Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)
Abstract Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challe...
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ftdoajarticles:oai:doaj.org/article:01ddead37cf949e0bfe561d3c74fc8c0 2023-05-15T15:08:15+02:00 Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866) Romuald Laso‐Jadart Kevin Sugier Emmanuelle Petit Karine Labadie Pierre Peterlongo Christophe Ambroise Patrick Wincker Jean‐Louis Jamet Mohammed‐Amin Madoui 2020-08-01T00:00:00Z https://doi.org/10.1002/ece3.6588 https://doaj.org/article/01ddead37cf949e0bfe561d3c74fc8c0 EN eng Wiley https://doi.org/10.1002/ece3.6588 https://doaj.org/toc/2045-7758 2045-7758 doi:10.1002/ece3.6588 https://doaj.org/article/01ddead37cf949e0bfe561d3c74fc8c0 Ecology and Evolution, Vol 10, Iss 16, Pp 8894-8905 (2020) allelic expression Arctic seas copepod metagenomics metatranscriptomics selection Ecology QH540-549.5 article 2020 ftdoajarticles https://doi.org/10.1002/ece3.6588 2022-12-31T16:24:04Z Abstract Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population‐scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009–2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10−30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population‐scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection. Article in Journal/Newspaper Arctic Zooplankton Directory of Open Access Journals: DOAJ Articles Arctic Ecology and Evolution 10 16 8894 8905 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
allelic expression Arctic seas copepod metagenomics metatranscriptomics selection Ecology QH540-549.5 |
spellingShingle |
allelic expression Arctic seas copepod metagenomics metatranscriptomics selection Ecology QH540-549.5 Romuald Laso‐Jadart Kevin Sugier Emmanuelle Petit Karine Labadie Pierre Peterlongo Christophe Ambroise Patrick Wincker Jean‐Louis Jamet Mohammed‐Amin Madoui Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866) |
topic_facet |
allelic expression Arctic seas copepod metagenomics metatranscriptomics selection Ecology QH540-549.5 |
description |
Abstract Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population‐scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009–2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10−30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population‐scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection. |
format |
Article in Journal/Newspaper |
author |
Romuald Laso‐Jadart Kevin Sugier Emmanuelle Petit Karine Labadie Pierre Peterlongo Christophe Ambroise Patrick Wincker Jean‐Louis Jamet Mohammed‐Amin Madoui |
author_facet |
Romuald Laso‐Jadart Kevin Sugier Emmanuelle Petit Karine Labadie Pierre Peterlongo Christophe Ambroise Patrick Wincker Jean‐Louis Jamet Mohammed‐Amin Madoui |
author_sort |
Romuald Laso‐Jadart |
title |
Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866) |
title_short |
Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866) |
title_full |
Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866) |
title_fullStr |
Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866) |
title_full_unstemmed |
Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866) |
title_sort |
investigating population‐scale allelic differential expression in wild populations of oithona similis (cyclopoida, claus, 1866) |
publisher |
Wiley |
publishDate |
2020 |
url |
https://doi.org/10.1002/ece3.6588 https://doaj.org/article/01ddead37cf949e0bfe561d3c74fc8c0 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Zooplankton |
genre_facet |
Arctic Zooplankton |
op_source |
Ecology and Evolution, Vol 10, Iss 16, Pp 8894-8905 (2020) |
op_relation |
https://doi.org/10.1002/ece3.6588 https://doaj.org/toc/2045-7758 2045-7758 doi:10.1002/ece3.6588 https://doaj.org/article/01ddead37cf949e0bfe561d3c74fc8c0 |
op_doi |
https://doi.org/10.1002/ece3.6588 |
container_title |
Ecology and Evolution |
container_volume |
10 |
container_issue |
16 |
container_start_page |
8894 |
op_container_end_page |
8905 |
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1766339641068224512 |