Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities
Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, anal...
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ftpubmed:oai:pubmedcentral.nih.gov:4457843 2023-05-15T18:18:28+02:00 Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities Majaneva, Markus Hyytiäinen, Kirsi Varvio, Sirkka Liisa Nagai, Satoshi Blomster, Jaanika 2015-06-05 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457843/ http://www.ncbi.nlm.nih.gov/pubmed/26047335 https://doi.org/10.1371/journal.pone.0130035 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457843/ http://www.ncbi.nlm.nih.gov/pubmed/26047335 http://dx.doi.org/10.1371/journal.pone.0130035 http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited CC-BY Research Article Text 2015 ftpubmed https://doi.org/10.1371/journal.pone.0130035 2015-06-14T00:12:28Z Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities. Text Sea ice PubMed Central (PMC) PLOS ONE 10 6 e0130035 |
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Research Article Majaneva, Markus Hyytiäinen, Kirsi Varvio, Sirkka Liisa Nagai, Satoshi Blomster, Jaanika Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities |
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Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities. |
format |
Text |
author |
Majaneva, Markus Hyytiäinen, Kirsi Varvio, Sirkka Liisa Nagai, Satoshi Blomster, Jaanika |
author_facet |
Majaneva, Markus Hyytiäinen, Kirsi Varvio, Sirkka Liisa Nagai, Satoshi Blomster, Jaanika |
author_sort |
Majaneva, Markus |
title |
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities |
title_short |
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities |
title_full |
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities |
title_fullStr |
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities |
title_full_unstemmed |
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities |
title_sort |
bioinformatic amplicon read processing strategies strongly affect eukaryotic diversity and the taxonomic composition of communities |
publisher |
Public Library of Science |
publishDate |
2015 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457843/ http://www.ncbi.nlm.nih.gov/pubmed/26047335 https://doi.org/10.1371/journal.pone.0130035 |
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Sea ice |
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Sea ice |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457843/ http://www.ncbi.nlm.nih.gov/pubmed/26047335 http://dx.doi.org/10.1371/journal.pone.0130035 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited |
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CC-BY |
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https://doi.org/10.1371/journal.pone.0130035 |
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PLOS ONE |
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e0130035 |
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