DOI: 10.5061/dryad.5d079
title: Data from: Fluorescent protein-mediated colour polymorphism in reef corals: multi-copy genes extend the adaptation/acclimatization potential to variable light environments

description: The genomic framework that enables corals to adjust to unfavourable
 conditions is crucial for coral reef survival in a rapidly changing
 climate. We have explored the striking intraspecific variability in the
 expression of coral pigments from the green fluorescent protein (GFP)
 family to elucidate the genomic basis for the plasticity of stress
 responses among reef corals. We show that multi-copy genes can greatly
 increase the dynamic range over which corals can modulate transcript
 levels in response to the light environment. Using the red fluorescent
 protein amilFP597 in the coral Acropora millepora as a model, we
 demonstrate that its expression increases with light intensity, but both
 the minimal and maximal gene transcript levels vary markedly among colour
 morphs. The pigment concentration in the tissue of different morphs is
 strongly correlated with the number of gene copies with a particular
 promoter type. These findings indicate that colour polymorphism in reef
 corals can be caused by the environmentally regulated expression of
 multi-copy genes. High-level expression of amilFP597 is correlated with
 reduced photodamage of zooxanthellae under acute light stress, supporting
 a photoprotective function of this pigment. The cluster of light-regulated
 pigment genes can enable corals to invest either in expensive high-level
 pigmentation, offering benefits under light stress, or to rely on low
 tissue pigment concentrations and use the conserved resources for other
 purposes, which is preferable in less light-exposed environments. The
 genomic framework described here allows corals to pursue different
 strategies to succeed in habitats with highly variable light stress
 levels. In summary, our results suggest that the intraspecific plasticity
 of reef corals’ stress responses is larger than previously thought.
description: Abs spectra of A
 milleporaAbsorption spectra of
 clarified tissue extracts of the HR and LR A. millepora morphs. The
 absorption spectrum of purified recombinant amilFP597 normalised to the
 peak value of the HR spectrum is included for
 comparison.amilFP597
 copiesCopy numbers of
 amilFP597 variant genes determined by semi-quantitative PCR amplification
 of a conserved genomic exon 3 fragment and by diagnostic restriction
 analysis with ApeK1.amilFP597 indel (+) and
 indel (-) promoter variantsSequences of all
 promoter clones of amilFP597 coding sequence.amilFP597 exon 3
 sequencesThe chromophore coding
 sequences of RFP-related genes of A. millepora were amplified using
 genomic DNA of LR, MR and HR morphs as the template with primers designed
 to conserved regions within exon 3 .amilFP597
 promoterAnalysis of the
 amilFP597 promoter copy ratios in six A. millepora morphs with different
 levels of redness.Sequences RFP full
 length genesAll raw sequences used
 to reconstruct the amilFP597 gene in A. millepora.Full-length sequences of
 indel (-) and indel (+) promoter variants of the amilFP597 gene were
 obtained for the MR morph. These sequences, extending from the promoter
 region to the 3’UTR, were produced by joining the sequences of two
 overlapping PCR products covering the 5’ region [promoter to exon 3
 amplified using primers pRFPlargeF (+) or pRFPsmallF (-) and RFP SP1] and
 the 3’ region (intron 2 to 3’UTR amplified using primers RFP_I2-3’U_F and
 RFP_I2-3’U_R2). Sequence differences in the overlap between the 5’ and 3’
 region fragments were used to assign the latter to either the indel (+) or
 indel (-) promoter variant genes. The promoter-exon 3 and intron 2-3’UTR
 fragments were cloned and sequenced on both strands using vector primers
 and by primer walking. The assembled sequences have been submitted to
 GenBank as accessions KC818413 [indel (-) gene] and KC818414 [indel (+)
 gene].Spectroscopic
 characteristics of GFP-like proteinsAll spectroscopic data
 utilised for the characterisation of amilFP597, amilCP506, amilCP564 and
 amilFP605