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      Insights into the genetic basis of predator‐induced response in Daphnia galeata

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          Abstract

          Phenotypic plastic responses allow organisms to rapidly adjust when facing environmental challenges—these responses comprise morphological, behavioral but also life‐history changes. Alteration of life‐history traits when exposed to predation risk have been reported often in the ecological and genomic model organism Daphnia. However, the molecular basis of this response is not well understood, especially in the context of fish predation. Here, we characterized the transcriptional profiles of two Daphnia galeata clonal lines with opposed life histories when exposed to fish kairomones. First, we conducted a differential gene expression, identifying a total of 125 candidate transcripts involved in the predator‐induced response, uncovering substantial intraspecific variation. Second, we applied a gene coexpression network analysis to find clusters of tightly linked transcripts revealing the functional relations of transcripts underlying the predator‐induced response. Our results showed that transcripts involved in remodeling of the cuticle, growth, and digestion correlated with the response to environmental change in D.  galeata. Furthermore, we used an orthology‐based approach to gain functional information for transcripts lacking gene ontology (GO) information, as well as insights into the evolutionary conservation of transcripts. We could show that our candidate transcripts have orthologs in other Daphnia species but almost none in other arthropods. The unique combination of methods allowed us to identify candidate transcripts, their putative functions, and evolutionary history associated with predator‐induced responses in Daphnia. Our study opens up to the question as to whether the same molecular signature is associated with fish kairomones‐mediated life‐history changes in other Daphnia species.

          Abstract

          Exposure of Daphnia galeata to fish kairomones modifies the expression of genes involved in remodeling of the cuticle, growth, and digestion. However, genotypes with opposed life histories under predation risk vary substantially in their response.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

            In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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              Trimmomatic: a flexible trimmer for Illumina sequence data

              Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                mathilde.cordellier@uni-hamburg.de
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                18 October 2020
                December 2020
                : 10
                : 23 ( doiID: 10.1002/ece3.v10.23 )
                : 13095-13108
                Affiliations
                [ 1 ] Institute of Marine Ecosystem and Fishery Science Universität Hamburg Hamburg Germany
                [ 2 ] Institute of Zoology Universität Hamburg Hamburg Germany
                Author notes
                [*] [* ] Correspondence

                Mathilde Cordellier, Institute of Zoology, Universität Hamburg, Martin‐Luther‐King Platz 3, 20146 Hamburg, Germany.

                Email: mathilde.cordellier@ 123456uni-hamburg.de

                Author information
                https://orcid.org/0000-0002-9539-2603
                https://orcid.org/0000-0001-7376-4560
                Article
                ECE36899
                10.1002/ece3.6899
                7713943
                33304520
                da5bf1b4-9ffe-48f9-9281-2f553de769ba
                © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 28 June 2020
                : 09 September 2020
                : 17 September 2020
                Page count
                Figures: 6, Tables: 2, Pages: 14, Words: 10578
                Funding
                Funded by: Volkswagen Foundation
                Award ID: 86030
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                December 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.5 mode:remove_FC converted:03.12.2020

                Evolutionary Biology
                daphniagaleata,gene coexpression,phenotypic plasticity,predator‐induced response,rna‐seq

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