Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation

Abstract

BackgroundMarine and freshwater zooplankton exhibit daily rhythmic patterns of behavior and physiology which may be regulated directly by the light:dark (LD) cycle and/or a molecular circadian clock. One of the best-studied zooplankton taxa, the freshwater crustacean Daphnia, has a 24 h diel vertical migration (DVM) behavior whereby the organism travels up and down through the water column daily. DVM plays a critical role in resource tracking and the behavioral avoidance of predators and damaging ultraviolet radiation. However, there is little information at the transcriptional level linking the expression patterns of genes to the rhythmic physiology/behavior of Daphnia.ResultsHere we analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 44 h time period under a 12:12 LD cycle (diel) conditions using a cosine-fitting algorithm. We used a comprehensive network modeling and analysis approach to identify novel co-regulated rhythmic genes that have similar network topological properties and functional annotations as rhythmic genes identified by the cosine-fitting analyses. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus enhancing current functional annotations available for genes in this ecologically relevant model species. Our results reveal that genes in many functional groupings exhibit 24 h rhythms in their expression patterns under diel conditions. We highlight the rhythmic expression of immunity, oxidative detoxification, and sensory process genes. We discuss differences in the chronobiology of D. pulex from other well-characterized terrestrial arthropods.ConclusionsThis research adds to a growing body of literature suggesting the genetic mechanisms governing rhythmicity in crustaceans may be divergent from other arthropod lineages including insects. Lastly, these results highlight the power of using a network analysis approach to identify differential gene expression and provide novel functional annotation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2998-2) contains supplementary material, which is available to authorized users.

Evolution to environmental contamination ablates the circadian clock of an aquatic sentinel species

“…We showed that per expression levels oscillate over 48 hr in complete darkness with a 20‐hr period, validating that D. pulex maintain an endogenous circadian rhythm. Further, our data corroborate more recent work that shows that D. pulex have expression of core clock genes (Bernatowicz et al., ; Rund et al., ). Bernatowicz et al.…”

“…In conjunction with the conservation of core clock genes, our data suggest that D. pulex maintain a molecular clock with similar architecture to those studied in other eukaryotic organisms (Partch, Green, & Takahashi, ; Tilden et al., ). Of note, the expression levels of per and clk in our control population closely resemble the expression of these genes in mosquitoes ( Anopheles gambiae ), relevant as the circadian rhythm of D. pulex is thought to be more like that of butterflies and mosquitos than that of Drosophila (Bernatowicz et al., ; Meireles‐Filho & Kyriacou, ; Rund et al., ; Tilden et al., ).…”

“…() and Rund et al. () also show an increase in per expression levels at approximately CT 12, or the beginning of the subjective night, as well as minimal oscillations in the clk gene. Though there are differences between these studies’ results and our own, these differences could be attributed to disparities in many key areas, including husbandry, experimental light conditions (constant dark vs. light–dark cycles), experimental duration (24 vs. 48 hr), experimental approach, and differences in the Daphnia clones.…”

“…Recent work suggests a circadian oscillation in D. pulex on the molecular level (Bernatowicz et al., ; Rund et al., ). However, a molecular clock in D. pulex has not been shown to persist without external cues, which is a requirement of endogenous clocks.…”

“…We found that both primer sets amplified the desired product in the light sample (sampled after 4 hr of light exposure; Figure 2a, lanes 2 and 3) as well as the dark sample (sampled after 16 hr in the dark; Figure 2a, lanes 4 and 5), demonstrating that per and tbp were expressed under our culture conditions. Recent work suggests a circadian oscillation in D. pulex on the molecular level (Bernatowicz et al, 2016;Rund et al, 2016). However, a molecular clock in D. pulex has not been shown to persist without external cues, which is a requirement of endogenous clocks.…”