title: Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus).
abstract: BACKGROUND
  With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs.
  
  
  RESULTS
  We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs' electric organ, main electric organ, and Hunter's electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species.
  
  
  CONCLUSIONS
  Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here.
authors.affiliation: Department of Genetics, University of Wisconsin, Madison, WI, 53706, USA. lltraeger@wisc.edu.|Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA. lltraeger@wisc.edu.
authors.forename: Lindsay L
authors.initials: LL
authors.lastname: Traeger
authors.affiliation: Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA. volkening@wisc.edu.|Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA. volkening@wisc.edu.
authors.forename: Jeremy D
authors.initials: JD
authors.lastname: Volkening
authors.affiliation: Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. hmoffett@partners.org.|Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. hmoffett@partners.org.
authors.forename: Howell
authors.initials: H
authors.lastname: Moffett
authors.affiliation: Department of Zoology, Michigan State University, East Lansing, MI, 48824, USA. jgallant@msu.edu.|BEACON Center for the Study of Evolution in Action, Lansing, USA. jgallant@msu.edu.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Gallant
authors.affiliation: Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. sleepy.howard@gmail.com.|Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. sleepy.howard@gmail.com.|Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA. sleepy.howard@gmail.com.
authors.forename: Po-Hao
authors.initials: PH
authors.lastname: Chen
authors.affiliation: Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. carl_novina@dfci.harvard.edu.|Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. carl_novina@dfci.harvard.edu.|Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA. carl_novina@dfci.harvard.edu.
authors.forename: Carl D
authors.initials: CD
authors.lastname: Novina
authors.affiliation: BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, 77005, USA. georgep@rice.edu.
authors.forename: George N
authors.initials: GN
authors.lastname: Phillips
authors.affiliation: Department of Pharmacology and Department of Neuroscience, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA. anand.20@osu.edu.
authors.forename: Rene
authors.initials: R
authors.lastname: Anand
authors.affiliation: Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77483, USA. gbwells@tamu.edu.
authors.forename: Gregg B
authors.initials: GB
authors.lastname: Wells
authors.affiliation: Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA. mpinch@nmsu.edu.
authors.forename: Matthew
authors.initials: M
authors.lastname: Pinch
authors.affiliation: Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA. rgueth@nmsu.edu.
authors.forename: Robert
authors.initials: R
authors.lastname: Güth
authors.affiliation: Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA. gunguez@nmsu.edu.
authors.forename: Graciela A
authors.initials: GA
authors.lastname: Unguez
authors.affiliation: Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA. jalbert@louisiana.edu.
authors.forename: James S
authors.initials: JS
authors.lastname: Albert
authors.affiliation: BEACON Center for the Study of Evolution in Action, Lansing, USA. h.zakon@austin.utexas.edu.|University of Texas, Austin, TX, 78712, USA. h.zakon@austin.utexas.edu.|The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, The Marine Biological Laboratory, Woods Hole, MA, 02543, USA. h.zakon@austin.utexas.edu.
authors.forename: Harold
authors.initials: H
authors.lastname: Zakon
authors.affiliation: Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA. msussman@wisc.edu.|Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA. msussman@wisc.edu.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Sussman
authors.affiliation: Systemix Institute, Redmond, WA, 98053, USA. manoj.samanta@systemix.org.
authors.forename: Manoj P
authors.initials: MP
authors.lastname: Samanta
mesh_terms: D000818:Animals; D004557:Electric Organ / Q000378:metabolism*; D004593:Electrophorus / Q000235:genetics / Q000378:metabolism*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D013020:South America; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger