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| Main Authors: | , , , , , |
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| Format: | Dataset Open Access |
| Language: | en |
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PANGAEA
2021
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| Online Access: | https://doi.org/10.1594/PANGAEA.938692 |
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| _version_ | 1867168213842788352 |
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| author | Milivojević, Tamara Rahman, Shirin Nurshan Raposo, Débora Siccha, Michael Kucera, Michal Morard, Raphael |
| author_facet | Milivojević, Tamara Rahman, Shirin Nurshan Raposo, Débora Siccha, Michael Kucera, Michal Morard, Raphael |
| collection | Datos científicos de ciencias marinas y ambientales |
| contents | 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 ~4 000 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. |
| format | Dataset Open Access |
| id | pangaea_https___doi_org_10_1594_PANGAEA_938692 |
| institution | PANGAEA |
| language | en |
| publishDate | 2021 |
| publisher | PANGAEA |
| record_format | pangaea |
| spellingShingle | 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, Raphael Center for Marine Environmental Sciences; Cruise/expedition; Depth, bottom/max; Depth, top/min; DEPTH, water; Elevation of event; Event label; Foraminifera; Gene copies per area; Gene copies per specimen; Gene copies per specimen, maximum; Gene copies per specimen, minimum; Gene copies per specimen, normalized, standard deviation; gene copy number; Genetic sequence; GeoB19612-2; GeoB19612-3; GeoB22361-2; Latitude of event; Longitude of event; M113/2; M113/2_44-2; M113/2_44-3; M124; M124_0344_K349; M133; M133_1678-1; M133_1685-1; M133_1775-1; M133_56-1; Maria S. Merian; MARUM; Meteor (1986); Mid sphere test volume; MSM66; MSM66_61-2; MSN; Multiple opening/closing net; Primers; quantitative PCR; Region, genetic; SACROSS; SpaDE; Species; Station label; Voucher Specimen Code 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 ~4 000 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. |
| title | High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR |
| topic | Center for Marine Environmental Sciences; Cruise/expedition; Depth, bottom/max; Depth, top/min; DEPTH, water; Elevation of event; Event label; Foraminifera; Gene copies per area; Gene copies per specimen; Gene copies per specimen, maximum; Gene copies per specimen, minimum; Gene copies per specimen, normalized, standard deviation; gene copy number; Genetic sequence; GeoB19612-2; GeoB19612-3; GeoB22361-2; Latitude of event; Longitude of event; M113/2; M113/2_44-2; M113/2_44-3; M124; M124_0344_K349; M133; M133_1678-1; M133_1685-1; M133_1775-1; M133_56-1; Maria S. Merian; MARUM; Meteor (1986); Mid sphere test volume; MSM66; MSM66_61-2; MSN; Multiple opening/closing net; Primers; quantitative PCR; Region, genetic; SACROSS; SpaDE; Species; Station label; Voucher Specimen Code |
| url | https://doi.org/10.1594/PANGAEA.938692 |