna Barcode ◽  
Marine Species ◽  
Biotic Index ◽  
Reference Database ◽  
Data Systems ◽  
Freshwater Macroinvertebrates ◽  
Public Data ◽  
Dna Metabarcoding

Molecular species identification with DNA metabarcoding can potentially accelerate, streamline and standardise biomonitoring routines. Currently, it is tested how this new technique can be implemented for the European Water Framework Directive (WFD) and the European Marine Strategy Framework Directive (MSFD). To connect the results from DNA metabarcoding with the current monitoring routines, an extensive, high-quality DNA barcode reference database is required. Hence, a gap-analysis of the Barcode of Life Data Systems (BOLD) was performed as part of the EU-COST Action DNAqua-Net (Weigand et al. 2019), which was updated in 2021. It aimed to analyse the completeness of BOLD for species on the national WFD monitoring lists and for marine species on the ERMS (European Register of Marine Species) and AMBI (AZTI Marine Biotic Index) lists. The data were supplemented by MitoFish for freshwater fish and Diat.barcode for diatoms. Several thousands of species were included in the gap-analysis, although not all countries currently apply species-level data for all WFD biological quality elements. The barcode coverage of the different taxonomic groups varied strongly, with high levels (> 80%) for fish and freshwater vascular plants, and low levels for diatoms and freshwater plathelminths (< 15%). As a general pattern, species monitored by several countries had a higher coverage compared to those monitored only by a single country. The gap-analysis focused additionally on the availability of metadata (e.g., geographical origin of the specimen or determiner name) for the barcodes. Hence, we analysed if the data were stored public (with access to metadata) or private (without access to metadata) in BOLD or if the data were mined from GenBank (metadata are potentially available but not easy to access). Although public data were stored for many species (43% of freshwater macroinvertebrates and 21% of AMBI marine species), the proportion of species without public metadata was not neglectable (22% of freshwater macroinvertebrates and 22% of AMBI marine species). Another issue that emerged from the gap-analysis was that several deposited barcodes were identified by reverse taxonomy (RT), i.e., specimens were molecularly identified via its DNA barcode and the barcode itself is stored in BOLD with the associated species name. This can be problematic as originally misidentified samples can lead to false RT-identifications, making the data appear more trustworthy than it actually is. For the analysed freshwater macroinvertebrates, 39% of all barcodes and 65% of all public data originated from RT, impacting 11% of all monitored species. As the information about RT is only available for publicly stored data, the real impact of RT might even be higher.

scholarly journals Diatom DNA barcodes for forensic discrimination of drowning incidents

2020 ◽  
Vol 367 (17) ◽  
Author(s):  
Mengyan Liu ◽  
Yi Zhao ◽  
Yuzhe Sun ◽  
Ping Wu ◽  
Shiliang Zhou ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Type Specimens ◽  
Internal Organs ◽  
Sequencing Platform ◽  
Next Generation Sequencing Platform ◽  
Urgent Task ◽  
Dna Metabarcoding ◽  
Generation Sequencing

ABSTRACT The presence of diatoms in victim's internal organs has been regarded as a gold biological evidence of drowning. The idea becomes true at the advent of DNA metabarcoding. Unfortunately, the DNA barcode of diatoms are far from being applicable due to neither consensus on the barcode and nor reliable reference library.In this study we tested 23 pairs of primers, including two new primer pairs, Baci18S (V4 of 18S) and BacirbcL (central region of rbcL), for amplifying fragments of 16S/18S, 23S/28S, COI, ITS and rbcL. A total of five pairs of primers performed satisfactory for diatoms. We used three of them, 18S605 (V2 + V3 of 18S), Baci18S and BacirbcL, to barcode four water samples using next generation sequencing platform. The results showed that these primers worked well for NGS metabarcoding of diatoms. We suggest that 18S605, Baci18S and BacirbcL be barcodes of diatoms and the corresponding primer pairs be used. Considering a quite high proportion of sequences deposited in GenBank were mislabeled, the most urgent task for DNA barcoding of diatoms is to create standard sequences using correctly identified specimens, ideally type specimens.

scholarly journals Splitting the leafmining shield-bearer moth genus Antispila Hübner (Lepidoptera, Heliozelidae): North American species with reduced venation placed in Aspilanta new genus, with a review of heliozelid morphology

ZooKeys ◽  
2020 ◽  
Vol 957 ◽  
pp. 105-161
Author(s):  
Erik J. van Nieukerken ◽  
Charles S. Eiseman
Keyword(s):  
Central America ◽  
New Genus ◽  
Dna Barcode ◽  
Single Species ◽  
Dna Barcodes ◽  
Host Family ◽  
Main Host ◽  
Candidate Species ◽  
Coi Sequences ◽  
Rich Fauna

The new genus Aspilantagen. n. is described to harbour Nearctic heliozelid moths with reduced venation, previously placed in Antispila Hübner, 1825, with type species Antispila oinophylla van Nieukerken & Wagner, 2012. The erection of this genus has become possible now that monophyly has been supported by a recent phylotranscriptomics analysis. Six species are combined in this genus: Aspilanta oinophylla (van Nieukerken & Wagner, 2012), comb. n., A. hydrangaeella (Chambers, 1874), comb. n., A. ampelopsifoliella (Chambers, 1874), comb. n., A. voraginella (Braun, 1927), comb. n., A. argentifera (Braun, 1927), comb. n., A. viticordifoliella (Clemens, 1860), comb. n. and two candidate species are recognised. DNA barcode COI sequences of Malaise trapped specimens suggest a rich fauna of Aspilanta in Central America. All are leafminers, with Vitaceae as main host family, and single species feeding respectively on Hydrangeaceae and Myricaceae. The species are briefly diagnosed, and data on biology, DNA barcodes and distribution are provided. To place the genus in context, a review of heliozelid morphology and phylogeny is presented and a key to Nearctic genera is given. The genus is confined to North and Central America, possibly also occurring in South America. Aspilanta oinophylla is also an invasive species on grapevine in Italy. The genus is sister to Coptodisca Walsingham, 1895. Another species is removed from Antispila: Heliozela eugeniella (Busck, 1900), comb. n., feeding on Eugenia (Myrtaceae), from Florida.

scholarly journals An Overview of DNA-Based Applications for the Assessment of Benthic Macroinvertebrates Biodiversity in Mediterranean Aquatic Ecosystems

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 112
Author(s):  
Eftychia Tzafesta ◽  
Francesco Zangaro ◽  
Valeria Specchia ◽  
Maurizio Pinna
Keyword(s):  
Benthic Macroinvertebrates ◽  
Aquatic Ecosystems ◽  
Biodiversity Monitoring ◽  
Biodiversity Data ◽  
Management Tools ◽  
Aquatic Biodiversity ◽  
Current State ◽  
Dna Metabarcoding ◽  
Ecosystem Condition ◽  
Macroinvertebrate Species

The loss of aquatic biodiversity is increasing at a rapid rate globally. There is a worldwide effort to protect, preserve and restore aquatic ecosystems. For efficient biodiversity monitoring and reliable management tools, comprehensive biodiversity data are required. The abundance and species diversity of benthic macroinvertebrates are commonly used as indicators of the aquatic ecosystem condition. Currently, macroinvertebrate species biodiversity assessment is based on morpho-taxonomy, which could be enhanced by recent advances in DNA-based tools for species identification. In particular, DNA metabarcoding has the potential to identify simultaneously many different taxa in a pool of species and to improve aquatic biomonitoring significantly, especially for indicator species. This review is focused on the current state of DNA-based aquatic biomonitoring using benthic macroinvertebrates in the Mediterranean region.

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