scholarly journals Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods

2020 ◽  
Vol 8 ◽  
Author(s):  
Matthew Bowser ◽  
Rebekah Brassfield ◽  
Annie Dziergowski ◽  
Todd Eskelin ◽  
Jennifer Hester ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
Native Species ◽  
High Throughput Sequencing ◽  
Deciduous Forest ◽  
Mixed Forest ◽  
Clustering Methods ◽  
Terrestrial Invertebrates ◽  
Creek Watershed ◽  
Natural Diversity

The Kenai National Wildlife Refuge has been given a broad conservation mandate to conserve natural diversity. A prerequisite for fulfilling this purpose is to be able to identify the species and communities that make up that biodiversity. We tested a set of varied methods for inventory and monitoring of plants, birds and terrestrial invertebrates on a grid of 40 sites in a 938 ha study area in the Slikok Creek watershed, Kenai Peninsula, Alaska. We sampled plants and lichens through observation and specimen-based methods. We surveyed birds using bird call surveys on variable circular plots. We sampled terrestrial arthropods by sweep net sampling, processing samples with High Throughput Sequencing methods. We surveyed for earthworms, using the hot mustard extraction method and identified worm specimens by morphology and DNA barcoding. We examined community membership using clustering methods and Nonmetric Multidimensional Scaling. We documented a total of 4,764 occurrences of 984 species and molecular operational taxonomic units: 87 vascular plants, 51 mosses, 12 liverworts, 111 lichens, 43 vertebrates, 663 arthropods, 9 molluscs and 8 annelid worms. Amongst these records, 102 of the arthropod species appeared to be new records for Alaska. We found three non-native species: Deroceras agreste (Linnaeus, 1758) (Stylommatophora: Agriolimacidae), Dendrobaena octaedra (Savigny, 1826) (Crassiclitellata: Lumbricidae) and Heterarthrus nemoratus (Fallén, 1808) (Hymenoptera: Tenthredinidae). Both D. octaedra and H. nemoratus were found at sites distant from obvious human disturbance. The 40 sites were grouped into five community groups: upland mixed forest, black spruce forest, open deciduous forest, shrub-sedge bog and willow. We demonstrated that, at least for a subset of species that could be detected using these methods, we were able to document current species distributions and assemblages in a way that could be efficiently repeated for the purposes of biomonitoring. While our methods could be improved and additional methods and groups could be added, our combination of techniques yielded a substantial portion of the data necessary for fulfilling Kenai National Wildlife Refuge's broad conservation purposes.

scholarly journals Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1055 ◽  
Author(s):  
Arturo Levican ◽  
Jenny C. Fisher ◽  
Sandra L. McLellan ◽  
Ruben Avendaño-Herrera
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Native Species ◽  
High Throughput Sequencing ◽  
Disease Outbreaks ◽  
Emerging Pathogens ◽  
Prophylactic Measures ◽  
Almost All ◽  
Conger Eel ◽  
Genypterus Chilensis

The red conger eel (Genypterus chilensis, Guichenot) is a native species included in the Chilean Aquaculture Diversification Program due to high commercial demand. In the context of intensified farming, prior reports link two disease outbreaks with emerging pathogens in the Vibrio and Tenacibaculum genera. However, the roles remain unclear for the bacterial community and each specific bacterium is associated with the rearing environment for healthy specimens. The success of red conger eel farming therefore warrants research into the bacterial composition of aquaculture conditions and the antimicrobial susceptibilities thereof. This study used culturing methods and high-throughput sequencing to describe the bacterial community associated with water in which G. chilensis was farmed. With culturing methods, the predominant genera were Vibrio (21.6%), Pseudolteromonas (15.7%), Aliivibrio (13.7%), and Shewanella (7.8%). Only a few bacterial isolates showed amylase, gelatinase, or lipase activity, and almost all showed inhibition zones to commonly-used antibiotics in aquaculture. By contrast, high-throughput sequencing established Paraperlucidibaca, Colwellia, Polaribacter, Saprospiraceae, and Tenacibaculum as the predominant genera, with Vibrio ranking twenty-seventh in abundance. High-throughput sequencing also established a link between previous outbreaks with increased relative abundances of Vibrio and Tenacibaculum. Therefore, monitoring the presence and abundance of these potential pathogens could be useful in providing prophylactic measures to prevent future outbreaks.

scholarly journals fluff: exploratory analysis and visualization of high-throughput sequencing data

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2209 ◽  
Author(s):  
Georgios Georgiou ◽  
Simon J. van Heeringen
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Command Line ◽  
Clustering Methods ◽  
Sequencing Data ◽  
Link Type ◽  
High Throughput Sequencing Data ◽  
Genome Wide ◽  
Genome Wide Data

Summary.In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available athttp://fluff.readthedocs.org.Availability.fluff is implemented in Python and runs on Linux. The source code is freely available for download athttps://github.com/simonvh/fluff.

