Supplementary Materials for - Science Advances · Supplementary Materials for Tidal heat pulses on a reef trigger a fine-tuned transcriptional response in corals to maintain homeostasis

advances.sciencemag.org/cgi/content/full/3/3/e1601298/DC1

Supplementary Materials for

Tidal heat pulses on a reef trigger a fine-tuned transcriptional response

in corals to maintain homeostasis

Lupita J. Ruiz-Jones and Stephen R. Palumbi

Published 8 March 2017, Sci. Adv. 3, e1601298 (2017)

DOI: 10.1126/sciadv.1601298

The PDF file includes:

fig. S1. Light intensity, temperature, and pH over the 17 days, and DO saturation

and depth for the first 14 days of the time series.

fig. S2. Temperature, pH, and DO saturation during the 1 hour before

transcriptome sampling for each day of the 17-day experiment.

fig. S3. The magnitude of day-to-night variability in temperature, pH, and DO

saturation for the time series.

fig. S4. Expression profiles in A. hyacinthus of the three environmentally

responsive modules during the time series.

fig. S5. Temperature profiles during the time series for each colony of A.

hyacinthus.

fig. S6. Results from the PCA of the 177 contigs in the UPR and calcium

homeostasis module for each colony of A. hyacinthus.

fig. S7. Minimum, mean, and maximum temperature and pH for each time point

in a day.

fig. S8. Trait heat map of the correlations between module eigengene values and

the environmental variables.

Legends for tables S1 to S3

table S4. The 37 unique functional enrichment genes for the UPR and calcium

homeostasis module in A. hyacinthus.

Legend for tables S5

table S6. The 34 unique functional enrichment genes for module RJ6 in A.

hyacinthus.

table S7. The number of contigs in modules RJ6, RJ9, and RJ11 that are present in

each of the gene modules identified by Rose and colleagues (18).

Other Supplementary Material for this manuscript includes the following:

(available at advances.sciencemag.org/cgi/content/full/3/3/e1601298/DC1)

table S1 (Microsoft Excel format). Contigs in each of the 13 modules for A.

hyacinthus and their module membership.

table S2 (Microsoft Excel format). Results from ANOVA tests looking at the

relationship of module expression in A. hyacinthus to multiple factors.

table S3 (Microsoft Excel format). Functional enrichment results for the UPR and

calcium homeostasis module in A. hyacinthus.

table S5 (Microsoft Excel format). Functional enrichment results for module RJ6

in A. hyacinthus.

SUPPLEMENTARY MATERIALS

fig. S1. Light intensity, temperature, and pH over the 17 days, and DO saturation and

depth for the first 14 days of the time series. The vertical lines mark 14:00 each day. The light

and temperature plots show averages for the three colonies (see fig. S5 for individual colony

temperature plots).

fig. S2. Temperature, pH, and DO saturation during the 1 hour before transcriptome

sampling for each day of the 17-day experiment. The temperature boxplots show the values

between 13:00 – 14:10 for each day (n = 8 time points). The pH boxplots show the values

between 13:00 – 14:20 (n = 5 time points). The dissolved oxygen saturation boxplots show the

values between 13:01 – 14:11 (n = 8 time points). Dissolved oxygen saturation data was

collected for the first 14 days.

fig. S3. The magnitude of day-to-night variability in temperature, pH, and DO saturation

for the time series. The standard deviations and ranges for temperature, pH, and dissolved

oxygen saturation during the 12 h prior to sampling are plotted for each day. For temperature,

each line represents one colony. Dissolved oxygen saturation data was collected for the first 14

days.

fig. S4. Expression profiles in A. hyacinthus of the three environmentally responsive

modules during the time series. Expression levels are represented by eigengenes for each day.

These three modules had significant expression associations to changes in the environment

(ANOVA, FDR corrected, all P < 0.01). In the text, Module RJ9 is also referred to as the UPR

and Calcium Homeostasis Module. Each color represents a different colony: AH06 = gold,

AH75 = blue, and AH88 = red. The number of contigs in each module is listed above each plot.

fig. S5. Temperature profiles during the time series for each colony of A. hyacinthus.

Temperature loggers were positioned with 30 cm of each colony. The vertical line marks 14:00.

fig. S6. Results from the PCA of the 177 contigs in the UPR and calcium homeostasis

module for each colony of A. hyacinthus. For each colony, principal components 1 and 2 are

plotted against each other and the proportion of variation explained by each is listed in each plot.

The numbers in the plots represent each of the 17 days of the time series.

fig. S7. Minimum, mean, and maximum temperature and pH for each time point in a day.

