title: Global discovery and characterization of small non-coding RNAs in marine microalgae.
abstract: BACKGROUND
  Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi.
  
  
  RESULTS
  Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions.
  
  
  CONCLUSIONS
  This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and maybe used for acclimation to environmental conditions.
authors.forename: Sara
authors.initials: S
authors.lastname: Lopez-Gomollon
authors.forename: Matthew
authors.initials: M
authors.lastname: Beckers
authors.forename: Tina
authors.initials: T
authors.lastname: Rathjen
authors.forename: Simon
authors.initials: S
authors.lastname: Moxon
authors.forename: Florian
authors.initials: F
authors.lastname: Maumus
authors.forename: Irina
authors.initials: I
authors.lastname: Mohorianu
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
authors.affiliation: School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK. t.dalmay@uea.ac.uk.
authors.forename: Tamas
authors.initials: T
authors.lastname: Dalmay
authors.forename: Thomas
authors.initials: T
authors.lastname: Mock
mesh_terms: D017377:Diatoms / Q000235:genetics* / Q000502:physiology; D020071:Interspersed Repetitive Sequences; D058086:Microalgae / Q000235:genetics* / Q000502:physiology; D018384:Oxidative Stress; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015854:Up-Regulation
chemical_list: D058727:RNA, Small Untranslated; D012343:RNA, Transfer