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

Published on Jan 1, 2019in Nature Communications 12.35
· DOI :10.1038/s41467-019-08703-2
Camilla Ferrari2
Estimated H-index: 2
(Max Planck Society),
Sebastian Proost16
Estimated H-index: 16
(Max Planck Society)
+ 9 AuthorsMarek Mutwil15
Estimated H-index: 15
(Max Planck Society)
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.
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Published on May 4, 2015in Plant Signaling & Behavior
Yuji Miyazaki5
Estimated H-index: 5
(Gakushuin University),
Tomoyuki Takase8
Estimated H-index: 8
(Gakushuin University),
Tomohiro Kiyosue31
Estimated H-index: 31
Hypocotyl cell elongation has been studied as a model to understand how cellular expansion contributes to plant organ growth. Hypocotyl elongation is affected by multiple environmental factors, including light quantity and light quality. Red light inhibits hypocotyl growth via the phytochrome signaling pathways. Proteins of the FLAVIN-BINDING KELCH REPEAT F-BOX 1 / LOV KELCH PROTEIN 2 / ZEITLUPE family are positive regulators of hypocotyl elongation under red light in Arabidopsis. These proteins...
7 Citations Source Cite
Published on Nov 1, 2011in Plant Journal 5.78
Esther Yakir7
Estimated H-index: 7
(Hebrew University of Jerusalem),
Miriam Hassidim16
Estimated H-index: 16
(Hebrew University of Jerusalem)
+ 3 AuthorsRachel M. Green9
Estimated H-index: 9
(Hebrew University of Jerusalem)
Summary The circadian system of plants regulates a wide range of rhythmic physiological and cellular output processes with a period of about 24 h. The rhythms are generated by an oscillator mechanism that, in Arabidopsis, consists of interlocking feedback loops of several components including CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION 1 (TOC1) and CCA1 HIKING EXPEDITION (CHE). Over recent years, researchers have gained a detailed picture of the ...
38 Citations Source Cite
Published on May 4, 2015in Plant Signaling & Behavior
Honghong Wu10
Estimated H-index: 10
Lana Shabala31
Estimated H-index: 31
Sergey Shabala63
Estimated H-index: 63
Mesophyll K+ retention ability has been recently reported as an important component of salinity stress tolerance in wheat. In order to investigate the role of ROS in regulating NaCl-induced K+ efflux in wheat leaf mesophyll, a series of pharmacological experiments was conducted using MV (methyl viologen, superoxide radical inducer), DPI (an inhibitor of NADPH oxidase), H2O2 (to mimic apoplastic ROS), and EGCG ((−)-Epigallocatechin gallate, ROS scavenger). Mesophyll pre-treatment with 10 μM MV re...
9 Citations Source Cite
Published on Dec 1, 2015in Genome Biology 13.21
David Emms8
Estimated H-index: 8
(University of Oxford),
Steven L. Kelly54
Estimated H-index: 54
(University of Oxford)
Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by pro...
377 Citations Source Cite
Published on May 4, 2015in Plant Signaling & Behavior
Julie M. Thole8
Estimated H-index: 8
(Saint Louis University),
Lucia C. Strader20
Estimated H-index: 20
(Washington University in St. Louis)
The advent of next generation sequencing has influenced every aspect of biological research. Many labs are now using whole genome sequencing in Arabidopsis thaliana as a means to quickly identify EMS-generated mutations present in isolated mutants. Following identification of these mutations, examination of T-DNA insertional alleles defective in candidate genes or complementation of the mutant phenotype with a wild type copy of candidate genes can be used to verify which mutation is causative fo...
8 Citations Source Cite
Published on Mar 31, 2011in PLOS Genetics 5.54
Reetika Rawat2
Estimated H-index: 2
(University of Minnesota),
Nozomu Takahashi1
Estimated H-index: 1
(University of Minnesota)
+ 5 AuthorsStacey L. Harmer28
Estimated H-index: 28
(University of Minnesota)
Circadian rhythms provide organisms with an adaptive advantage, allowing them to regulate physiological and developmental events so that they occur at the most appropriate time of day. In plants, as in other eukaryotes, multiple transcriptional feedback loops are central to clock function. In one such feedback loop, the Myb-like transcription factors CCA1 and LHY directly repress expression of the pseudoresponse regulator TOC1 by binding to an evening element (EE) in the TOC1 promoter. Another k...
93 Citations Source Cite
Published on Dec 1, 2014in BMC Plant Biology 3.93
Mine Nose3
Estimated H-index: 3
Atsushi Watanabe15
Estimated H-index: 15
(Kyushu University)
Background The circadian clock and diurnal dynamics of the transcriptome are presumed to play important roles in the regulation of physiological, biological and developmental processes synchronized with diurnal and annual cycles of plant environments. However, little is known about the circadian clock and its regulation in gymnosperms, including conifers. Here we present the diurnal transcriptome dynamics of Japanese cedar (Cryptomeria japonica (L.f.) D.Don) in both active (summer) and dormant (...
9 Citations Source Cite
Published on Mar 1, 2004in Plant Journal 5.78
Oliver Thimm9
Estimated H-index: 9
(Max Planck Society),
Oliver Bläsing17
Estimated H-index: 17
(Max Planck Society)
+ 7 AuthorsMark Stitt110
Estimated H-index: 110
(Max Planck Society)
Summary mapman is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed ‘BINs’, ‘subBINs’). A first build of transcriptscavenger groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cel...
1,960 Citations Source Cite
Published on Jul 1, 2002in Nature Genetics 27.13
Lani F. Wu25
Estimated H-index: 25
(Harvard University),
Timothy R. Hughes80
Estimated H-index: 80
(University of Toronto)
+ 3 AuthorsSteven J. Altschuler27
Estimated H-index: 27
(Harvard University)
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
316 Citations Source Cite
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