Barcoding
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Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High-quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1-5P' DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high-quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.
- MeSH
- členovci genetika MeSH
- databáze nukleových kyselin * MeSH
- entomologie MeSH
- polymerázová řetězová reakce MeSH
- respirační komplex IV genetika MeSH
- sekvenční analýza DNA MeSH
- soudní vědy * MeSH
- taxonomické DNA čárové kódování * MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
This review is focused on identification of bacterial species by their antigenes by barcoding oligonucleotides by application of magnetic micro and nanoparticles. In the first part of this review is discussed the structures and types of magnetic particles and their synthesis. In the next and the most important part we described the principle and the existing status of barcoding system and antigenes markers for identification of organisms such as animals, plants and microorganisms.
- Klíčová slova
- biobarcode assay, magnetické mikročástice, DNA barkódování,
- MeSH
- kovové nanočástice * MeSH
- magnetické nanočástice MeSH
- magnetismus * MeSH
- molekulární sondy - techniky MeSH
- oligonukleotidy MeSH
- protilátky MeSH
- sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
- taxonomické DNA čárové kódování * metody využití MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
Understanding interactions between herbivores and parasitoids is essential for successful biodiversity protection and monitoring and for biological pest control. Morphological identifications employ insect rearing and are complicated by insects' high diversity and crypsis. DNA barcoding has been successfully used in studies of host-parasitoid interactions as it can substantially increase the recovered real host-parasitoid diversity distorted by overlooked species complexes, or by species with slight morphological differences. However, this approach does not allow the simultaneous detection and identification of host(s) and parasitoid(s). Recently, high-throughput sequencing has shown high potential for surveying ecological communities and trophic interactions. Using mock samples comprising insect larvae and their parasitoids, we tested the potential of DNA metabarcoding for identifying individuals involved in host-parasitoid interactions to different taxonomic levels, and compared it to standard DNA barcoding and morphological approaches. For DNA metabarcoding, we targeted the standard barcoding marker cytochrome oxidase subunit I using highly degenerate primers, 2*300 bp sequencing on a MiSeq platform, and RTAX classification using paired-end reads. Additionally, using a large host-parasitoid dataset from a Central European floodplain forest, we assess the completeness and usability of a local reference library by confronting the number of Barcoding Index Numbers obtained by standard barcoding with the number of morphotypes. Overall, metabarcoding recovery was high, identifying 92.8% of the taxa present in mock samples, and identification success within individual taxonomic levels did not significantly differ among metabarcoding, standard barcoding, and morphology. Based on the current local reference library, 39.4% parasitoid and 90.7% host taxa were identified to the species level. DNA barcoding estimated higher parasitoid diversity than morphotyping, especially in groups with high level of crypsis. This study suggests the potential of metabarcoding for effectively recovering host-parasitoid diversity, together with more accurate identifications obtained from building reliable and comprehensive reference libraries, especially for parasitoids.
Pear psyllids (Hemiptera: Psylloidea: Psyllidae: Cacopsylla spp.) belong to the most serious pests of pear (Pyrus spp.). They damage pear trees by excessive removal of phloem sap, by soiling the fruits with honeydew which, in turn, provides a substrate for sooty mould, and by transmission of Candidatus Phytoplasma spp., the causal agents of the pear decline disease. The morphological similarity, the presence of seasonal dimorphism that affects adult colour, size and wing morphology and uncritical use of species names, led to much confusion in the taxonomy of pear psyllids. As a result, pear psyllids have been frequently misidentified. Many of the entries attributed to Cacopsylla pyricola and other species in the GenBank are misidentifications which led to additional, unnecessary confusion. Here we analysed DNA barcodes of 11 pear psyllid species from eastern Asia, Europe and Iran using four mitochondrial gene fragments (COI 658 bp, COI 403 bp, COI-tRNAleu-COII 580 bp and 16S rDNA 452 bp). The efficiency of identification was notably high and considerable barcoding gaps were observed in all markers. Our results confirm the synonymies of the seasonal forms of Cacopsylla jukyungi ( = C. cinereosignata, winter form) and C. maculatili ( = C. qiuzili, summer form) previously suggested based on morphology. Some previous misidentifications (C. chinensis from China, Japan and Korea = misidentification of C. jukyungi; C. pyricola and C. pyrisuga from East Asia = misidentification of C. jukyungi and C. burckhardti, respectively; C. pyricola from Iran = misidentification of C. bidens, C. pyri and Cacopsylla sp.) are also corrected. There is no evidence for the presence of European pear psyllid species in East Asia.
- MeSH
- druhová specificita MeSH
- Hemiptera chemie genetika MeSH
- hmyzí geny MeSH
- mitochondriální geny MeSH
- taxonomické DNA čárové kódování metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Biodiversity research in tropical ecosystems-popularized as the most biodiverse habitats on Earth-often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.
