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.