The strength and pattern of natural selection on gene expression in rice.

Abstract:

:Levels of gene expression underpin organismal phenotypes1,2, but the nature of selection that acts on gene expression and its role in adaptive evolution remain unknown1,2. Here we assayed gene expression in rice (Oryza sativa)3, and used phenotypic selection analysis to estimate the type and strength of selection on the levels of more than 15,000 transcripts4,5. Variation in most transcripts appears (nearly) neutral or under very weak stabilizing selection in wet paddy conditions (with median standardized selection differentials near zero), but selection is stronger under drought conditions. Overall, more transcripts are conditionally neutral (2.83%) than are antagonistically pleiotropic6 (0.04%), and transcripts that display lower levels of expression and stochastic noise7-9 and higher levels of plasticity9 are under stronger selection. Selection strength was further weakly negatively associated with levels of cis-regulation and network connectivity9. Our multivariate analysis suggests that selection acts on the expression of photosynthesis genes4,5, but that the efficacy of selection is genetically constrained under drought conditions10. Drought selected for earlier flowering11,12 and a higher expression of OsMADS18 (Os07g0605200), which encodes a MADS-box transcription factor and is a known regulator of early flowering13-marking this gene as a drought-escape gene11,12. The ability to estimate selection strengths provides insights into how selection can shape molecular traits at the core of gene action.

journal_name

Nature

journal_title

Nature

authors

Groen SC,Ćalić I,Joly-Lopez Z,Platts AE,Choi JY,Natividad M,Dorph K,Mauck WM 3rd,Bracken B,Cabral CLU,Kumar A,Torres RO,Satija R,Vergara G,Henry A,Franks SJ,Purugganan MD

doi

10.1038/s41586-020-1997-2

subject

Has Abstract

pub_date

2020-02-01 00:00:00

pages

572-576

issue

7796

eissn

0028-0836

issn

1476-4687

pii

10.1038/s41586-020-1997-2

journal_volume

578

pub_type

杂志文章

相关文献

NATURE文献大全
  • Renewing Felsenstein's phylogenetic bootstrap in the era of big data.

    abstract::Felsenstein's application of the bootstrap method to evolutionary trees is one of the most cited scientific papers of all time. The bootstrap method, which is based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-018-0043-0

    authors: Lemoine F,Domelevo Entfellner JB,Wilkinson E,Correia D,Dávila Felipe M,De Oliveira T,Gascuel O

    更新日期:2018-04-01 00:00:00

  • Substance P regulates the vasodilator activity of calcitonin gene-related peptide.

    abstract::The 37-amino-acid calcitonin gene-related peptide (CGRP) occurs as a result of alternative processing of mRNA from the calcitonin gene. The potency of CGRP as a vasodilator and the occurrence of the peptide in nerves associated with blood vessels suggest an important role for CGRP in the regulation of blood flow. The ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/335073a0

    authors: Brain SD,Williams TJ

    更新日期:1988-09-01 00:00:00

  • U.S. agrigenetics: suit filed against NIH.

    abstract::Three environmental groups have filed suit against the National Institutes of Health in an attempt to block an experiment approved in April by the NIH Recombinant DNA Advisory Committee. The experiment, designed by researchers at the University of California, Berkeley, to enhance the frost resistance of crops, would ...

    journal_title:Nature

    pub_type: 新闻

    doi:10.1038/305262a0

    authors: David P

    更新日期:1983-09-22 00:00:00

  • Solvent-induced distortions and the curvature of alpha-helices.

    abstract::The alpha-helix defined in 1951 by Pauling et al. on the basis of model building and X-ray fibre diffraction data has 3.65 residues per turn (n) achieved with planar peptides, torsion angles of phi = -48 degrees and psi = -57 degrees and hydrogen bonds which are close to linear. Although X-ray analyses of proteins hav...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/306281a0

    authors: Blundell T,Barlow D,Borkakoti N,Thornton J

    更新日期:1983-11-17 00:00:00

  • A motif in the alphabeta T-cell receptor controls positive selection by modulating ERK activity.

    abstract::Positive selection allows thymocytes that recognize an individual's own major histocompatibility complex (self-MHC) molecules to survive and differentiate, whereas negative selection removes overtly self-reactive thymocytes. Although both forms of thymic selection are mediated by the alphabeta T-cell receptor (TCR) an...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/35019094

    authors: Werlen G,Hausmann B,Palmer E

    更新日期:2000-07-27 00:00:00

  • Nitric oxide mediates network oscillations of olfactory interneurons in a terrestrial mollusc.

    abstract::The interneuronal messenger nitric oxide (NO) may play a central role in the processing of olfactory information. Several circuit elements in the mammalian olfactory bulb contain NO synthase or its functional equivalent, NADPH diaphorase. The effects of NO on cellular excitability or circuit dynamics in the olfactory ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/369061a0

    authors: Gelperin A

    更新日期:1994-05-05 00:00:00

  • Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA.

    abstract::DNA mismatch repair is critical for increasing replication fidelity in organisms ranging from bacteria to humans. MutS protein, a member of the ABC ATPase superfamily, recognizes mispaired and unpaired bases in duplex DNA and initiates mismatch repair. Mutations in human MutS genes cause a predisposition to hereditary...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/35037509

    authors: Obmolova G,Ban C,Hsieh P,Yang W

    更新日期:2000-10-12 00:00:00

  • Mechanosensitivity of mammalian auditory hair cells in vitro.

