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Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Published on Jan 1, 2019in Nature Communications 11.88
· DOI :10.1038/s41467-019-08703-2
Camilla Ferrari2
Estimated H-index: 2
(MPG: Max Planck Society),
Sebastian Proost17
Estimated H-index: 17
(MPG: Max Planck Society)
+ 9 AuthorsMarek Mutwil17
Estimated H-index: 17
(MPG: Max Planck Society)
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Abstract
Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.
  • References (80)
  • Citations (1)
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References80
Newest
Published on Dec 1, 2018in Scientific Reports 4.01
Hokuto Nakayama4
Estimated H-index: 4
(UC Davis: University of California, Davis),
Tomoaki Sakamoto9
Estimated H-index: 9
(Nara Institute of Science and Technology)
+ 8 AuthorsNeelima Sinha40
Estimated H-index: 40
(UC Davis: University of California, Davis)
Because natural variation in wild species is likely the result of local adaptation, it provides a valuable resource for understanding plant-environmental interactions. Rorippa aquatica (Brassicaceae) is a semi-aquatic North American plant with morphological differences between several accessions, but little information available on any physiological differences. Here, we surveyed the transcriptomes of two R. aquatica accessions and identified cryptic physiological differences between them. We fi...
Akiva Shalit-Kaneh2
Estimated H-index: 2
(UC Davis: University of California, Davis),
Roderick W. Kumimoto13
Estimated H-index: 13
(UC Davis: University of California, Davis)
+ 1 AuthorsStacey L. Harmer27
Estimated H-index: 27
(UC Davis: University of California, Davis)
Although circadian oscillators in diverse eukaryotes all depend on interlinked transcriptional feedback loops, specific components are not conserved across higher taxa. Moreover, the circadian network in the model plant Arabidopsis thaliana is notably more complex than those found in animals and fungi. Here, we combine mathematical modeling and experimental approaches to investigate the functions of two classes of Myb-like transcription factors that antagonistically regulate common target genes....
Published on Jul 1, 2018in Cell 36.22
Tomoaki Nishiyama27
Estimated H-index: 27
(Kanazawa University),
Hidetoshi Sakayama12
Estimated H-index: 12
(Kobe University)
+ 57 AuthorsDaniel Lang29
Estimated H-index: 29
Summary Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii ; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlle...
Published on Apr 1, 2018in Developmental Cell 9.19
Jorge Fung-Uceda1
Estimated H-index: 1
(CSIC: Spanish National Research Council),
Kyounghee Lee8
Estimated H-index: 8
(SKKU: Sungkyunkwan University)
+ 3 AuthorsPaloma Díaz-Mas32
Estimated H-index: 32
(CSIC: Spanish National Research Council)
Summary The circadian clock and cell cycle as separate pathways have been well documented in plants. Elucidating whether these two oscillators are connected is critical for understanding plant growth. We found that a slow-running circadian clock decelerates the cell cycle and, conversely, a fast clock speeds it up. The clock component TOC1 safeguards the G 1 -to-S transition and controls the timing of the mitotic cycle at early stages of leaf development. TOC1 also regulates somatic ploidy at la...
Published on Mar 16, 2018in Science 41.04
Ludovic S. Mure6
Estimated H-index: 6
(Salk Institute for Biological Studies),
Hiep D. Le10
Estimated H-index: 10
(Salk Institute for Biological Studies)
+ 8 AuthorsOuria Dkhissi-Benyahya2
Estimated H-index: 2
(UCBL: Claude Bernard University Lyon 1)
INTRODUCTION The interaction among cell-autonomous circadian oscillators—daily cycles of activity–rest and feeding–fasting—produces diurnal rhythms in gene expression in almost all animal tissues. These rhythms control the timing of a wide range of functions across different organs and brain regions, affording optimal fitness. Chronic disruption of these rhythms predisposes to and are hallmarks of numerous diseases and affective disorders. RATIONALE Time-series gene expression studies in a limit...
Published on Dec 1, 2017in BMC Bioinformatics 2.51
Sebastian Proost17
Estimated H-index: 17
(MPG: Max Planck Society),
Agnieszka Krawczyk1
Estimated H-index: 1
(MPG: Max Planck Society),
Marek Mutwil17
Estimated H-index: 17
(MPG: Max Planck Society)
Background Since experimental elucidation of gene function is often laborious, various in silico methods have been developed to predict gene function of uncharacterized genes. Since functionally related genes are often expressed in the same tissues, conditions and developmental stages (co-expressed), functional annotation of characterized genes can be transferred to co-expressed genes lacking annotation. With genome-wide expression data available, the construction of co-expression networks, wher...
Published on Oct 1, 2017in New Phytologist 7.30
Anna Malin Linde1
Estimated H-index: 1
(Uppsala University),
D. Magnus Eklund13
Estimated H-index: 13
(Uppsala University)
+ 9 AuthorsTokitaka Oyama22
Estimated H-index: 22
(Kyoto University)
While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anth...
Published on Oct 1, 2017in Journal of Biological Rhythms 2.47
Michael E. Hughes17
Estimated H-index: 17
(WashU: Washington University in St. Louis),
Katherine C. Abruzzi1
Estimated H-index: 1
(Brandeis University)
+ 90 AuthorsJustin Blau26
Estimated H-index: 26
(NYU: New York University)
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze...
Published on Jul 13, 2017in Frontiers in Plant Science 4.11
Pedro Reyes2
Estimated H-index: 2
(University of Seville),
Francisco José Romero Campero19
Estimated H-index: 19
(University of Seville)
+ 2 AuthorsFederico Valverde19
Estimated H-index: 19
(University of Seville)
Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage...
Cited By1
Newest
Published in bioRxiv
Camilla Ferrari2
Estimated H-index: 2
(MPG: Max Planck Society),
Devendra Shivhare1
Estimated H-index: 1
(NTU: Nanyang Technological University)
+ -3 AuthorsTakayuki Tohge50
Estimated H-index: 50
(Nara Institute of Science and Technology)
The lycophyte Selaginella moellendorffii represents early vascular plants and is studied to understand the evolution of higher plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, little is known about the gene expression and transcriptional coordination of Selaginella genes, which precludes us from understanding the evolution of transcriptional programs behind these traits. We here present a gene expression atlas comprising all major organs, tissue type...
Published on Jun 18, 2019in bioRxiv
Camilla Ferrari2
Estimated H-index: 2
(MPG: Max Planck Society),
Marek Mutwil17
Estimated H-index: 17
(MPG: Max Planck Society)
The glaucophyte Cyanophora paradoxa represents the most basal member of the Archaeplastida kingdom, however the function and expression of most of its genes are unknown. This information is needed to uncover how functional gene modules, i.e. groups of genes performing a given function, evolved in the plant kingdom. We have generated a gene expression atlas capturing responses of Cyanophora to various abiotic stresses. This data was included in the CoNekT-Plants database, enabling comparative tra...
Published on Jun 3, 2019in bioRxiv
Jonathan Wei Xiong Ng (NTU: Nanyang Technological University), Qiao Wen Tan (NTU: Nanyang Technological University)+ 1 AuthorsMarek Mutwil17
Estimated H-index: 17
(NTU: Nanyang Technological University)
Almost all organisms coordinate some aspects of their biology through the diurnal cycle. Photosynthetic organisms, and plants especially, have established complex programs that coordinate physiological, metabolic and developmental processes with the changing light. The diurnal regulation of the underlying transcriptional processes is observed when groups of functionally related genes (gene modules) are expressed at a specific time of the day. However, studying the diurnal regulation of these gen...