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

Samuel S C Rund; Boyoung Yoo; Camille Alam; Taryn Green; Melissa T Stephens; Erliang Zeng; Gary F George; Aaron D Sheppard; Giles E Duffield; Tijana Milenković; Michael E Pfrender

doi:10.1186/s12864-016-2998-2

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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

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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

Samuel S C Rund, Boyoung Yoo, Camille Alam, Taryn Green, Melissa T Stephens, Erliang Zeng, Gary F George, Aaron D Sheppard, Giles E Duffield, Tijana Milenković, …

BMC genomics, Vol.17(1), pp.653-653

08/18/2016

DOI: 10.1186/s12864-016-2998-2

PMCID: PMC4991082

PMID: 27538446

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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.

Algorithms

Animals

Daphnia - physiology

Oligonucleotide Array Sequence Analysis - methods

Molecular Sequence Annotation

Gene Expression Regulation

Periodicity

Circadian Clocks

Gene Expression Profiling - methods

Arthropod Proteins - genetics

Gene Regulatory Networks

Daphnia - genetics

Details

Title: Subtitle: 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
Creators: Samuel S C Rund - Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
Boyoung Yoo - Present Address: Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
Camille Alam - Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
Taryn Green - Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
Melissa T Stephens - Notre Dame Genomics and Bioinformatics Core Facility, University of Notre Dame, Notre Dame, IN, 46556, USA
Erliang Zeng - Present Address: Department of Computer Science, University of South Dakota, Vermillion, SD, 57069, USA
Gary F George - Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
Aaron D Sheppard - Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
Giles E Duffield - Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
Tijana Milenković - Interdisciplinary Center for Network Science and Applications (iCeNSA), University of Notre Dame, Notre Dame, IN, 46556, USA
Michael E Pfrender - Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, 46556, USA. Michael.Pfrender.1@nd.edu
Resource Type: Journal article
Publication Details: BMC genomics, Vol.17(1), pp.653-653
DOI: 10.1186/s12864-016-2998-2
PMID: 27538446
PMCID: PMC4991082
NLM abbreviation: BMC Genomics
ISSN: 1471-2164
eISSN: 1471-2164
Publisher: England
Grant note: 095831 / Wellcome Trust Wellcome Trust R24 GM078274 / NIGMS NIH HHS R01 GM087508 / NIGMS NIH HHS
Language: English
Date published: 08/18/2016
Academic Unit: Preventive and Community Dentistry; Roy J. Carver Department of Biomedical Engineering; Iowa Neuroscience Institute; Biostatistics; Dental Research
Record Identifier: 9984065472002771

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