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Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle
Bilcke, G.; Osuna-Cruz, C.M.; Silva, M.S.; Poulsen, N.; D'hondt, S.; Bulankova, P.; Vyverman, W.; De Veylder, L.; Vandepoele, K. (2021). Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. Plant J. 107(1): 315-336. https://dx.doi.org/10.1111/tpj.15291
In: The plant journal. Blackwell Publishing: York. ISSN 0960-7412; e-ISSN 1365-313X
Peer reviewed article  
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Trefwoord
    Seminavis robusta D.B.Danielidis & D.G.Mann, 2002 [WoRMS]
Author keywords
    benthic; cell wall; circadian clock; diatoms; diurnal rhythms; phylostratigraphy; transcriptomics
Auteurs  Top 
  • Bilcke, G.
  • Osuna-Cruz, C.M.
  • Silva, M.S.
  • Poulsen, N.
  • D'hondt, S.
  • Bulankova, P.
  • Vyverman, W., meer
  • De Veylder, L.
  • Vandepoele, K.
Abstract
    Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23 328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24 h. Phylostratigraphic analysis found that rhythmic genes are enriched in highly conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall-associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for the study of diurnal regulation in photosynthetic eukaryotes.
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