International Barcode of Life: Focus on big biodiversity in South Africa

Genome ◽  
2017 ◽  
Vol 60 (11) ◽  
pp. 875-879 ◽  
Author(s):  
Sarah J. Adamowicz ◽  
Peter M. Hollingsworth ◽  
Sujeevan Ratnasingham ◽  
Michelle van der Bank
Keyword(s):  
South Africa ◽  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Global Scale ◽  
Species Interaction ◽  
Full Potential ◽  
Data Generation ◽  
African Flora

Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20–24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna. Within Africa and elsewhere, DNA barcoding and related techniques are being increasingly used for wildlife forensics and for the validation of commercial products, such as medicinal plants and seafood species. A striking trend of the conference is the dramatic rise of studies on environmental DNA (eDNA) and on diverse uses of high-throughput sequencing techniques. Emerging techniques in these areas are opening new avenues for environmental biomonitoring, managing species-at-risk and invasive species, and revealing species interaction networks in unprecedented detail. Contributors call for the development of validated community standards for high-throughput sequence data generation and analysis, to enable the full potential of these methods to be realized for understanding and managing biodiversity on a global scale.

scholarly journals Detecting HTS Barcode Contamination

2018 ◽  
Author(s):  
Mallory A. Clark ◽  
Sara H. Stankiewicz ◽  
Vincent Barronette ◽  
Darrell O. Ricke
Keyword(s):  
Clinical Research ◽  
Dna Barcoding ◽  
High Throughput ◽  
Cancer Diagnosis ◽  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Cross Contamination ◽  
Cost Efficiencies ◽  
Forensic Samples ◽  
Multiple Samples

AbstractDNA barcoding enables multiple samples to be characterized in parallel with high throughput sequencing (HTS) experiments for cost efficiencies. Cross-contamination of DNA barcode reagents can result in the detection of HTS sequences for barcodes that were not originally added to a particular sample. Cross-contamination of data between multiplexed samples can also occur. Avoidance and detection of contaminated barcodes is relevant for DNA forensic samples analysis, accurate cancer diagnosis, clinical research applications, metagenomic analysis, etc. We present recommendations for the avoidance of contamination and a tool, TallyBarcodes, to aid in the detection of DNA barcode contamination.

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 High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

2020 ◽  
Vol 230 (2) ◽  
pp. 185-201 ◽  
Author(s):  
Susan R. Kennedy ◽  
Stefan Prost ◽  
Isaac Overcast ◽  
Andrew J. Rominger ◽  
Rosemary G. Gillespie ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Spider Communities

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.

Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive Species Early Detection

2021 ◽  
Author(s):  
Joel Hoffman ◽  
Christy Meredith ◽  
Erik Pilgrim ◽  
Anett S Trebitz ◽  
Chelsea Hatzenbuhler ◽  
...  
Keyword(s):  
Invasive Species ◽  
Early Detection ◽  
High Throughput ◽  
Native Species ◽  
High Throughput Sequencing ◽  
Larval Fish ◽  
Hot Spot ◽  
Species Introduction ◽  
Species Detection ◽  
Taxonomic Assignments

When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy, and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction ‘hot-spot’ in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.

Barcoding the food chain: from Sanger to high-throughput sequencing

Genome ◽  
2016 ◽  
Vol 59 (11) ◽  
pp. 946-958 ◽  
Author(s):  
Joanne E. Littlefair ◽  
Elizabeth L. Clare
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
Food Chain ◽  
High Throughput Sequencing ◽  
Human Mobility ◽  
Environmental Dna ◽  
Universal Primers ◽  
Individual Species ◽  
Parasitic Infections ◽  
Forensic Evaluation

Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace “environmental DNA”, and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.

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