This file is part of the following reference:

Seneca, François (2010) The molecular stress response in the Indo-Pacific model scleractinian coral, Acropora

millepora. PhD thesis, James Cook University.

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Appendices

152

Appendices

Supplementary Table S.1. Primers used for the genes under investigation in the qRTPCR experiment. The

best Tblastx match and E value are shown for the EST sequence corresponding to the indicated accession

number. The Symbiodinium-specific PCNA primers were designed on the same sequences used in Boldt

et al. (2009).

Supplementary Table S.2. Ranking of the candidate ICGs according to their M and CV values (Hellemans

et al. 2007) calculated between healthy-looking and severely bleached samples across the nine colonies

used in qRTPCR experiment.

Appendices

153

Supplementary Table S.3. MIQE checklist (Bustin et al. 2009).

Appendices

154

Supplementary Fig. S.1. Consistent difference between average quantification cycles of healthy (dark

grey) and bleached (light grey) samples in nine colonies, for the best performing ICGs: GAPDH, rpL9

and S7

Appendices

155

Supplementary Fig. S.2. Maximum likelihood tree of the USP domain sequences in animals. The

numbers on the nodes indicate their support by a SH-like likelihood ratio test.

Appendices

156

Supplementary Fig. S.3. Maximum likelihood tree of the USP domain sequences in animals. The

numbers on the nodes indicate their bootstrap support.

Appendices

157

Supplementary Fig. S.4. Bayesian tree of the USP domain sequences in all species. The numbers on

each node represent the posterior probability.

Appendices

158

Supplementary Fig. S.5. Maximum likelihood tree of the USP domain sequences in all species. The

numbers on the nodes indicate their support by a SH-like likelihood ratio test.

Appendices

159

Supplementary Fig. S.6. Maximum likelihood tree of the USP domain sequences in all species. The

numbers on the nodes indicate their bootstrap support.

Appendices

160

Supplementary Fig. S.7. Likelihood mapping assessing the monophyly of animal USPs. 79.1% of

10,000 random quartets are consistent with metazoan (a) and non-metazoan sequences (b) grouping

separately.

Appendices

161

Appendices

162

Supplementary Fig. S.8. Multiple sequences alignment of USP domains. Vertical bars indicate an

intron between two amino acid positions, left slanted bars indicate that a codon has 1 nucleotide in the 5'

exon and 2 nucleotides in the 3' exon, right slanted bars indicate that a codon has 2 nucleotide in the 5'

exon and 1 nucleotides in the 3' exon. The boxes above the alignment denote the approximate position of

alpha helices (pink) and beta strands (blue) in the secondary structure of 1MJH. Asterisks under the

alignment highlight the position of residues involved in ATP binding in 1MJH. The arrow under the

alignment points at the position of the intron conserved between plants and animals.