Relevant bibliographies by topics / Meta-barcoding

Academic literature on the topic 'Meta-barcoding'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Meta-barcoding"

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Keller, Alexander, Sonja Hohlfeld, Andreas Kolter, Jörg Schultz, Birgit Gemeinholzer, and Markus J. Ankenbrand. "BCdatabaser: on-the-fly reference database creation for (meta-)barcoding." Bioinformatics 36, no. 8 (January 6, 2020): 2630–31. http://dx.doi.org/10.1093/bioinformatics/btz960.

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Abstract Summary DNA barcoding and meta-barcoding have become irreplaceable in research and applications, where identification of taxa alone or within a mixture, respectively, becomes relevant. Pioneering studies were in the microbiological context, yet nowadays also plants and animals become targeted. Given the variety of markers used, formatting requirements for classifiers and constant growth of primary databases, there is a need for dedicated reference database creation. We developed a web and command-line interface to generate such on-the-fly for any applicable marker and taxonomic group with optional filtering, formatting and restriction specific for (meta-)barcoding purposes. Also, databases optionally receive a DOI, making them well-documented with meta-data, publicly sharable and citable. Availability and implementation source code: https://www.github.com/molbiodiv/bcdatabaser, webservice: https://bcdatabaser.molecular.eco, documentation: https://molbiodiv.github.io/bcdatabaser.
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Jo, Hyunbin, Dong-Kyun Kim, Kiyun Park, and Ihn-Sil Kwak. "Discrimination of Spatial Distribution of Aquatic Organisms in a Coastal Ecosystem Using eDNA." Applied Sciences 9, no. 17 (August 21, 2019): 3450. http://dx.doi.org/10.3390/app9173450.

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The nonlinearity and complexity of coastal ecosystems often cause difficulties when analyzing spatial and temporal patterns of ecological traits. Environmental DNA (eDNA) monitoring has provided an alternative to overcoming the aforementioned issues associated with classical monitoring. We determined aquatic community taxonomic composition using eDNA based on a meta-barcoding approach that characterizes the general ecological features in the Gwangyang Bay coastal ecosystem. We selected the V9 region of the 18S rDNA gene (18S V9), primarily because of its broad range among eukaryotes. Our results produced more detailed spatial patterns in the study area previously categorized (inner bay, main channel of the bay and outer bay) by Kim et al. (2019). Specifically, the outer bay zone was clearly identified by CCA using genus-level identification of aquatic organisms based on meta-barcoding data. We also found significant relationships between environmental factors. Therefore, eDNA monitoring based on meta-barcoding approach holds great potential as a complemental monitoring tool to identify spatial taxonomic distribution patterns in coastal areas.
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Balech, Bachir, Anna Sandionigi, Caterina Manzari, Emiliano Trucchi, Apollonia Tullo, Flavio Licciulli, Giorgio Grillo, et al. "Tackling critical parameters in metazoan meta-barcoding experiments: a preliminary study based on coxI DNA barcode." PeerJ 6 (June 13, 2018): e4845. http://dx.doi.org/10.7717/peerj.4845.

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Nowadays DNA meta-barcoding is a powerful instrument capable of quickly discovering the biodiversity of an environmental sample by integrating the DNA barcoding approach with High Throughput Sequencing technologies. It mainly consists of the parallel reading of informative genomic fragment/s able to discriminate living entities. Although this approach has been widely studied, it still needs optimization in some necessary steps requested in its advanced accomplishment. A fundamental element concerns the standardization of bioinformatic analyses pipelines. The aim of the present study was to underline a number of critical parameters of laboratory material preparation and taxonomic assignment pipelines in DNA meta-barcoding experiments using the cytochrome oxidase subunit-I (coxI) barcode region, known as a suitable molecular marker for animal species identification. We compared nine taxonomic assignment pipelines, including a custom in-house method, based on Hidden Markov Models. Moreover, we evaluated the potential influence of universal primers amplification bias in qPCR, as well as the correlation between GC content with taxonomic assignment results. The pipelines were tested on a community of known terrestrial invertebrates collected by pitfall traps from a chestnut forest in Italy. Although the present analysis was not exhaustive and needs additional investigation, our results suggest some potential improvements in laboratory material preparation and the introduction of additional parameters in taxonomic assignment pipelines. These include the correct setup of OTU clustering threshold, the calibration of GC content affecting sequencing quality and taxonomic classification, as well as the evaluation of PCR primers amplification bias on the final biodiversity pattern. Thus, careful attention and further validation/optimization of the above-mentioned variables would be required in a DNA meta-barcoding experimental routine.
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ANDERSEN, KENNETH, KAREN LISE BIRD, MORTEN RASMUSSEN, JAMES HAILE, HENRIK BREUNING-MADSEN, KURT H. KJAER, LUDOVIC ORLANDO, M. THOMAS P. GILBERT, and ESKE WILLERSLEV. "Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity." Molecular Ecology 21, no. 8 (September 14, 2011): 1966–79. http://dx.doi.org/10.1111/j.1365-294x.2011.05261.x.

