Diurnal transcript profiling of the diatomSeminavis robustareveals adaptations to a benthic lifestyle

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 (lincRNAs) showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24h. Phylostratigraphic analysis found that rhythmic genes are enriched in deeply 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 diurnal regulation in photosynthetic eukaryotes.

Rhythms and Clocks in Marine Organisms

“…Algae also exhibit moon-related cycles. Migratory rhythms in intertidal sediments synchronized with diurnal and tidal cycles have been reported in different diatom species (Mitbavkar & Anil 2004, Round & Palmer 1966, and semidiurnal (12-h) gene expression periodicity has been documented in the diatom Seminavis robusta (Bilcke et al 2021), likely reflecting adaptations to the tides in coastal ecosystems. Sexual reproduction is another process tangled with moon rhythms in algae.…”

The molecular basis for pore pattern morphogenesis in diatom silica

“…3), which are widely occurring protein-protein interaction motifs involved in numerous cellular functions including protein interactions on the cytosolic surface of membranes 35 . Interestingly, transcriptomic studies in the diatom Seminavis robusta also implicated ankyrin repeat domain bearing proteins in cell wall formation 36 , which suggest that these types of proteins might be general components of the diatom machinery for silica biogenesis. We performed a phylogenetic analysis of the three ankyrin repeat domain bearing VSP1.0 proteins (Tp23225, Tp5147, Tp21058) using the Marine Microbial Eukaryotic Transcriptome Sequencing Project data base 61 , as well as the PLAZA diatoms data base 62 .…”

Differential expression patterns of long noncoding RNAs in a pleiomorphic diatom and relation to hyposalinity

“…Hundreds of thousands of lncRNAs have been identi ed across the Eukarya domain of life, from unicellular protists and yeasts, to plants to animals 9,[19][20][21] . In diatoms a few studies have shown the occurrence of lncRNAs [22][23][24][25][26] . In the model marine diatom Phaeodactylum tricornutum, several lncRNAs (both lincRNAs and NATs) have been shown to be expressed under speci c environmental stresses like phosphate and nitrogen depletion, temperature variations and atmospheric CO 2 pressure variation [22][23][24][25][26] .…”

“…In diatoms a few studies have shown the occurrence of lncRNAs [22][23][24][25][26] . In the model marine diatom Phaeodactylum tricornutum, several lncRNAs (both lincRNAs and NATs) have been shown to be expressed under speci c environmental stresses like phosphate and nitrogen depletion, temperature variations and atmospheric CO 2 pressure variation [22][23][24][25][26] . Additionally, several thousands of lncRNA have recently been identi ed in a benthic diatom (Seminavis robusta), which show not only a speci c expression in response to environmental stresses but also a diurnal responsiveness (rhythmic activation according to a day/night cycle) 25 .…”