Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?
A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. W...
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ftzenodo:oai:zenodo.org:4975297 2023-05-15T17:58:57+02:00 Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? Deagle, Bruce E. Thomas, Austen C. Shaffer, Amanda K. Trites, Andrew W. Jarman, Simon N. 2013-03-19 https://zenodo.org/record/4975297 https://doi.org/10.5061/dryad.953hv unknown doi:10.1111/1755-0998.12103 https://zenodo.org/communities/dryad https://zenodo.org/record/4975297 https://doi.org/10.5061/dryad.953hv oai:zenodo.org:4975297 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode Captive Populations Diet Analysis info:eu-repo/semantics/other dataset 2013 ftzenodo https://doi.org/10.5061/dryad.953hv10.1111/1755-0998.12103 2023-03-10T15:25:17Z A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis. Ion Torrent diet dataFASTQ sequence files and additional data described in the ReadMe file1 MER paper functionsFunctions needed to run R code2 MER R code databaseR code3 MER R code summaryR code Dataset Phoca vitulina Zenodo |
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Captive Populations Diet Analysis |
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Captive Populations Diet Analysis Deagle, Bruce E. Thomas, Austen C. Shaffer, Amanda K. Trites, Andrew W. Jarman, Simon N. Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? |
topic_facet |
Captive Populations Diet Analysis |
description |
A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis. Ion Torrent diet dataFASTQ sequence files and additional data described in the ReadMe file1 MER paper functionsFunctions needed to run R code2 MER R code databaseR code3 MER R code summaryR code |
format |
Dataset |
author |
Deagle, Bruce E. Thomas, Austen C. Shaffer, Amanda K. Trites, Andrew W. Jarman, Simon N. |
author_facet |
Deagle, Bruce E. Thomas, Austen C. Shaffer, Amanda K. Trites, Andrew W. Jarman, Simon N. |
author_sort |
Deagle, Bruce E. |
title |
Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? |
title_short |
Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? |
title_full |
Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? |
title_fullStr |
Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? |
title_full_unstemmed |
Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? |
title_sort |
data from: quantifying sequence proportions in a dna-based diet study using ion torrent amplicon sequencing: which counts count? |
publishDate |
2013 |
url |
https://zenodo.org/record/4975297 https://doi.org/10.5061/dryad.953hv |
genre |
Phoca vitulina |
genre_facet |
Phoca vitulina |
op_relation |
doi:10.1111/1755-0998.12103 https://zenodo.org/communities/dryad https://zenodo.org/record/4975297 https://doi.org/10.5061/dryad.953hv oai:zenodo.org:4975297 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.953hv10.1111/1755-0998.12103 |
_version_ |
1766167686199377920 |