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Terrat, S., S. Dequiedt, W. Horrigue, M. Lelievre, C. Cruaud, N. P. A. Saby, C. Jolivet, et al. "Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding." Heredity 114, no. 5 (October 8, 2014): 468–75. http://dx.doi.org/10.1038/hdy.2014.91.

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Liu, Yin, Xiaowei Li, Yufeng Chen, Guangzhou Geng, Junjie Li, Yongtian Wang, and Lingling Huang. "Imaging-based optical barcoding for relative humidity sensing based on meta-tip." Nanophotonics 11, no. 1 (November 2, 2021): 111–18. http://dx.doi.org/10.1515/nanoph-2021-0529.

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Abstract In a wide range of applications such as healthcare treatment, environmental monitoring, food processing and storage, and semiconductor chip manufacturing, relative humidity (RH) sensing is required. However, traditional fiber-optic humidity sensors face the challenges of miniaturization and indirectly obtaining humidity values. Here, we propose and demonstrate an optical barcode technique by cooperating with RH meta-tip, which can predict the humidity values directly. Such RH meta-tip is composed of fiber-optic sensor based on surface plasmon resonance (SPR) effect and graphene oxide film as humidity sensitizer. While SPR sensor is composed of multimode fiber (MMF) integrated with metallic metasurface. Dynamic time warping (DTW) algorithm is used to obtain the warp path distance (WPD) sequence between the measured reflection spectrum and the spectra of the precalibrated database. The distance sequence is transformed into a pseudo-color barcode, and the humidity value is corresponded to the lowest distance, which can be read by human eyes. The RH measurement depends on the collective changes of the reflection spectrum rather than tracking a single specific resonance peak/dip. This work can open up new doors to the development of a humidity sensor with direct RH recognition by human eyes.
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Byers, Philicity R. M., Rodger C. Evans, Zoë Migicovsky, and Allison K. Walker. "Fungal symbionts of endangered Crocanthemum canadense (Cistaceae) in Nova Scotia." Botany 99, no. 7 (July 2021): 403–19. http://dx.doi.org/10.1139/cjb-2020-0187.

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Crocanthemum canadense (L.) Britton (Cistaceae) is critically imperiled in Nova Scotia. The decline of Nova Scotian Crocanthemum canadense is largely due to the loss of the Annapolis Valley sand barrens habitat. Fungal symbionts may aid in nutrient and water acquisition as well as plant defenses. The role of fungal associations with Crocanthemum canadense is unknown; our goal was to identify fungal symbionts to inform ongoing conservation research. We isolated fungi from eighteen Crocanthemum canadense plants collected from Greenwood, Nova Scotia. Using internal transcribed spacer (ITS) rDNA barcoding of fungal cultures, we identified 58 fungal taxa. ITS2 meta-amplicon barcoding of roots and rhizosphere soil revealed 241 fungi with basidiomycetes accounting for 53.8% of reads. Chaetothyriales sp., Mycetinis scorodonius, Acidomelania panicicola, and Scleroderma citrinum were the most abundant root associates based on meta-amplicon data. We quantified percent root colonization of arbuscular mycorrhizal fungi (AMF) using root staining and microscopy. The average AMF colonization rate of the roots was 29.6% (n = 18). Our research provides a foundation for understanding the fungal community in this declining habitat and the first account of fungal symbionts in the above- and below-ground tissues and rhizosphere of Crocanthemum canadense. Identifying fungi influencing endangered Nova Scotian Crocanthemum canadense is valuable for developing conservation strategies.
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Prodinger, Florian, Hisashi Endo, Yasuhiro Gotoh, Yanze Li, Daichi Morimoto, Kimiho Omae, Kento Tominaga, et al. "An Optimized Metabarcoding Method for Mimiviridae." Microorganisms 8, no. 4 (April 2, 2020): 506. http://dx.doi.org/10.3390/microorganisms8040506.

