Results 11 to 20 of about 24,742 (210)

An Optimized Metabarcoding Method for Mimiviridae [PDF]

Microorganisms, 2020
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
Florian Prodinger, Hisashi Endo, Yasuhiro Gotoh, Yanze Li, Daichi Morimoto, Kimiho Omae, Kento Tominaga, Romain Blanc-Mathieu, Yoshihito Takano, Tetsuya Hayashi, Keizo Nagasaki, Takashi Yoshida, Hiroyuki Ogata   +12 more
openaire   +4 more sources

VTAM: A robust pipeline for validating metabarcoding data using controls

Computational and Structural Biotechnology Journal, 2023
To obtain accurate estimates for biodiversity and ecological studies, metabarcoding studies should be carefully designed to minimize both false positive (FP) and false negative (FN) occurrences.
Aitor González, Vincent Dubut, Emmanuel Corse, Reda Mekdad, Thomas Dechatre, Ulysse Castet, Raphaël Hebert, Emese Meglécz   +7 more
doaj   +1 more source

Comparison between COI Metabarcoding and Reverse Metabarcoding with Nanopore’s MinION

Metabarcoding have emerged as a vital tool for assessing biodiversity and early detecting invasive species. It is a technique where a certain marker gene, or barcode, is amplified from a DNA sample, sequenced and subsequently classified by comparisons to
Erixon, Rebecka
core   +2 more sources

Abundance estimation with DNA metabarcoding – recent advancements for terrestrial arthropods [PDF]

, 2023
Biodiversity is declining at alarming rates worldwide and large-scale monitoring is urgently needed to understand changes and their drivers. While classical taxonomic identification of species is time and labour intensive, the combination with DNA-based ...
Dieker,Petra, Zizka,Vera, Scherges,Alice, Dieker, Petra, Scherges, Alice, Bourlat,Sarah J., Bourlat, Sarah J., Sickel,Wiebke, Sickel, Wiebke, Zizka, Vera   +9 more
core   +1 more source

Quantification of marine benthic communities with metabarcoding [PDF]

Molecular Ecology Resources, 2021
AbstractDNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the
Lise Klunder, Judith D. L. van Bleijswijk, Loran Kleine Schaars, Henk W. van der Veer, Pieternella C. Luttikhuizen, Allert I. Bijleveld   +5 more
openaire   +3 more sources

Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

Ecological Indicators, 2021
Diatoms (Bacillariophyceae) are characterized by silicified cell walls that favor their long-term preservation in sediments, therefore widely used as bioindicators of present and past water conditions.
Wengang Kang, Sten Anslan, Nicole Börner, Anja Schwarz, Robin Schmidt, Sven Künzel, Patrick Rioual, Paula Echeverría-Galindo, Miguel Vences, Junbo Wang, Antje Schwalb   +10 more
doaj   +1 more source

Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera)

Scientific Reports, 2022
The soil fauna of the tropics remains one of the least known components of the biosphere. Long-term monitoring of this fauna is hampered by the lack of taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding.
Yves Basset, Mehrdad Hajibabaei, Michael T. G. Wright, Anakena M. Castillo, David A. Donoso, Simon T. Segar, Daniel Souto-Vilarós, Dina Y. Soliman, Tomas Roslin, M. Alex Smith, Greg P. A. Lamarre, Luis F. De León, Thibaud Decaëns, José G. Palacios-Vargas, Gabriela Castaño-Meneses, Rudolf H. Scheffrahn, Marleny Rivera, Filonila Perez, Ricardo Bobadilla, Yacksecari Lopez, José Alejandro Ramirez Silva, Maira Montejo Cruz, Angela Arango Galván, Héctor Barrios   +23 more
doaj   +1 more source

Internal transcribed spacer primer evaluation for vascular plant metabarcoding [PDF]

Metabarcoding and Metagenomics, 2021
The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring ...
Andreas Kolter, Birgit Gemeinholzer
doaj   +3 more sources

An Illumina metabarcoding pipeline for fungi [PDF]

Ecology and Evolution, 2014
AbstractHigh‐throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired‐end reads on ...
Bálint, Miklós, Schmidt, Philipp-André, Sharma, Rahul, Thines, Marco, Schmitt, Imke   +4 more
openaire   +3 more sources

Diversity and ecology of protists revealed by metabarcoding [PDF]

Current Biology, 2021
Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding
Burki F, Sandin MM, Jamy M
openaire   +4 more sources