High-Throughput Sequencing—The Key to Rapid Biodiversity Assessment of Marine Metazoa?
Publication Date
October 19, 2015
Journal
PLOS ONE
Authors
Inga Mohrbeck, Michael J. Raupach, Pedro Martínez Arbizu, Thomas Knebelsberger, et al
Volume
10
Issue
10
Pages
e0140342
DOI
https://dx.plos.org/10.1371/journal.pone.0140342
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0140342
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26479071
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610693
Europe PMC
http://europepmc.org/abstract/MED/26479071
Web of Science
000363026600008
Scopus
84949506102
Mendeley
http://www.mendeley.com/research/highthroughput-sequencingthe-key-rapid-biodiversity-assessment-marine-metazoa
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/2365321"], "description"=>"<p>Cluster analysis conducted on modified reference libraries (characterized by 5-mer, 4-mer, 3-mer and 2-mer homopolymers, respectively) using different similarity thresholds (97–100%, at 1% intervals).</p>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579803, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140342.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cluster_analysis_conducted_on_modified_reference_libraries_characterized_by_5_mer_4_mer_3_mer_and_2_mer_homopolymers_respectively_using_different_similarity_thresholds_97_8211_100_at_1_intervals_/1579803", "title"=>"Cluster analysis conducted on modified reference libraries (characterized by 5-mer, 4-mer, 3-mer and 2-mer homopolymers, respectively) using different similarity thresholds (97–100%, at 1% intervals).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-19 02:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2365334", "https://ndownloader.figshare.com/files/2365335"], "description"=>"<div><p>The applications of traditional morphological and molecular methods for species identification are greatly restricted by processing speed and on a regional or greater scale are generally considered unfeasible. In this context, high-throughput sequencing, or metagenetics, has been proposed as an efficient tool to document biodiversity. Here we evaluated the effectiveness of 454 pyrosequencing in marine metazoan community analysis using the 18S rDNA: V1-V2 region. Multiplex pyrosequencing of the V1-V2 region was used to analyze two pooled samples of DNA, one comprising 118 and the other 37 morphologically identified species, and one natural sample taken directly from a North Sea zooplankton community. A DNA reference library comprising all species represented in the pooled samples was created by Sanger sequencing, and this was then used to determine the optimal similarity threshold for species delineation. The optimal threshold was found at 99% species similarity, with 85% identification success. Pyrosequencing was able to identify between fewer species: 67% and 78% of the species in the two pooled samples. Also, a large number of sequences for three species that were not included in the pooled samples were amplified by pyrosequencing, suggesting preferential amplification of some genotypes and the sensitivity of this approach to even low levels of contamination. Conversely, metagenetic analysis of the natural zooplankton sample identified many more species (particularly gelatinous zooplankton and meroplankton) than morphological analysis of a formalin-fixed sample from the same sampling site, suggesting an increased level of taxonomic resolution with pyrosequencing. The study demonstrated that, based on the V1-V2 region, 454 sequencing does not provide accurate species differentiation and reliable taxonomic classification, as it is required in most biodiversity monitoring. The analysis of artificially prepared samples indicated that species detection in pyrosequencing datasets is complicated by potential PCR-based biases and that the V1-V2 marker is poorly resolved for some taxa.</p></div>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579816, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0140342.s001", "https://dx.doi.org/10.1371/journal.pone.0140342.s002"], "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_High_Throughput_Sequencing_8212_The_Key_to_Rapid_Biodiversity_Assessment_of_Marine_Metazoa_/1579816", "title"=>"High-Throughput Sequencing—The Key to Rapid Biodiversity Assessment of Marine Metazoa?", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-10-19 02:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2365332"], "description"=>"<p>Identifications of the pyrosequenced sample determined by searching against a V1-V2 reference library (99% similarity) and the GenBank database (MEGABLAST search > 90% identity).</p>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579814, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140342.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_taxonomic_composition_of_a_morphologically_analyzed_individuals_m_3_and_a_pyrosequenced_zooplankton_sample_as_aliquots_ZPHTS1_and_ZPHTS2_no_of_reads_per_species_/1579814", "title"=>"Comparison of taxonomic composition of a morphologically analyzed (individuals/m<sup>3</sup>) and a pyrosequenced zooplankton sample, as aliquots ZPHTS1 and ZPHTS2 (no. of reads per species).