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      Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change

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          Abstract

          Ovary-to-testis transformation in a sex-changing fish involves transcriptomic and epigenomic reprogramming.

          Abstract

          Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis and that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.

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          Most cited references74

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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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              Fast gapped-read alignment with Bowtie 2.

              As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                July 2019
                10 July 2019
                : 5
                : 7
                : eaaw7006
                Affiliations
                [1 ]Department of Anatomy, University of Otago, Dunedin, New Zealand.
                [2 ]Department of Biological Sciences and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA.
                [3 ]Department of Biochemistry, University of Otago, Dunedin, New Zealand.
                [4 ]School of Life Sciences, La Trobe University, Bundoora, VIC 3168, Australia.
                Author notes
                [* ]Corresponding author. Email: ericavtodd@ 123456gmail.com (E.V.T.); ojavieror@ 123456gmail.com (O.O.-R.); neil.gemmell@ 123456otago.ac.nz (N.J.G.)
                [†]

                These authors contributed equally as co-first authors.

                [‡]

                These authors contributed equally as co-senior authors.

                Author information
                http://orcid.org/0000-0001-7870-1286
                http://orcid.org/0000-0002-8076-0346
                http://orcid.org/0000-0001-5513-1970
                http://orcid.org/0000-0001-5576-3476
                http://orcid.org/0000-0001-6277-726X
                http://orcid.org/0000-0003-1174-6054
                http://orcid.org/0000-0002-6735-225X
                http://orcid.org/0000-0002-0928-501X
                http://orcid.org/0000-0003-0671-3637
                Article
                aaw7006
                10.1126/sciadv.aaw7006
                6620101
                31309157
                99b13863-39e4-419e-88ce-b2c3793838e1
                Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                History
                : 16 January 2019
                : 05 June 2019
                Funding
                Funded by: doi http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 1257791
                Funded by: doi http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 1257761
                Funded by: doi http://dx.doi.org/10.13039/501100009193, Marsden Fund;
                Award ID: UOO1308
                Categories
                Research Article
                Research Articles
                SciAdv r-articles
                Organismal Biology
                Custom metadata
                Fritzie Benzon

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