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Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological profiling of Mimiviridae, we previously proposed a meta-barcoding approach based on 82 degenerate primer pairs (i.e., MEGAPRIMER) targeting the DNA polymerase gene of Mimiviridae. The method detected a larger number of operational taxonomic units (OTUs) in environmental samples than previous methods. However, it required large quantities of DNA and was laborious due to the use of individual primer pairs. Here, we examined coastal seawater samples using varying PCR conditions and purification protocols to streamline the MEGAPRIMER method. Mixing primer pairs in “cocktails” reduced the required amount of environmental DNA by 90%, while reproducing the results obtained by the original protocol. We compared the results obtained by the meta-barcoding approach with quantifications using qPCR for selected OTUs. This revealed possible amplification biases among different OTUs, but the frequency profiles for individual OTUs across multiple samples were similar to those obtained by qPCR. We anticipate that the newly developed MEGAPRIMER protocols will be useful for ecological investigation of Mimiviridae in a larger set of environmental samples.
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Santoferrara, Luciana F., Ewelina Rubin, and George B. Mcmanus. "Global and local DNA (meta)barcoding reveal new biogeography patterns in tintinnid ciliates." Journal of Plankton Research 40, no. 3 (April 12, 2018): 209–21. http://dx.doi.org/10.1093/plankt/fby011.

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Sato, Jun J., Takuya Shimada, Daisuke Kyogoku, Taketo Komura, Shigeru Uemura, Takashi Saitoh, and Yuji Isagi. "Dietary niche partitioning between sympatric wood mouse species (Muridae: Apodemus) revealed by DNA meta-barcoding analysis." Journal of Mammalogy 99, no. 4 (June 14, 2018): 952–64. http://dx.doi.org/10.1093/jmammal/gyy063.

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Dissertations / Theses on the topic "Meta-barcoding"

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Sickel, Wiebke [Verfasser], and Alexander [Gutachter] Keller. "High-throughput biodiversity assessment - Powers and limitations of meta-barcoding / Wiebke Sickel ; Gutachter: Alexander Keller." Würzburg : Universität Würzburg, 2017. http://d-nb.info/1125884665/34.

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Sickel, Wiebke. "High-throughput biodiversity assessment - Powers and limitations of meta-barcoding." Doctoral thesis, 2016. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-144573.

