title: 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: 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. 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.
  
  
  
  Here 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.
  
  
  
  This 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.
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.|Centre for Immunity, Infection and Evolution, Institute of Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK.|Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.
authors.forename: Samuel S C
authors.initials: SS
authors.lastname: Rund
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.|Present Address: Department of Computer Science, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Boyoung
authors.initials: B
authors.lastname: Yoo
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Camille
authors.initials: C
authors.lastname: Alam
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Taryn
authors.initials: T
authors.lastname: Green
authors.affiliation: Notre Dame Genomics and Bioinformatics Core Facility, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Melissa T
authors.initials: MT
authors.lastname: Stephens
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.|Notre Dame Genomics and Bioinformatics Core Facility, University of Notre Dame, Notre Dame, IN, 46556, USA.|Present Address: Department of Biology, University of South Dakota, Vermillion, SD, 57069, USA.|Present Address: Department of Computer Science, University of South Dakota, Vermillion, SD, 57069, USA.
authors.forename: Erliang
authors.initials: E
authors.lastname: Zeng
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Gary F
authors.initials: GF
authors.lastname: George
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Aaron D
authors.initials: AD
authors.lastname: Sheppard
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Giles E
authors.initials: GE
authors.lastname: Duffield
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.|Interdisciplinary Center for Network Science and Applications (iCeNSA), University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Tijana
authors.initials: T
authors.lastname: Milenković
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA. Michael.Pfrender.1@nd.edu.|Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA. Michael.Pfrender.1@nd.edu.|Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, 46556, USA. Michael.Pfrender.1@nd.edu.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Pfrender
mesh_terms: D000465:Algorithms; D000818:Animals; D060829:Arthropod Proteins / Q000235:genetics; D057906:Circadian Clocks; D003621:Daphnia / Q000235:genetics / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010507:Periodicity
chemical_list: D060829:Arthropod Proteins
keywords: Biological networks; Circadian; Diel; Diel Vertical Migration (DVM); Functional enrichment analysis; Gene expression; Network centrality; Network clustering; Protein function prediction