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      Gene expression plasticity facilitates acclimatization of a long-lived Caribbean coral across divergent reef environments

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          Abstract

          Local adaptation can increase fitness under stable environmental conditions. However, in rapidly changing environments, compensatory mechanisms enabled through plasticity may better promote fitness. Climate change is causing devastating impacts on coral reefs globally and understanding the potential for adaptive and plastic responses is critical for reef management. We conducted a four-year, three-way reciprocal transplant of the Caribbean coral Siderastrea siderea across forereef, backreef, and nearshore populations in Belize to investigate the potential for environmental specialization versus plasticity in this species. Corals maintained high survival within forereef and backreef environments, but transplantation to nearshore environments resulted in high mortality, suggesting that nearshore environments present strong environmental selection. Only forereef-sourced corals demonstrated evidence of environmental specialization, exhibiting the highest growth in the forereef. Gene expression profiling 3.5 years post-transplantation revealed that transplanted coral hosts exhibited profiles more similar to other corals in the same reef environment, regardless of their source location, suggesting that transcriptome plasticity facilitates acclimatization to environmental change in S. siderea. In contrast, algal symbiont ( Cladocopium goreaui) gene expression showcased functional variation between source locations that was maintained post-transplantation. Our findings suggest limited acclimatory capacity of some S. siderea populations under strong environmental selection and highlight the potential limits of coral physiological plasticity in reef restoration.

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

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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

                Contributors
                kdcastil@email.unc.edu
                colleenbove@gmail.com
                daviessw@bu.edu
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                3 April 2024
                3 April 2024
                2024
                : 14
                : 7859
                Affiliations
                [1 ]Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, ( https://ror.org/0130frc33) Chapel Hill, NC USA
                [2 ]Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, ( https://ror.org/0130frc33) Chapel Hill, NC USA
                [3 ]Department of Biology, Boston University, ( https://ror.org/05qwgg493) Boston, MA USA
                [4 ]Department of Marine and Environmental Sciences, Marine Sciences Center, Northeastern University, ( https://ror.org/04t5xt781) Nahant, MA USA
                Article
                57319
                10.1038/s41598-024-57319-0
                10991280
                38570591
                7f6a7fd9-a92d-46b1-95bc-ec41edb0df36
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 16 March 2023
                : 17 March 2024
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000192, National Oceanic and Atmospheric Administration;
                Award ID: NA13OAR4310186
                Funded by: NSF
                Award ID: OCE-1459522
                Award ID: OCE-1357665
                Award Recipient :
                Funded by: Boston University Microbiome Initiative
                Funded by: FundRef http://dx.doi.org/10.13039/100009559, Life Sciences Research Foundation;
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2024

                Uncategorized
                acclimatization,caribbean coral,reciprocal transplant,transcriptome plasticity,environmental variability,environmental specialization,ecophysiology,climate-change ecology,coral reefs

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