Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle
- Author
- Gust Bilcke (UGent) , Cristina Osuna, Marta Santana Silva, Nicole Poulsen, Sofie D'hondt (UGent) , Petra Bulánková (UGent) , Wim Vyverman (UGent) , Lieven De Veylder (UGent) and Klaas Vandepoele (UGent)
- Organization
- Project
- 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.
- Keywords
- Plant Science, Genetics, Cell Biology, benthic, cell wall, circadian clock, diatoms, diurnal rhythms, phylostratigraphy, transcriptomics, GENE-EXPRESSION, CELL-CYCLE, SEXUAL REPRODUCTION, CIRCADIAN-RHYTHMS, DIVISION, RNA, MIGRATION, MICROPHYTOBENTHOS, PREDICTION, MICROALGAE
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8710601
- MLA
- Bilcke, Gust, et al. “Diurnal Transcript Profiling of the Diatom Seminavis Robusta Reveals Adaptations to a Benthic Lifestyle.” PLANT JOURNAL, vol. 107, no. 1, 2021, pp. 315–36, doi:10.1111/tpj.15291.
- APA
- Bilcke, G., Osuna, C., Santana Silva, M., Poulsen, N., D’hondt, S., Bulánková, P., … Vandepoele, K. (2021). Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. PLANT JOURNAL, 107(1), 315–336. https://doi.org/10.1111/tpj.15291
- Chicago author-date
- Bilcke, Gust, Cristina Osuna, Marta Santana Silva, Nicole Poulsen, Sofie D’hondt, Petra Bulánková, Wim Vyverman, Lieven De Veylder, and Klaas Vandepoele. 2021. “Diurnal Transcript Profiling of the Diatom Seminavis Robusta Reveals Adaptations to a Benthic Lifestyle.” PLANT JOURNAL 107 (1): 315–36. https://doi.org/10.1111/tpj.15291.
- Chicago author-date (all authors)
- Bilcke, Gust, Cristina Osuna, Marta Santana Silva, Nicole Poulsen, Sofie D’hondt, Petra Bulánková, Wim Vyverman, Lieven De Veylder, and Klaas Vandepoele. 2021. “Diurnal Transcript Profiling of the Diatom Seminavis Robusta Reveals Adaptations to a Benthic Lifestyle.” PLANT JOURNAL 107 (1): 315–336. doi:10.1111/tpj.15291.
- Vancouver
- 1.Bilcke G, Osuna C, Santana Silva M, Poulsen N, D’hondt S, Bulánková P, et al. Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle. PLANT JOURNAL. 2021;107(1):315–36.
- IEEE
- [1]G. Bilcke et al., “Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle,” PLANT JOURNAL, vol. 107, no. 1, pp. 315–336, 2021.
@article{8710601,
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.}},
author = {{Bilcke, Gust and Osuna, Cristina and Santana Silva, Marta and Poulsen, Nicole and D'hondt, Sofie and Bulánková, Petra and Vyverman, Wim and De Veylder, Lieven and Vandepoele, Klaas}},
issn = {{0960-7412}},
journal = {{PLANT JOURNAL}},
keywords = {{Plant Science,Genetics,Cell Biology,benthic,cell wall,circadian clock,diatoms,diurnal rhythms,phylostratigraphy,transcriptomics,GENE-EXPRESSION,CELL-CYCLE,SEXUAL REPRODUCTION,CIRCADIAN-RHYTHMS,DIVISION,RNA,MIGRATION,MICROPHYTOBENTHOS,PREDICTION,MICROALGAE}},
language = {{eng}},
number = {{1}},
pages = {{315--336}},
title = {{Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle}},
url = {{http://dx.doi.org/10.1111/tpj.15291}},
volume = {{107}},
year = {{2021}},
}
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