scholarly journals Expedited Assessment of Terrestrial Arthropod Diversity by Coupling Malaise Traps with DNA Barcoding

2017 ◽  
Author(s):  
JR deWaard ◽  
V Levesque-Beaudin ◽  
SL deWaard ◽  
NV Ivanova ◽  
JTA McKeown ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
National Park ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
List Type ◽  
Arthropod Diversity ◽  
Sequencing Technologies ◽  
Data Release ◽  
Speed And Accuracy ◽  
Malaise Traps

SummaryMonitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches.The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance.Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 20,000 specimens representing 2200 species.These protocols can support arthropod monitoring programs at regional, national, and continental scales.

scholarly journals Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 85-95 ◽  
Author(s):  
Jeremy R. deWaard ◽  
Valerie Levesque-Beaudin ◽  
Stephanie L. deWaard ◽  
Natalia V. Ivanova ◽  
Jaclyn T.A. McKeown ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
National Park ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Arthropod Diversity ◽  
Sequencing Technologies ◽  
Data Release ◽  
Speed And Accuracy ◽  
Malaise Traps

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.

scholarly journals Access COI barcode efficiently using high throughput Single-End 400 bp sequencing

2018 ◽  
Author(s):  
Chentao Yang ◽  
Shangjin Tan ◽  
Guangliang Meng ◽  
David G. Bourne ◽  
Paul A. O’Brien ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Development ◽  
Full Length ◽  
List Type ◽  
Sequencing Data ◽  
Test Plate ◽  
Function Modules ◽  
Sequencing Platforms

SummaryOver the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, constraints in barcoding costs led to unbalanced efforts which prevented accurate taxonomic identification for biodiversity studies.We present a high throughput sequencing approach based on the HIFI-SE pipeline which takes advantage of Single-End 400 bp (SE400) sequencing data generated by BGISEQ-500 to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons. HIFI-SE was written in Python and included four function modules of filter, assign, assembly and taxonomy.We applied the HIFI-SE to a test plate which contained 96 samples (30 corals, 64 insects and 2 blank controls) and delivered a total of 86 fully assembled HIFI COI barcodes. By comparing to their corresponding Sanger sequences (72 sequences available), it showed that most of the samples (98.61%, 71/72) were correctly and accurately assembled, including 46 samples that had a similarity of 100% and 25 of ca. 99%.Our approach can produce standard full-length barcodes cost efficiently, allowing DNA barcoding for global biomes which will advance DNA-based species identification for various ecosystems and improve quarantine biosecurity efforts.

scholarly journals The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia

2018 ◽  
Vol 6 ◽  
Author(s):  
Bruno Cancian de Araujo ◽  
Stefan Schmidt ◽  
Olga Schmidt ◽  
Thomas von Rintelen ◽  
Rosichon Ubaidillah ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
National Park ◽  
Large Scale ◽  
Dna Barcode ◽  
Cost Benefit ◽  
Good Picture ◽  
Large Scale Assessment ◽  
Indonesian Archipelago ◽  
Technological Advances ◽  
Malaise Traps

The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. From September 2015 until April 2016, 34 Malaise traps were placed in different localities in the south-eastern part of the Halimun-Salak National Park. A total of 4,531 specimens were processed for DNA barcoding and in total, 2,382 individuals produced barcode compliant records, representing 1,195 exclusive BINs or putative species in 98 insect families. A total of 1,149 BINs were new to BOLD. Of 1,195 BINs detected, 804 BINs were singletons and more than 90% of the BINs incorporated less than five specimens. The astonishing heterogeneity of BINs, as high as 1.1 exclusive BIN per specimen of Diptera successfully processed, shows that the cost/benefit relationship of the discovery of new species in those areas is very low. In four genera of Chalcidoidea, a superfamily of the Hymenoptera, the number of discovered species was higher than the number of species known from Indonesia, suggesting that our samples contain many species that are new to science. Those numbers shows how fast molecular pipelines contribute substantially to the objective inventorying of the fauna giving us a good picture of how potentially diverse tropical areas might be.

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol

2020 ◽  
Author(s):  
Simon Poirier ◽  
Sébastien Déjean ◽  
Cédric Midoux ◽  
Kim-Anh Lê Cao ◽  
Olivier Chapleur
Keyword(s):  
Anaerobic Digestion ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
List Type ◽  
Community Patterns ◽  
Microbial Indicators ◽  
Sequencing Technologies ◽  
External Data ◽  
Wide Range ◽  
Process Failure

