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.
Highlights
Marine 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
Global transcription analysis and JTK_CYCLE analysis To perform an analysis of D. pulex rhythmic gene expression under laboratory conditions, we profiled genome-wide expression patterns of mature, egg-bearing females maintained on a 12:12 LD cycle with abrupt LD transitions
Our analysis revealed that Daphnia express a great number and diversity of genes in a highly rhythmic manner, including genes involved in sensory processes, response to oxidative stress, and immune-related genes
Summary
Marine 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. As organisms progress through their 24 h day, they experience a daily cycle of environmental changes, including rhythms in temperature, light, predation risk, and resource availability. To respond to these daily environmental changes, organisms modulate their biology in a rhythmic manner driven by both the coordinated action of an endogenous circadian pacemaker or clock, as well as the direct effect of the environmental light:dark cycle (LD cycle) [1,2,3,4,5,6,7,8]. Under both circadian and/or diel conditions, as much as 5 % of the transcripts expressed in the fruit fly Drosophila melanogaster head and 4 % in the honeybee Apis mellifera head are rhythmically expressed [14,15,16]
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