DOI: 10.5061/dryad.r24b1
title: Data from: The coral immune response facilitates protection against microbes during tissue regeneration

description: Increasing physical damage on coral reefs from predation, storms and
 anthropogenic disturbances highlights the need to understand the impact of
 injury on the coral immune system. In this study, we examined the
 regulation of the coral immune response over 10 days following physical
 trauma artificially inflicted on in situ colonies of the coral Acropora
 aspera, simultaneously with bacterial colonization of the lesions. Corals
 responded to injury by increasing the expression of immune system-related
 genes involved in the Toll-like and NOD-like receptor signalling pathways
 and the lectin–complement system in three phases (&lt;2, 4 and 10 days
 post-injury). Phenoloxidase activity was also significantly upregulated in
 two phases (&lt;3 and 10 days post-injury), as were levels of
 non-fluorescent chromoprotein. In addition, green fluorescent protein
 expression was upregulated in response to injury from 4 days post-injury,
 while cyan fluorescent protein expression was reduced. No shifts in the
 composition of coral-associated bacterial communities were evident
 following injury based on 16S rRNA gene amplicon pyrosequencing.
 Bacteria-specific fluorescence in situ hybridization also showed no
 evidence of bacterial colonization of the wound or regenerating tissues.
 Coral tissues showed near-complete regeneration of lesions within 10 days.
 This study demonstrates that corals exhibit immune responses that support
 rapid recovery following physical injury, maintain coral microbial
 homeostasis and prevent bacterial infestation that may compromise coral
 fitness.
description: 16S rRNA amplicon
 sequencing - QIIME analysisThis archive file
 contains all input and output files required for and produced by the QIIME
 pipeline in the 'dataset' folder. The quality file Wound.qual
 and the sequence file Wound.fna along with the mapping files Map.txt and
 Map_corrected2.txt are the primary input files. Output files include the
 complete selection of OTU tables (otu_table.biom,
 Normalised_otu_table.biom as well the weighted and unweighted Unifrac
 tables). Additional special files required for analysis can be found in
 the 'input' folder. The script 'QIIME Analysis
 script.txt' was used for data analysis and the file 'Sample
 names.txt' should be used to determine the biological sample /
 treatment corresponding to each sample. Sequences have been deposited in
 the NCBI Sequence Read Archive (SRA) database under study accession number
 SRP052969.16S amplicon data - QIIME
 analysis.zipImmune parameter
 dataThis archive file
 contains the data files for the expression levels of the range of immune
 parameters presented in the manuscript: 1) Chromoprotein expression
 levels, 2) Fluorescent protein expression levels, 3) Immune gene
 expression levels and 4) PO and tpPO activity levels. Each file contains a
 description of the samples and sample names used.Immune
 parameters.zipFluorescent Protein
 Analysis MethodologyThis archive file
 contains the files required for the fluorescent protein spectral analysis.
 The input file Wounding_Aaspera_fl.csv containing the raw fluorescence
 values and sample protein concentration is provided along with the
 reference fluorescent protein data file modelspecs_interp_25sh.csv (based
 on the spectrum of purified Acropora millepora fluorescent proteins) and
 the spectral decomposition script specs_regression_WF.R. The reference
 fluorescent protein data and the script were provided by Mikhail
 Matz.