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-19 02:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2365328"], "description"=>"<p>For each cluster comprising more than one sequence a representative sequence* is presented.</p>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579810, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140342.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_delineation_results_for_the_Sanger_generated_reference_library_at_a_98_similarity_threshold_/1579810", "title"=>"Species delineation results for the Sanger-generated reference library at a 98% similarity threshold.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-19 02:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2365322"], "description"=>"<p><b>(A)</b> Dataset showing strong positive correlation between aliquot 1 (<i>x</i>-axis) and aliquot 2 (<i>y</i>-axis) of pooled ALLDNA sample (Spearman r = 0.98, P < 0.001). (<b>B)</b> Dataset showing strong positive correlation between aliquot 1 (<i>x</i>-axis) and aliquot 2 (<i>y</i>-axis) of pooled ZPDNA sample (Spearman r = 0.94, P < 0.001).</p>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579804, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140342.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Read_coverage_distribution_of_sample_aliquots_inferred_from_pyrosequencing_after_clustering_against_the_reference_library_at_99_similarity_/1579804", "title"=>"Read coverage distribution of sample aliquots inferred from pyrosequencing after clustering against the reference library at 99% similarity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-19 02:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2365331"], "description"=>"<p>GS FLX sequences generated for each aliquot.</p>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579812, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140342.t003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GS_FLX_sequences_generated_for_each_aliquot_/1579812", "title"=>"GS FLX sequences generated for each aliquot.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-19 02:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2365327"], "description"=>"<p>Higher taxa composition and number of different species per taxa analyzed for the Sanger-sequence reference library used in the pooled DNA samples.</p>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579809, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140342.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Higher_taxa_composition_and_number_of_different_species_per_taxa_analyzed_for_the_Sanger_sequence_reference_library_used_in_the_pooled_DNA_samples_/1579809", "title"=>"Higher taxa composition and number of different species per taxa analyzed for the Sanger-sequence reference library used in the pooled DNA samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-19 02:52:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2365325"], "description"=>"<p>The tree, based on consensus sequences of the Sanger-generated reference library, was generated by the Neighbor-Joining algorithm / p-distance model. Clustering against the reference library was performed at 99% sequence similarity threshold using the program cd-hit-est-2d. Percentage of pyrosequencing reads for each species detected in each sample is shown by color-coded rectangles. Black asterisks denote species included in the artificially prepared ZPDNA sample. Red asterisks denote species not included, but detected in the ZPDNA sample. <b>B) Figure 3A continued. C) Figure 3B continued</b>.</p>", "links"=>[], "tags"=>["metagenetic analysis", "sampling site", "zooplankton sample", "biodiversity monitoring", "species identification", "species detection", "454 sequencing", "taxonomic resolution", "species differentiation", "taxonomic classification", "similarity threshold", "marine metazoan community analysis", "Multiplex pyrosequencing", "processing speed", "Marine Metazoa", "18 S rDNA", "Sanger sequencing", "454 pyrosequencing", "document biodiversity", "North Sea zooplankton community", "37 morphologically", "gelatinous zooplankton", "DNA reference library", "species delineation", "Rapid Biodiversity Assessment", "pyrosequencing datasets"], "article_id"=>1579807, "categories"=>["Uncategorised"], "users"=>["Inga Mohrbeck", "Michael J. Raupach", "Pedro Martínez Arbizu", "Thomas Knebelsberger", "Silke Laakmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140342.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Species_composition_of_North_Sea_metazoa_from_four_aliquots_of_pooled_known_DNA_samples_ALLDNA_ZPDNA_and_two_aliquots_of_one_field_collected_zooplankton_sample_ZPHTS_as_assigned_by_454_sequencing_of_the_18S_rDNA_V1_V2_region_/1579807", "title"=>"A) Species composition of North Sea metazoa from four aliquots of pooled, known DNA samples (ALLDNA, ZPDNA) and two aliquots of one field-collected zooplankton sample (ZPHTS), as assigned by 454 sequencing of the 18S rDNA: V1-V2 region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-19 02:52:07"}

PMC Usage Stats | Further Information

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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