Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866).

Autor: Laso-Jadart R; Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS, Univ Evry Université Paris-Saclay Evry France.; Research Federation for the study of Global Ocean Systems Ecology and Evolution FR2022/Tara Oceans GO-SEE Paris France., Sugier K; Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS, Univ Evry Université Paris-Saclay Evry France., Petit E; CEA, Genoscope Institut de Biologie François Jacob Université Paris-Saclay Evry France., Labadie K; CEA, Genoscope Institut de Biologie François Jacob Université Paris-Saclay Evry France., Peterlongo P; CNRS, Inria, IRISA - UMR 6074 Univ Rennes Rennes France., Ambroise C; LaMME, CNRS Université Paris-Saclay Univ Evry Evry France., Wincker P; Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS, Univ Evry Université Paris-Saclay Evry France.; Research Federation for the study of Global Ocean Systems Ecology and Evolution FR2022/Tara Oceans GO-SEE Paris France., Jamet JL; Mediterranean Institute of Oceanology (MIO) AMU-UTLN UM110 CNRS UMR7294, IRD UMR235 Equipe Ecologie Marine et Biodiversité (EMBIO) Université de Toulon Toulon Cedex 9 France., Madoui MA; Génomique Métabolique, Genoscope Institut François Jacob, CEA, CNRS, Univ Evry Université Paris-Saclay Evry France.; Research Federation for the study of Global Ocean Systems Ecology and Evolution FR2022/Tara Oceans GO-SEE Paris France.
Jazyk: angličtina
Zdroj: Ecology and evolution [Ecol Evol] 2020 Aug 04; Vol. 10 (16), pp. 8894-8905. Date of Electronic Publication: 2020 Aug 04 (Print Publication: 2020).
DOI: 10.1002/ece3.6588
Abstrakt: 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.
Competing Interests: The authors declare no competing interests.
(© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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