Daily temporal homeostasis in the coral Acropora digitifera

This study aimed to identify the daily biological processes that occur under ambient conditions in the coral Acropora digitifera and present the biorhythm circadian "map"of biological processes that are entrained by environmental cues and the daily shifts in external conditions. On March 3rd, 2017, five mature Acropora digitifera colonies were collected from Sesoko Island, Okinawa, Japan at a three meter depth. Coral colonies were kept in direct flow-through seawater, pumped directly from the reef flat, and acclimatized for 72 hours before sampling. Coral tanks were placed outside and subjected to the natural diel cycle and moon phase. Sampling continued for 24 hours with two hour intervals (13 sampling points).RNA was extracted from 39 coral nubbins and sequenced on an Illumina NextSeq machine. We performed Variance analysis and clustering and were able to generate a gene list of 1,454 differentially expressed genes at each quarter of the day. These highly variable genes were assigned to clusters by their expression over time using a Dirichlet process Gaussian process model, which generated 67 gene clusters. We found cyclic regulating processes which help maintain the coral's physiology while adjusting to the daily external fluctuations. Our results could help shed some light on what are the environmental cues that corals react to and adapt their physiology, behavior, and biochemistry accordingly. This study aimed to identify the daily biological processes that occur under ambient conditions in the coral Acropora digitifera and present the biorhythm circadian map of biological processes that are entrained by environmental cues and the daily shifts in external conditions. On March 3rd, 2017, five mature Acropora digitifera colonies were collected from Sesoko Island, Okinawa, Japan at a three-meter depth. Coral colonies were kept in direct flow-through seawater, pumped directly from the reef flat, and acclimatized for 72 hours before sampling. Coral tanks were placed outside and subjected to the natural diel cycle and moon phase. Sampling continued for 24 hours with two-hour intervals (13 sampling points). RNA was extracted from 39 coral nubbins and sequenced on an Illumina NextSeq machine. We performed Variance analysis and clustering and were able to generate a gene list of 1,454 differentially expressed genes at each quarter of the day. These highly variable genes were assigned to clusters by their expression over time using a Dirichlet process Gaussian process model, which generated 67 gene clusters. We found cyclic regulating processes which help maintain the coral's physiology while adjusting to the daily external fluctuations. Our results could help shed some light on what are the environmental cues that corals react to and adapt their physiology, behavior, and biochemistry accordingly.