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      Transcriptomic Analysis of Thermally Stressed Symbiodinium Reveals Differential Expression of Stress and Metabolism Genes

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          Abstract

          Endosymbioses between dinoflagellate algae ( Symbiodinium sp.) and scleractinian coral species form the foundation of coral reef ecosystems. The coral symbiosis is highly susceptible to elevated temperatures, resulting in coral bleaching, where the algal symbiont is released from host cells. This experiment aimed to determine the transcriptional changes in cultured Symbiodinium, to better understand the response of cellular mechanisms under future temperature conditions. Cultures were exposed to elevated temperatures (average 31°C) or control conditions (24.5°C) for a period of 28 days. Whole transcriptome sequencing of Symbiodinium cells on days 4, 19, and 28 were used to identify differentially expressed genes under thermal stress. A large number of genes representing 37.01% of the transcriptome (∼23,654 unique genes, FDR < 0.05) with differential expression were detected at no less than one of the time points. Consistent with previous studies of Symbiodinium gene expression, fold changes across the transcriptome were low, with 92.49% differentially expressed genes at ≤2-fold change. The transcriptional response included differential expression of genes encoding stress response components such as the antioxidant network and molecular chaperones, cellular components such as core photosynthesis machinery, integral light-harvesting protein complexes and enzymes such as fatty acid desaturases. Differential expression of genes encoding glyoxylate cycle enzymes were also found, representing the first report of this in Symbiodinium. As photosynthate transfer from Symbiodinium to coral hosts provides up to 90% of a coral’s daily energy requirements, the implications of altered metabolic processes from exposure to thermal stress found in this study on coral- Symbiodinium associations are unknown and should be considered when assessing the stability of the symbiotic relationship under future climate conditions.

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          Most cited references 78

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          Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

          Background New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. Results More than 600,000 reads produced in a single 454 sequencing run were assembled into ~40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified ~11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed ~8,500 pairs of orthologs and ~100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. Conclusion The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.
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            A comparison of the 1998 and 2002 coral bleaching events on the Great Barrier Reef: spatial correlation, patterns, and predictions

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              A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai'i.

              Dinoflagellates in the genus Symbiodinium are crucial components of coral reef ecosystems in their roles as endosymbionts of corals and other marine invertebrates. The genus Symbiodinium encompasses eight lineages (clades A-H), and multiple sub-clade types. Symbiodinium in clades A, B, C, and D are most commonly associated with metazoan hosts while clades C, D, F, G, and H with large soritid foraminifera. Recent studies have described a diversity of new Symbiodinium types within each clades, but no new clades have been reported since 2001. Here, we describe a new clade of Symbiodinium isolated from soritid foraminifera from Hawai'i. Published by Elsevier Inc.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                28 February 2017
                2017
                : 8
                Affiliations
                1College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville QLD, Australia
                2Comparative Genomics Centre, James Cook University, Townsville QLD, Australia
                3ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville QLD, Australia
                4Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra ACT, Australia
                Author notes

                Edited by: Basil J. Nikolau, Iowa State University, USA

                Reviewed by: Ryo Nakabayashi, RIKEN, Japan; Emilie Villar, Centre National de la Recherche Scientifique, France

                *Correspondence: Sarah L. Gierz, sarah.gierz@ 123456my.jcu.edu.au

                This article was submitted to Plant Metabolism and Chemodiversity, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2017.00271
                5328969
                28293249
                Copyright © 2017 Gierz, Forêt and Leggat.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 4, Tables: 0, Equations: 0, References: 111, Pages: 20, Words: 0
                Funding
                Funded by: Australian Research Council 10.13039/501100000923
                Award ID: CE140100020
                Award ID: DP130101421
                Award ID: DP160100271
                Categories
                Plant Science
                Original Research

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