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      Photoperiod-dependent developmental reprogramming of the transcriptional response to seawater entry in Atlantic salmon ( Salmo salar)

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          Abstract

          The developmental transition of juvenile salmon from a freshwater resident morph (parr) to a seawater (SW) migratory morph (smolt), known as smoltification, entails a reorganization of gill function to cope with the altered water environment. Recently, we used RNAseq to characterize the breadth of transcriptional change which takes place in the gill in the FW phase of smoltification. This highlighted the importance of extended exposure to short, winter-like photoperiods (SP) followed by a subsequent increase in photoperiod for completion of transcriptional reprogramming in FW and efficient growth following transfer to SW. Here, we extend this analysis to examine the consequences of this photoperiodic history-dependent reprogramming for subsequent gill responses upon exposure to SW. We use RNAseq to analyze gill samples taken from fish raised on the photoperiod regimes we used previously and then challenged by SW exposure for 24 hours. While fish held on constant light (LL) throughout were able to hypo-osmoregulate during a 24 hours SW challenge, the associated gill transcriptional response was highly distinctive from that in fish which had experienced a 7-week period of exposure to SP followed by a return to LL (SPLL) and had consequently acquired the characteristics of fully developed smolts. Fish transferred from LL to SP, and then held on SP for the remainder of the study was unable to hypo-osmoregulate, and the associated gill transcriptional response to SW exposure featured many transcripts apparently regulated by the glucocorticoid stress axis and by the osmo-sensing transcription factor NFAT5. The importance of these pathways for the gill transcriptional response to SW exposure appears to diminish as a consequence of photoperiod mediated induction of the smolt phenotype, presumably reflecting preparatory developmental changes taking place during this process.

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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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            UpSetR: an R package for the visualization of intersecting sets and their properties

            Abstract Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability and implementation: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/. Contact: nils@hms.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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              GOplot: an R package for visually combining expression data with functional analysis.

              Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive-yet detailed understanding of the results remains challenging. This is mainly due to the lack of publicly available tools for the visualization of this type of information. Here we present an R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press
                2160-1836
                April 2021
                12 March 2021
                12 March 2021
                : 11
                : 4
                : jkab072
                Affiliations
                [1 ] Department of Arctic and Marine Biology, UiT -The Arctic University of Norway , Tromsø NO-9037, Norway
                [2 ] Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences , Ås NO-1432, Norway
                [3 ] School of Biological Sciences, University of Aberdeen , Aberdeen AB24 2TZ, UK
                [4 ] Centre for Integrative Genetics, Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences , Ås NO-1432, Norway
                Author notes
                Corresponding author: david.hazlerigg@ 123456uit.no
                Author information
                https://orcid.org/0000-0003-1020-4018
                https://orcid.org/0000-0003-4884-8409
                Article
                jkab072
                10.1093/g3journal/jkab072
                8049429
                33710311
                25aa1267-97d4-4b78-b871-b77bc4f7d59b
                © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 09 October 2020
                : 28 January 2021
                Page count
                Pages: 9
                Funding
                Funded by: Norway for funding;
                Award ID: 241016
                Categories
                Investigation
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140
                AcademicSubjects/SCI00010
                AcademicSubjects/SCI00960

                Genetics
                smoltification,smolting,osmoregulation,gills,atlantic salmon,photoperiod,nfat5,glucocorticoid
                Genetics
                smoltification, smolting, osmoregulation, gills, atlantic salmon, photoperiod, nfat5, glucocorticoid

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