High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR
Abstract Metabarcoding has become the workhorse of community ecology. Sequencing a taxonomically informative DNA fragment from environmental samples gives fast access to community composition across taxonomic groups, but it relies on the assumption that the number of sequences for each taxon correla...
Published in: | ISME Communications |
---|---|
Main Authors: | , , , , , |
Other Authors: | , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Oxford University Press (OUP)
2021
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1038/s43705-021-00067-3 https://www.nature.com/articles/s43705-021-00067-3.pdf https://www.nature.com/articles/s43705-021-00067-3 https://academic.oup.com/ismecommun/article-pdf/1/1/63/55651664/43705_2021_article_67.pdf |
id |
croxfordunivpr:10.1038/s43705-021-00067-3 |
---|---|
record_format |
openpolar |
spelling |
croxfordunivpr:10.1038/s43705-021-00067-3 2024-06-23T07:56:16+00:00 High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR Milivojević, Tamara Rahman, Shirin Nurshan Raposo, Débora Siccha, Michael Kucera, Michal Morard, Raphaël Max-Planck-Gesellschaft Deutsche Forschungsgemeinschaft Max-Planck-Gesellschaft Deutsche Forschungsgemeinschaft 2021 http://dx.doi.org/10.1038/s43705-021-00067-3 https://www.nature.com/articles/s43705-021-00067-3.pdf https://www.nature.com/articles/s43705-021-00067-3 https://academic.oup.com/ismecommun/article-pdf/1/1/63/55651664/43705_2021_article_67.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 ISME Communications volume 1, issue 1 ISSN 2730-6151 journal-article 2021 croxfordunivpr https://doi.org/10.1038/s43705-021-00067-3 2024-06-04T06:07:55Z Abstract Metabarcoding has become the workhorse of community ecology. Sequencing a taxonomically informative DNA fragment from environmental samples gives fast access to community composition across taxonomic groups, but it relies on the assumption that the number of sequences for each taxon correlates with its abundance in the sampled community. However, gene copy number varies among and within taxa, and the extent of this variability must therefore be considered when interpreting community composition data derived from environmental sequencing. Here we measured with single-cell qPCR the SSU rDNA gene copy number of 139 specimens of five species of planktonic foraminifera. We found that the average gene copy number varied between of ~4000 to ~50,000 gene copies between species, and individuals of the same species can carry between ~300 to more than 350,000 gene copies. This variability cannot be explained by differences in cell size and considering all plausible sources of bias, we conclude that this variability likely reflects dynamic genomic processes acting during the life cycle. We used the observed variability to model its impact on metabarcoding and found that the application of a correcting factor at species level may correct the derived relative abundances, provided sufficiently large populations have been sampled. Article in Journal/Newspaper Planktonic foraminifera Oxford University Press ISME Communications 1 1 |
institution |
Open Polar |
collection |
Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
description |
Abstract Metabarcoding has become the workhorse of community ecology. Sequencing a taxonomically informative DNA fragment from environmental samples gives fast access to community composition across taxonomic groups, but it relies on the assumption that the number of sequences for each taxon correlates with its abundance in the sampled community. However, gene copy number varies among and within taxa, and the extent of this variability must therefore be considered when interpreting community composition data derived from environmental sequencing. Here we measured with single-cell qPCR the SSU rDNA gene copy number of 139 specimens of five species of planktonic foraminifera. We found that the average gene copy number varied between of ~4000 to ~50,000 gene copies between species, and individuals of the same species can carry between ~300 to more than 350,000 gene copies. This variability cannot be explained by differences in cell size and considering all plausible sources of bias, we conclude that this variability likely reflects dynamic genomic processes acting during the life cycle. We used the observed variability to model its impact on metabarcoding and found that the application of a correcting factor at species level may correct the derived relative abundances, provided sufficiently large populations have been sampled. |
author2 |
Max-Planck-Gesellschaft Deutsche Forschungsgemeinschaft Max-Planck-Gesellschaft Deutsche Forschungsgemeinschaft |
format |
Article in Journal/Newspaper |
author |
Milivojević, Tamara Rahman, Shirin Nurshan Raposo, Débora Siccha, Michael Kucera, Michal Morard, Raphaël |
spellingShingle |
Milivojević, Tamara Rahman, Shirin Nurshan Raposo, Débora Siccha, Michael Kucera, Michal Morard, Raphaël High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR |
author_facet |
Milivojević, Tamara Rahman, Shirin Nurshan Raposo, Débora Siccha, Michael Kucera, Michal Morard, Raphaël |
author_sort |
Milivojević, Tamara |
title |
High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR |
title_short |
High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR |
title_full |
High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR |
title_fullStr |
High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR |
title_full_unstemmed |
High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR |
title_sort |
high variability in ssu rdna gene copy number among planktonic foraminifera revealed by single-cell qpcr |
publisher |
Oxford University Press (OUP) |
publishDate |
2021 |
url |
http://dx.doi.org/10.1038/s43705-021-00067-3 https://www.nature.com/articles/s43705-021-00067-3.pdf https://www.nature.com/articles/s43705-021-00067-3 https://academic.oup.com/ismecommun/article-pdf/1/1/63/55651664/43705_2021_article_67.pdf |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
ISME Communications volume 1, issue 1 ISSN 2730-6151 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_doi |
https://doi.org/10.1038/s43705-021-00067-3 |
container_title |
ISME Communications |
container_volume |
1 |
container_issue |
1 |
_version_ |
1802649243438022656 |