Transcriptome-wide Changes in Coral Gene Expression at Noon and Midnight Under Field Conditions

Abstract

Reef-building corals experience high daily variation in their environment, food availability, and physiological activities such as calcification and photosynthesis by endosymbionts. On Ofu Island, American Samoa, we investigated day-night differences in gene expression under field conditions of changing pH, temperature, light, and oxygen. Using RNASeq techniques, we compared two replicate transcriptomes from a single coral colony of Acropora hyacinthus over six noons and five midnights. We identified 344 contigs with significant expression differences across 16,800 contigs in the transcriptome, most with small fold-changes. However, there were 21 contigs with fold-changes ranging from 10 to 141. The largest changes were in a set of transcription factors strongly associated with day-night gene regulation in other animals, including cryptochromes, thyrotroph embryonic factor, and D site-binding protein. We also found large daytime increases in a set of genes involved in glucose transport and glycogen storage. We found small expression differences in genes associated with aerobic ATP production and hypoxia response, along with slightly higher expression of most calcification genes at noon. Although >40-fold-changes in expression occur in important transcription factors, downstream gene regulation seems very stable in corals from day to night compared to other animals studied.

Tidal heat pulses on a reef trigger a fine-tuned transcriptional response in corals to maintain homeostasis

“…Furthermore, by sampling once a day, we controlled for circadian and day-night gene expression oscillations [for example, see the studies of Levy et al . ( 33 ) and Ruiz-Jones and Palumbi ( 34 )]. Across all 51 field samples of A. hyacinthus , there were 17,315 contigs with a mean read depth greater than five.…”

“…For 17 consecutive days (14 to 30 August 2013), we sampled the transcriptomes of the three colonies at 1400. Our intent for sampling once a day was to control for oscillating expression patterns due to circadian rhythm [for example, see the study of Levy et al ( 33 )] and day-night gene regulation [for example, see the study of Ruiz-Jones and Palumbi ( 34 )]. It took approximately 10 min to sample the colonies (American Samoan Department of Marine and Wildlife Resources permit number 2012-65 and National Park Service Scientific Research and Collecting Permit number NPSA-2012-SCI-0008).…”

Transcriptome dynamics over a lunar month in a broadcast spawning acroporid coral

“…; Oren et al . ; Ruiz‐Jones & Palumbi ), the lack of data on lunar‐associated cycles blocks our ability to detect potential cycle overlaps that may act in a similar manner to drive biological processes that are regulated by the moon, such as broadcast spawning. We report here an RNA‐seq analysis of transcription in the reef‐building coral Acropora gemmifera (Brook 1892) over an entire lunar month, under stabilized environmental conditions.…”

Site-specific variation in gene expression from Symbiodinium spp. associated with offshore and inshore Porites astreoides in the lower Florida Keys is lost with bleaching and disease stress

“…Although data was not statistically significant (Table 5), cumulative trends demonstrate increased expression of five of the six zooxanthellae genes relative to the experimental control in response to heat stress, a trend also found in the literature [62]. During acute temperature exposure, symbiont cells show a “knee-jerk” reaction in which cumulative gene expression increases one or two-fold, increasing photosynthetic capacity, DNA synthesis and lipid metabolism (Fig 3)[62,63]. …”