<scp>COInr</scp> and <scp>mkCOInr</scp>: Building and customizing a nonredundant barcoding reference database from <scp>BOLD</scp> and <scp>NCBI</scp> using a semi‐automated pipeline

Meglécz, Emese

doi:10.1111/1755-0998.13756

Cited by 14 publications

(7 citation statements)

References 95 publications

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“…Therefore, it is essential to integrate these two primary databases creating a custom database for more accurate taxonomic assignment of metabarcoding sequences. mkCOInr v.0.2.0 (Meglecz, 2023) was employed to create such custom database following operation document. The COI sequences were downloaded from these two nucleotide databases in November 13, 2023, respectively.…”

Section: Construction Of Custom Reference Databasementioning

confidence: 99%

Environmental DNA from ethanol eluent of flowers reveals a widespread diversity in cowpea associated animal communities in Hainan Island

Chen,

Yu,

et al. 2024

Preprint

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Cowpea (Vigna unguiculata (L.) Walp.), as an economical crop, is one of the important pillar industries of rural revitalization strategy in China. However, cowpea planting in China is often infested and damaged by many insects during growth, especially in Hainan region with a warm and wet tropical climate. Traditional monitoring methods with technical limitation could only detect a few common significant agricultural pests, how many kinds of species associated with cowpea is unknown. Here, we employed environmental DNA (eDNA) metabarcoding to characterize cowpea associated animal community-level diversity among six planting areas in Hainan. In all, 62 species were detected, of which 99.05% was Arthropoda, suggesting that Arthropods are the main groups interacting with cowpea. Moreover, we also detected 28 pests on cowpea, predominantly belonging to Thysanoptera, Lepidoptera, Diptera and Hemiptera, of which 20 pests were first reported and need more extra attention. Furthermore, clustering results indicated that there is a certain diversity of cowpea associated animals in different regions of Hainan, but the species composition was similar in the large planting areas due to the indiscriminate use of pesticides, which need further develop scientific pesticide applications to ensure adequate species diversity. This study represents the first molecular approach to investigate the cowpea associated animal communities and provides basic information for further scientific pesticide applications.

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Section: Construction Of Custom Reference Databasementioning

confidence: 99%

Environmental DNA from ethanol eluent of flowers reveals a widespread diversity in cowpea associated animal communities in Hainan Island

Chen,

Yu,

et al. 2024

Preprint

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“…org). The invertebrate COI reference sequence database was curated to include all taxa within families known to occur in Wisconsin and neighboring states and trimmed to remove primers using the mkCOInr sequence database and pipeline developed by Megléz (Meglécz, 2023). To control for contamination, the maximum number of reads for each ASV found in field, extraction, and PCR controls were removed from all the other samples.…”

Section: Bioinformaticsmentioning

confidence: 99%

Comparison of qPCR and metabarcoding for environmental DNA surveillance of a freshwater parasite

Johnson,

Tetzlaff,

Katz

et al. 2024

Ecology and Evolution

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Analysis of environmental DNA (eDNA) has been successfully used across freshwater ecological parasitology to inform management of ecologically and economically important species. However, most studies have used species‐specific quantitative polymerase chain reaction (qPCR) assays to detect target taxa. While generally effective, this approach limits the amount of community and management‐supporting data that can be obtained from eDNA samples. If eDNA metabarcoding could be conducted with the same accuracy of a single species approach, researchers could simultaneously detect a target species while obtaining vast community data from eDNA samples. We sampled 38 freshwater sites on Fort McCoy, Wisconsin and compared qPCR to metabarcoding for eDNA detection of the ectoparasitic gill louse Salmincola edwardsii, an obligate parasite of Salvelinus fishes (chars). We found no evidence to suggest S. edwardsii occupancy or detection probabilities differed between qPCR and metabarcoding. Further, we found that the number of S. edwardsii reads from metabarcoding were negatively predictive of CT values from qPCR (CT value indicates cycle a significant amount of target eDNA is detected, with lower CTs indicative of more DNA), demonstrating that our metabarcoding reads positively predicted qPCR DNA quantities. However, the number of reads was not predictive of overall qPCR score (number of positive qPCR replicates). In addition to S. edwardsii, metabarcoding led to the detection of a vast community of over 2600 invertebrate taxa. We underscore the necessity for conducting similar analyses across environments and target species, as the ecology of eDNA will vary on a per‐study basis. Our results suggest that eDNA metabarcoding provides a highly sensitive and accurate method for detecting parasitic gill lice while also illuminating the broader biological community and co‐occurrence of species in the environment.

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“…This database construction was facilitated by python package nucleotide or NCBI sequence downloader (NSDPY; Hebert and Meglécz, 2022). Additionally, we obtained a non-redundant COI database (COInr) from https://doi.org/10.5281/zen odo.6555985 (Meglécz, 2023). Taxonomic assignments were based on the top hits with a sequence identity of at least 97%.…”

Section: Sequence Filtering and Taxonomic Assignationmentioning

confidence: 99%

Metabarcoding reveals waterbird diet in a French Ramsar wetland: implications for ecosystem management

Fablet,

Pellerin,

Zarzoso-Lacoste

et al. 2024

Knowl. Manag. Aquat. Ecosyst.

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Environmental and/or climate changes, occurring at a global or local scale, can significantly impact the diets, health, and population dynamics of waterbirds. This study aimed to develop an effective tool, using DNA metabarcoding of fecal samples, for monitoring waterbird diets during the breeding season in a Ramsar freshwater wetland in Northern France. We collected bird feces across eight marshes with varying anthropic usage. The majority of samples (69%) were from five waterbird species: Eurasian coot (Fulica atra), Eurasian moorhen (Gallinula chloropus), mallard (Anas platyrhynchos), mute swan (Cygnus olor), and grey heron (Ardea cinerea). DNA was extracted from 116 samples, with plant and invertebrate primers used to undertake multi-marker metabarcoding. Despite a negative impact of uric acid on DNA amplification, we observed significant dietary variations among bird species and sampling sites. Wetland bird diets primarily consisted of four arthropod families, dominated by Chironomidae and Asellidae. The number of plant families detected was higher, consisting of 33 families, with Poaceae highly prevalent within wetland bird diets. This study shows that using DNA metabarcoding to explore interactions between waterbirds and trophic resources is a promising approach to assist wetland management and assess the effect of environmental changes.

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COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline

Abstract: Reference databases of particular genes or markers are used for DNA-based identification and thus have various applications in

Cited by 14 publications

References 95 publications

Environmental DNA from ethanol eluent of flowers reveals a widespread diversity in cowpea associated animal communities in Hainan Island

Environmental DNA from ethanol eluent of flowers reveals a widespread diversity in cowpea associated animal communities in Hainan Island

Comparison of qPCR and metabarcoding for environmental DNA surveillance of a freshwater parasite

Metabarcoding reveals waterbird diet in a French Ramsar wetland: implications for ecosystem management

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