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

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.

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

Genome ◽

10.1139/gen-2018-0093 ◽

2019 ◽

Vol 62 (3) ◽

pp. 85-95 ◽

Cited By ~ 12

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.

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Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide

New Phytologist ◽

10.1111/nph.12243 ◽

2013 ◽

Vol 199 (1) ◽

pp. 288-299 ◽

Cited By ~ 528

Author(s):

Björn D. Lindahl ◽

R. Henrik Nilsson ◽

Leho Tedersoo ◽

Kessy Abarenkov ◽

Tor Carlsen ◽

...

Keyword(s):

High Throughput ◽

Fungal Community ◽

High Throughput Sequencing ◽

Community Analysis

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Perchlorate reduction by hydrogen autotrophic bacteria and microbial community analysis using high-throughput sequencing

Biodegradation ◽

10.1007/s10532-015-9754-1 ◽

2015 ◽

Vol 27 (1) ◽

pp. 47-57 ◽

Cited By ~ 16

Author(s):

Dongjin Wan ◽

Yongde Liu ◽

Zhenhua Niu ◽

Shuhu Xiao ◽

Daorong Li

Keyword(s):

Microbial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Community Analysis ◽

Microbial Community Analysis ◽

Perchlorate Reduction ◽

Autotrophic Bacteria

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

10.1101/498618 ◽

2018 ◽

Cited By ~ 1

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.

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

Biodiversity Data Journal ◽

10.3897/bdj.8.e50124 ◽

2020 ◽

Vol 8 ◽

Cited By ~ 1

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.

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Detecting HTS Barcode Contamination

10.1101/482166 ◽

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.

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