Time is in 12 min intervals for temperature and in 20 min intervals for pH. Generated from a

196-day temperature time series and a 76-day pH time series; both of which were collected from

the same area of the back-reef where we conducted our field experiment.

fig. S8. Trait heat map of the correlations between module eigengene values and the

environmental variables. For the 13 gene modules, the correlations between module eigengenes

across all 51 samples and the 1 h mean prior to sampling and 12 h standard deviation for light

intensity (PAR), temperature (°C), pH, dissolved oxygen saturation (%), and depth (m). False

discovery rate corrected P values are reported in parenthesis. Modules are labeled ME1 through

ME13. SD; standard deviation.

table S4. The 37 unique functional enrichment genes for the UPR and calcium homeostasis

module in A. hyacinthus. Functional enrichment analysis was done in Database for Annotation,

Visualization and Integrated Discovery (v6.7). These are the genes responsible for the significant

gene ontology terms (Benjamini-Hochberg adjusted P < 0.05). Some UniProt accessions are

associated with multiple contigs.

UniProt

Accession Contig Name Description

Q03669 contig98302 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2

P14211 contig176450_105992 Calreticulin

O23184 contig115941_181836 Calcium-binding protein CML19

P51868 contig20122 Calsequestrin-2

Q8BH97 contig189685 Reticulocalbin-3

Q9H2B2 contig116802_21164 Synaptotagmin-4

O43581 contig112078 Synaptotagmin-7

O43581

contig16340_137404_

71412_180832_15195

9 Synaptotagmin-7

Q5NVI9 contig169440 DnaJ homolog subfamily A member 1

Q13217 contig149217 DnaJ homolog subfamily C member 3

P08110

contig152263_170651

_208957 Endoplasmin

P27420 contig219137 Heat shock 70 kDa protein C

Q18688 contig213914 Heat shock protein 90

P11501 contig183708 Heat shock protein HSP 90-alpha

Q7ZUW2 contig174767 Hypoxia up-regulated protein 1

Q7ZUW2 contig178720_177820 Hypoxia up-regulated protein 1

Q925U4 contig169860 ER degradation-enhancing alpha-mannosidase-like 1

Q9TT38 contig172456 Cytosolic phospholipase A2

Q7T0T9 contig204384_69966 Cytosolic phospholipase A2

Q3TBT3 contig151962 Transmembrane protein 173

P24367 contig213182 Peptidyl-prolyl cis-trans isomerase B

P45877 contig165620 Peptidyl-prolyl cis-trans isomerase C

Q9EPK6 contig99157 Nucleotide exchange factor SIL1

Q8WXF0 contig146692 Serine/arginine-rich splicing factor 12

Q91XE9 contig204685 Cyclic AMP-responsive element-binding protein 3-like protein 3

Q4V8Y6 contig183849 Endoplasmic reticulum-Golgi intermediate compartment protein 1

Q9DC16 contig82989 Endoplasmic reticulum-Golgi intermediate compartment protein 1

Q6AYY8 contig170925_178536 Acetyl-coenzyme A transporter 1

O16025 contig117567 Allene oxide synthase-lipoxygenase protein

Q99JG3 contig117970_92676 Annexin A13

table S4. Continued

UniProt


Q5RDD8 contig111238_205222 Calumenin

Q6XLQ7 contig176437 Calumenin

P52826 contig152777_153218 Carnitine O-acetyltransferase

Q7SXF6 contig151481 Cysteine-rich with EGF-like domain protein 2

O97125 contig187488 Heat shock protein 68

Q5R687 contig79655 Insulin-induced gene 2 protein

P22758 contig203152 Protein-glutamine gamma-glutamyltransferase K

Q86WA9 contig147342 Sodium-independent sulfate anion transporter

O18405 contig150949 Surfeit locus protein 4 homolog

table S6. The 34 unique functional enrichment genes for module RJ6 in A. hyacinthus.

Functional enrichment analysis was done in Database for Annotation, Visualization and

Integrated Discovery (v6.7). These are the genes responsible for the significant gene ontology

terms (Benjamini-Hochberg adjusted P < 0.05). Some UniProt accessions are associated with

multiple contigs.