AbstractAnaerobic digestion (AD) is a microbial process that can efficiently degrade organic waste into renewable energies such as methane-rich biogas. However, the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds, leading to process failure and economic losses. High-throughput sequencing technologies enable the identification of microbial indicators of digesters inhibition and can provide new insights into the key phylotypes at stake during AD process. But yet, current studies have used different inocula, substrates, geographical sites and types of reactors, resulting in indicators that are not robust or reproducible across independent studies. In addition, such studies focus on the identification of a single microbial indicator that is not reflective of the complexity of AD. Our study proposes the first analysis of its kind that seeks for a robust signature of microbial indicators of phenol and ammonia inhibitions, whilst leveraging on 4 independent in-house and external AD microbial studies. We applied a recent multivariate integrative method on two-in-house studies to identify such signature, then predicted the inhibitory status of samples from two datasets with more than 90% accuracy. Our study demonstrates how we can efficiently analyze existing studies to extract robust microbial community patterns, predict AD inhibition, and deepen our understanding of AD towards better AD microbial management.HighlightsRobust biomarkers of AD inhibition were tagged by integrating independent 16S studiesIncrease of the Clostridiales relative abundance is an early warning of AD inhibitionCloacimonetes is associated with good performance of biomethane productionMultivariate model predicts ammonia inhibition with 90% accuracy in external data

scholarly journals Diversity, phylogeny and DNA barcoding of brachyuran crabs in artificially created mangrove environments

2020 ◽  
Author(s):  
Ganesh Manikantan ◽  
Chinnamani PrasannaKumar ◽  
J. Vijaylaxmi ◽  
S. R. Pugazhvendan ◽  
Narra Prasanthi
Keyword(s):  
Dna Barcoding ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Mangrove Ecosystem ◽  
Crab Species ◽  
Vegetative Cover ◽  
Mangrove Species ◽  
Association Index ◽  
Brachyuran Crab ◽  
Brachyuran Crabs

AbstractGlobally, at the rate of 1-2 percent per annum, mangrove coverings are disappearing and 35 percent have been lost in the last 20 years due to changes in climate and human activities. No mangrove-associated crabs were found when the mangroves were artificially transplanted 25 years ago in the Vellar estuary. This mangrove ecosystem was sampled for brachyuran biodiversity estimation, species abundance, composition and evaluation of the effectiveness of DNA barcoding in brachyuran crabs species identification. A total of 2844 crabs were collected, representing 35 species within 8 families belonging to 20 genera. Four brachyuran crab species, that is, Uca lactae, U. Triangularis, Selatium brockii, and Neosarmatium asiaticum account for >70% of the total abundance. An approximate 87.5% of crab species estimated to occur by various species estimator were recovered in the present study. Between Uca lactea and U. triangularis, the maximum association index value was observed (97.7%). Cluster analysis grouped the sampled stations according to the types of mangrove species, clearly influencing the structure and composition of the brachyuran crabs. In general, vegetative cover composed of multiple species of mangroves is preferred for the abundance of all collected crabs species, and particularly Neosarmatium asiaticum. Analysis of DNA barcoding indicates that 40% of the brachyuran species gathered in this sample were first barcoded. The advent of new high-throughput sequencing technologies will change biomonitoring applications and surveys drastically in the near future, making reference datasets like ours relevant.

scholarly journals High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Régis Vivien ◽  
Laure Apothéloz-Perret-Gentil ◽  
Jan Pawlowski ◽  
Inge Werner ◽  
Michel Lafont ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Genetic Identification ◽  
Dna Barcodes ◽  
Biological Quality ◽  
Dna Metabarcoding ◽  
Morphological Approach

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.

To the flora of сonjugates (Streptophyta, Conjugatophyceae) of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia)

2014 ◽  
Vol 48 ◽  
pp. 81-88
Author(s):  
A. F. Luknitskaya
Keyword(s):  
Species Distribution ◽  
National Park ◽  
Species Abundance ◽  
Water Bodies ◽  
Number Of Species ◽  
First Time

76 species, 3 varieties and 1 form from 21 genera of Streptophyta, Conjugatophyceae (Actinotaenium, Bambusina, Closterium, Cosmarium, Cylindrocystis, Euastrum, Gonatozygon, Haplotaenium, Micrasterias, Mougeotia, Netrium, Penium, Planotaenium, Pleurotaenium, Raphidiastrum, Spirogyra, Spirotaenia, Staurastrum, Staurodesmus, Tetmemorus, Xanthidium) were found in the basins of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia). The list of species is annotated with data on the species distribution in 55 collecting sites of 29 water bodies of the national park, and species abundance in collected samples according to Luknitskaya (2009). Among above mentioned genera, the genus Cosmarium is represented by the greatest number of species (20). Staurastrum chaetoceros has been found for the first time for the Novgorod Region.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Application of Oxford Nanopore Technology to Plant Virus Detection

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1424
Author(s):  
Lia W. Liefting ◽  
David W. Waite ◽  
Jeremy R. Thompson
Keyword(s):  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Plant Virus Detection ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Virus Diagnostics ◽  
Post Entry ◽  
Read Accuracy

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.

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