title: RNA-seq analysis identifies potential modulators of gravity response in spores of Ceratopteris (Parkeriaceae): evidence for modulation by calcium pumps and apyrase activity.
abstract: OBJECTIVE
  Gravity regulates the magnitude and direction of a trans-cell calcium current in germinating spores of Ceratopteris richardii. Blocking this current with nifedipine blocks the spore's downward polarity alignment, a polarization that is fixed by gravity ∼10 h after light induces the spores to germinate. RNA-seq analysis at 10 h was used to identify genes potentially important for the gravity response. The data set will be valuable for other developmental and phylogenetic studies.
  
  
  METHODS
  De novo Newbler assembly of 958 527 reads from Roche 454 sequencing was executed. The sequences were identified and analyzed using in silico methods. The roles of endomembrane Ca(2+)-ATPase pumps and apyrases in the gravity response were further tested using pharmacological agents.
  
  
  RESULTS
  Transcripts related to calcium signaling and ethylene biosynthesis were identified as notable constituents of the transcriptome. Inhibiting the activity of endomembrane Ca(2+)-ATPase pumps with 2,5-di-(t-butyl)-1,4-hydroquinone diminished the trans-cell current, but increased the orientation of the polar axis to gravity. The effects of applied nucleotides and purinoceptor antagonists gave novel evidence implicating extracellular nucleotides as regulators of the gravity response in these fern spores.
  
  
  CONCLUSIONS
  In addition to revealing general features of the transcriptome of germinating spores, the results highlight a number of calcium-responsive and light-receptive transcripts. Pharmacologic assays indicate endomembrane Ca(2+)-ATPases and extracellular nucleotides may play regulatory roles in the gravity response of Ceratopteris spores.
authors.affiliation: The University of Texas at Austin, 1 University Station A6700, Austin, Texas 78712, USA.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Bushart
authors.forename: Ashley E
authors.initials: AE
authors.lastname: Cannon
authors.forename: Aeraj
authors.initials: A
authors.lastname: Ul Haque
authors.forename: Phillip
authors.initials: P
authors.lastname: San Miguel
authors.forename: Kathy
authors.initials: K
authors.lastname: Mostajeran
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Clark
authors.forename: D Marshall
authors.initials: DM
authors.lastname: Porterfield
authors.forename: Stanley J
authors.initials: SJ
authors.lastname: Roux
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D001081:Apyrase / Q000235:genetics / Q000378:metabolism*; D002118:Calcium / Q000378:metabolism*; D000252:Calcium-Transporting ATPases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*; D016764:Cell Polarity / Q000187:drug effects; D030541:Databases, Genetic; D004791:Enzyme Inhibitors / Q000494:pharmacology; D005110:Extracellular Space / Q000187:drug effects / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant / Q000235:genetics; D006112:Gravitation; D008969:Molecular Sequence Data; D055519:Photoreceptors, Plant / Q000378:metabolism; D029625:Pteridaceae / Q000166:cytology / Q000187:drug effects / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction / Q000187:drug effects; D013170:Spores / Q000187:drug effects
chemical_list: D004791:Enzyme Inhibitors; D055519:Photoreceptors, Plant; D012333:RNA, Messenger; D000255:Adenosine Triphosphate; D001081:Apyrase; D000252:Calcium-Transporting ATPases; D002118:Calcium