- MeSH
- biodiverzita * MeSH
- DNA analýza genetika MeSH
- ekosystém MeSH
- můry klasifikace genetika MeSH
- taxonomické DNA čárové kódování metody MeSH
- tropické klima * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Geografické názvy
- Gabon MeSH
Horse flies (Diptera: Tabanidae) are of medical and veterinary importance since they transmit a range of pathogens. The horse fly fauna of tropical Africa is still poorly known, and in some geographical areas has not been studied for decades. This study summarizes the results of tabanid collections performed in three West African countries where only sparse data were previously available, the Central African Republic (CAR), Gabon and Liberia. Of 1093 collected specimens, 28 morphospecies and 26 genospecies belonging to six genera were identified, including the first findings of eleven morphospecies in the countries where horse flies were collected: Philoliche (Subpangonia) gravoti Surcouf, 1908 and Tabanus ianthinus Surcouf, 1907 are new records for Liberia; Ancala fasciata f. mixta (Surcouf, 1914), Tabanus fraternus Macquart, 1846, and T. triquetrornatus Carter, 1915 for CAR; Chrysops longicornis Macquart, 1838, Haematopota albihirta Karsch, 1887, H. bowdeni Oldroyd, 1952, and H. brucei Austen, 1908 for Gabon; and Tabanus secedens f. regnaulti Surcouf, 1912 and T. thoracinus Palisot de Beauvois, 1807 for Gabon and Liberia. Species identification of all 28 morphospecies based on morphological features was further supplemented by barcoding of cytochrome oxidase I (COI). Based on the COI sequences of 115 specimens representing 74 haplotypes, a phylogenetic tree was constructed to illustrate the relationships among the tabanid species found and to demonstrate their intra- and interspecific divergences. Our study enriches the current number of barcoded tabanids with another 22 genospecies. Based on the analysis of molecular data we question the taxonomic relevance of the morphological forms Ancala fasciata f. mixta and Tabanus secedens f. regnaulti. A parasitological survey based on nested PCR of 18S rRNA revealed a high (˜25%) prevalence of Trypanosoma theileri in the studied horse flies, accompanied by two species of monoxenous trypanosomatids, Crithidia mellificae and Blastocrithidia sp.
- MeSH
- Diptera klasifikace genetika parazitologie MeSH
- fylogeneze MeSH
- taxonomické DNA čárové kódování MeSH
- Trypanosoma genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- západní Afrika MeSH
Several species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel & Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.
- MeSH
- brouci genetika MeSH
- fylogeneze MeSH
- genetická variace MeSH
- haplotypy MeSH
- klasifikace metody MeSH
- mitochondriální DNA chemie MeSH
- sekvenční analýza DNA MeSH
- sekvenční seřazení MeSH
- taxonomické DNA čárové kódování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Torotrogla merulae Skoracki, Dabert et Ehrnsberger, 2000 and T. rubeculi Skoracki, 2004 have been considered as distinct steno- and monoxenous quill mite species (Acari: Prostigmata: Syringophilidae) parasitizing the thrushes of the genus Turdus Linnaeus and the European robin Erithacus rubecula (Linnaeus), respectively. Morphological and molecular studies on the taxonomical status of these two species provided contradictory results. Well defined differences in morphology were not supported by substantial genetic distance in nucleotide sequences of the DNA barcode (mitochondrial cytochrome c oxidase subunit I, COI, and D2 domain of the nuclear 28S rRNA gene), by the topology of the phylogenetic trees (neighbor-joining, maximum parsimony, maximum likelihood) and the network analyses of the COI haplotype genealogy (median-joining, statistical parsimony) that reveal rubeculi populations nested within merulae haplotypes. Since detected differences between T. merulae and T. rubeculi populations (1.6-2.4% for COI and 0.1% for D2) are comparable to the intraspecific level observed in majority of currently recognized European Torotrogla species and are much lower than the interspecific distances observed in the genus, we postulate their conspecificity. Because main morphological distinctions concern the structures used for feeding, we hypothesize that they are the result of phenotypic plasticity evoked by specific and different environmental conditions prevailing on the host bodies (thickness of the feather quill wall).
- MeSH
- fylogeneze MeSH
- haplotypy MeSH
- infestace roztoči parazitologie MeSH
- peří parazitologie MeSH
- ptáci MeSH
- roztoči anatomie a histologie klasifikace genetika MeSH
- taxonomické DNA čárové kódování * MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
A new species of Eudicella White, 1839 (Coleoptera: Scarabaeidae: Cetoniinae), is described from Uganda and Kenya: E. nana new species. Morphological and genetic analyses of the new taxon and phenotypically allied species are given. Eudicella nana is compared with its hypothesized sister species, E. darwiniana Kraatz, 1880, and diagnostic characters that distinguish it from other species occurring in the same region are provided.
- MeSH
- brouci anatomie a histologie klasifikace genetika MeSH
- DNA genetika MeSH
- druhová specificita MeSH
- taxonomické DNA čárové kódování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Keňa MeSH
- Uganda MeSH
Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.
- MeSH
- bezobratlí genetika klasifikace MeSH
- biodiverzita MeSH
- ekosystém MeSH
- koupací pláže MeSH
- metagenomika metody MeSH
- respirační komplex IV * genetika MeSH
- taxonomické DNA čárové kódování * metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Nizozemsko MeSH
- Severní moře MeSH