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Traditional species identification based on morphological characters is laborious and requires expert knowledge. It is further complicated in the case of species assemblages or degraded and processed material. DNA-barcoding, species identification based on genetic data, has become a suitable alternative, yet species assemblages are still difficult to study. In the past decade meta-barcoding has widely been adopted for the study of species communities, due to technological advances in modern sequencing platforms and because manual separation of individual specimen is not required. Here, meta-barcoding is put into context and applied to the study of bee-collected pollen as well as bacterial communities. These studies provide the basis for a critical evaluation of the powers and limitations of meta-barcoding. Advantages identified include species identification without the need for expert knowledge as well as the high throughput of samples and sequences. In microbiology, meta-barcoding can facilitate directed cultivation of taxa of interest identified with meta-barcoding data. Disadvantages include insufficient species resolution due to short read lengths and incomplete reference databases, as well as limitations in abundance estimation of taxa and functional profiling. Despite these, meta-barcoding is a powerful method for the analysis of species communities and holds high potential especially for automated biomonitoring
Traditionelle Methoden der Identifizierung von Organismen anhand von morphologischen Merkmalen sind arbeits- und zeitaufwendig und benötigen Expertenkenntnisse der Morphologie. Weitere Probleme liegen in der Analyse von Artgemeinschaften und prozessiertem Material. DNA-barcoding, Artbestimmung anhand von genetischen Merkmalen, hat sich als Alternative herausgebildet, jedoch sind Artgemeinschaften nach wie vor schwierig zu analysieren. Im vergangenen Jahrzehnt wurde meta-barcoding zur Analyse von Artgemeinschaften entwickelt; insbesondere durch die Weiterentwicklung moderner Sequenziergeräte und da eine Auftrennung der Organismen innerhalb einer Gemeinschaft nicht mehr notwendig ist. In der vorliegenden Arbeit wurde zunächst ein Überblick über meta-barcoding erstellt. Die Methode wurde dann für die Analyse von Bienen-gesammeltem Pollen und Bakteriengemeinschaften angewandt. Diese Studien bilden eine gute Basis, um die Vor- und Nachteile von meta-barcoding kritisch zu bewerten. Vorteile beinhalten unter anderem, dass Organismen bestimmt werden können, ohne dass Expertenkenntnisse notwendig sind, sowie der hohe Durchsatz von Proben und Sequenzen. In der Mikrobiologie kann meta-barcoding eine gerichtete Kultivierung von Bakterien erleichtern, die durch meta-barcoding als Zielorganismen indentifiziert wurden. Nachteile finden sich in der manchmal noch unzureichenden Unterscheidung nah ver- wandter Arten aufgrund von kurzen Sequenzlängen und lückenhaften Referenzdatenbanken, sowie Einschränkungen in der Abschätzung von Abundanzen und Funktionen der Organismen innerhalb der Artgemeinschaft. Trotz dieser Problematiken ist meta-barcoding eine leistungsstarke Methode für die Analyse von Artgemeinschaften und ist besonders vielversprechend für automatisiertes Bio-Monitoring
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Akankunda, Trace. "Meta-barcoding for assessment of risks posed by genetically modified crops to farmland arthropods." Thesis, 2015. http://hdl.handle.net/2440/95093.

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The rate of adoption of genetically modified (GM) crops continues to grow at unprecedented rates 19 years after their first commercialisation. As global coverage of GM crops increases, concerns about their potential effects on the environment and specifically agro-ecosystem health intensify. To address these concerns, researchers have called for increased monitoring of agro-ecosystems to detect unforeseen adverse effects of GM crops. To date, only Europe has a statutory requirement for developers of GM products to conduct post market environmental monitoring (PMEM) in order to assess potential risks associated with their products. This might be due to lack of robust and cost effective methods for conducting PMEM. Here we propose the use of a modified meta-barcoding pipeline on an Illumina MiSeq platform as a comprehensive and cost effective approach for conducting PMEM on farmland arthropod communities. We test the method’s capacity to generate baseline data on a selection of indicator arthropod groups following guidelines issued by the European Food Safety Authority (EFSA). We use arthropod communities of coffee plantations in the south and south-western regions of Uganda as an exemplar for the approach. We modify the sample preparation steps of the meta-barcoding pipeline to reduce sequencing cost and successfully adapt the MiSeq Reporter program to classify arthropods using COI sequence reads produced by the MiSeq. We compile baseline data on the diversity and distribution s of six generalist predators, two parasitoids, two pollinators, four common pests and three herbivores of the coffee crop system using incidence counts. We demonstrate the method’s capacity to monitor arthropod communities at the genus and species level and discuss the application of the baseline data collected for GM risk assessment.
Thesis (M.Bio.(PB)) -- University of Adelaide, Masters of Biotechnology (Plant Biotechnology), School of Agriculture, Food and Wine, 2015
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Book chapters on the topic "Meta-barcoding"

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Bruno, Fosso, Marzano Marinella, and Monica Santamaria. "e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling." In Methods in Molecular Biology, 257–78. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2291-8_16.

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