UniProt


B7PAD9 contig192794 Putative uncharacterized protein

O89114 contig104770 DnaJ homolog subfamily B member 5



O89114 contig170561_190070 DnaJ homolog subfamily B member 5


O89114 contig219229_106934 DnaJ homolog subfamily B member 5


P05627 contig211469_148901_120483 Transcription factor AP-1

P11308 contig175601 Transcriptional regulator ERG



P13346 contig182044 Protein fosB

P17431 contig177051 Zinc finger protein 36, C3H1 type-like 1

P17431 contig209414 Zinc finger protein 36, C3H1 type-like 1

P21272 contig116059 CCAAT/enhancer-binding protein beta



P24610

contig209407_108765_77238_964

85 Paired box protein Pax-3

P26632 contig68383_180363_132010 Early growth response protein 1

P38529 contig145533 Heat shock factor protein 1




P41156 contig68724 Protein C-ets-1

P41158 contig109454_149736 ETS domain-containing protein Elk-4

P41969 contig150730 ETS domain-containing protein Elk-1

P59055 contig156842 Cysteine/serine-rich nuclear protein 3

P59055 contig79663 Cysteine/serine-rich nuclear protein 3

P79145 contig145275_179145 cAMP-responsive element modulator

P79145 contig180769 cAMP-responsive element modulator

table S6. Continued

UniProt


P97360 contig105526 Transcription factor ETV6

P97360 contig170228_212502 Transcription factor ETV6

P97360 contig177469_209841 Transcription factor ETV6

Q00709 contig176326 Apoptosis regulator Bcl-2

Q01196 contig145294_114125 Runt-related transcription factor 1

Q04688 contig189533_109443_15068 DNA-binding protein Ets97D

Q0IH87 contig105296_171521 Paired box protein Pax-3-B

Q0IH87 contig154274_177837 Paired box protein Pax-3-B

Q13887 contig158041 Krueppel-like factor 5




Q24180

contig170318_10188_144982_210

582 Deformed epidermal autoregulatory factor 1

Q24180 contig75580 Deformed epidermal autoregulatory factor 1

Q2MJB4 contig104395_153016 Doublesex- and mab-3-related transcription factor A2

Q2MJB4

contig44815_68504_129659_2050

01 Doublesex- and mab-3-related transcription factor A2

Q4V5A3 contig204704 Homeobox protein unplugged

Q6P788 contig109698 Cyclic AMP-dependent transcription factor ATF-5

Q6P788 contig174339 Cyclic AMP-dependent transcription factor ATF-5

Q8C172 contig155787_170803 Ceramide synthase 6

Q8R3Y8

contig155851_69784_130543_130

414 Interferon regulatory factor 2-binding protein 1

Q8R5K6 contig163512_152421_180625 Protein Tob1

Q90XW6 contig115684 Iroquois-class homeodomain protein irx-4-A



Q99676 contig202444_149735_68940 Zinc finger protein 184

Q9HAW4 contig107904_151594 Claspin

Q9MZT6 contig139133 Myc proto-oncogene protein

Q9PVY8

contig205137_147819_210532_11

0623 Forkhead box protein C2-B

Q9WTP3 contig152086_121449 SAM pointed domain-containing Ets transcription factor

table S7. The number of contigs in modules RJ6, RJ9, and RJ11 that are present in each of

the gene modules identified by Rose and colleagues (18). Our Modules RJ6, RJ9, and RJ11 are

enriched for genes in Module Rose1 (general heat stress response), Module Rose8 (DNA repair),

and Module Rose12 (bleaching related) (Fisher’s exact test for over-representation P < 0.005);

denoted by asterisks. Not all the contigs in our modules were present in the Rose et al. (2016)

module data set (note the totals in the last row). Module RJ9 is referred to as the UPR and

Calcium Homeostasis Module in the text.

Rose Modules Number of contigs in Rose Modules Module RJ6 Module RJ9 Module RJ11

1 * 2459 94 91 40

2 1430 8 2 0

3 1368 1 5 0

4 1355 4 3 0

5 1141 8 9 3

6 1026 0 0 0

7 1022 6 3 3

8 * 874 33 15 2

9 798 2 1 0

10 442 1 2 0

11 384 1 1 0

12 * 277 47 14 21

13 162 2 0 0

14 162 3 8 0

15 153 1 1 2

16 138 2 2 1

17 105 13 1 1

18 81 0 0 0

19 80 0 3 0

20 44 0 0 0

21 42 0 0 0

22 27 0 0 0

23 26 0 0 0

Total 13596 226 161 73

Supplemental tables provided separately

table S1. Contigs in each of the 13 modules for A. hyacinthus and their module

membership.

table S2. Results from ANOVA tests looking at the relationship of module expression in A.

hyacinthus to multiple factors.

table S3. Functional enrichment results for the UPR and calcium homeostasis module in A.

hyacinthus.

table S5. Functional enrichment results for module RJ6 in A. hyacinthus.

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Supplementary Materials for - Science Advances · Supplementary Materials for Tidal heat pulses on a reef trigger a fine-tuned transcriptional response in corals to maintain homeostasis