    abstract::Intracellular responses recorded in vitro from the cochleas of anaesthetized mammals have shown that the mechanoreceptive inner and outer hair cells are sharply tuned, accounting for many of the properties of the afferent fibres in the auditory nerve. However, in vivo it has not been possible to measure directly the e...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/321517a0

    authors: Russell IJ,Richardson GP,Cody AR

    更新日期:1986-05-29 00:00:00

  • Publisher Correction: Magnetoelectric inversion of domain patterns.

    abstract::Four incorrect figure citations in this Letter have been corrected online. ...

    journal_title:Nature

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41586-018-0560-x

    authors: Leo N,Carolus V,White JS,Kenzelmann M,Hudl M,Tolédano P,Honda T,Kimura T,Ivanov SA,Weil M,Lottermoser T,Meier D,Fiebig M

    更新日期:2018-11-01 00:00:00

  • Dynamical transition of myoglobin revealed by inelastic neutron scattering.

    abstract::Structural fluctuations in proteins on the picosecond timescale have been studied in considerable detail by theoretical methods such as molecular dynamics simulation, but there exist very few experimental data with which to test the conclusions. We have used the technique of inelastic neutron scattering to investigate...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/337754a0

    authors: Doster W,Cusack S,Petry W

    更新日期:1989-02-23 00:00:00

  • Retinotopic order in the absence of axon competition.

    abstract::The retinotectal projection has long been studied experimentally and theoretically, as a model for the formation of topographic brain maps. Neighbouring retinal ganglion cells (RGCs) project their axons to neighbouring positions in the optic tectum, thus re-establishing a continuous neural representation of visual spa...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature06816

    authors: Gosse NJ,Nevin LM,Baier H

    更新日期:2008-04-17 00:00:00

  • A Mott insulator of fermionic atoms in an optical lattice.

    abstract::Strong interactions between electrons in a solid material can lead to surprising properties. A prime example is the Mott insulator, in which suppression of conductivity occurs as a result of interactions rather than a filled Bloch band. Proximity to the Mott insulating phase in fermionic systems is the origin of many ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature07244

    authors: Jördens R,Strohmaier N,Günter K,Moritz H,Esslinger T

    更新日期:2008-09-11 00:00:00

  • The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells.

    abstract::Null mutations of glass specifically remove photoreceptor cells, leaving other cell types intact. We have isolated the glass gene and have shown that its transcript encodes a putative protein of 604 amino acids with five zinc-fingers. The glass product may be a transcription factor required for the development of a si...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/340531a0

    authors: Moses K,Ellis MC,Rubin GM

    更新日期:1989-08-17 00:00:00

  • Single amino-acid changes in HIV envelope affect viral tropism and receptor binding.

    abstract::Infection by the human immunodeficiency virus (HIV) is initiated by the binding of its extracellular envelope glycoprotein, gp120, to the CD4 antigen on target cells. To map the residues of the HIV-1 glycoprotein that are critical for binding and to analyse the effects of binding on viral infectivity, we created 15 mu...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/340571a0

    authors: Cordonnier A,Montagnier L,Emerman M

    更新日期:1989-08-17 00:00:00

  • Ecosystem resilience despite large-scale altered hydroclimatic conditions.

    abstract::Climate change is predicted to increase both drought frequency and duration, and when coupled with substantial warming, will establish a new hydroclimatological model for many regions. Large-scale, warm droughts have recently occurred in North America, Africa, Europe, Amazonia and Australia, resulting in major effects...

    journal_title:Nature

    pub_type: 历史文章,杂志文章

    doi:10.1038/nature11836

    authors: Ponce Campos GE,Moran MS,Huete A,Zhang Y,Bresloff C,Huxman TE,Eamus D,Bosch DD,Buda AR,Gunter SA,Scalley TH,Kitchen SG,McClaran MP,McNab WH,Montoya DS,Morgan JA,Peters DP,Sadler EJ,Seyfried MS,Starks PJ

    更新日期:2013-02-21 00:00:00

  • Ecology: human role in Russian wild fires.

    abstract::Anomalies in temperature and precipitation in northern Russia over the past few years have been viewed as manifestations of anthropogenic climate change, prompting suggestions that this may also account for exceptional forest fires in the region. Here we examine the number of forest-fire events across the boreal Russi...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/440436a

    authors: Mollicone D,Eva HD,Achard F

    更新日期:2006-03-23 00:00:00

  • Widespread changes in protein synthesis induced by microRNAs.

    abstract::Animal microRNAs (miRNAs) regulate gene expression by inhibiting translation and/or by inducing degradation of target messenger RNAs. It is unknown how much translational control is exerted by miRNAs on a genome-wide scale. We used a new proteomic approach to measure changes in synthesis of several thousand proteins i...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature07228

    authors: Selbach M,Schwanhäusser B,Thierfelder N,Fang Z,Khanin R,Rajewsky N

    更新日期:2008-09-04 00:00:00

  • Cryopyrin activates the inflammasome in response to toxins and ATP.

    abstract::A crucial part of the innate immune response is the assembly of the inflammasome, a cytosolic complex of proteins that activates caspase-1 to process the proinflammatory cytokines interleukin (IL)-1beta and IL-18. The adaptor protein ASC is essential for inflammasome function, binding directly to caspase-1 (refs 3, 4)...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature04515

    authors: Mariathasan S,Weiss DS,Newton K,McBride J,O'Rourke K,Roose-Girma M,Lee WP,Weinrauch Y,Monack DM,Dixit VM

    更新日期:2006-03-09 00:00:00

  • Author Correction: Universal resilience patterns in complex networks.

    abstract::In this Letter, in Fig. 3c and f the Saccharomyces cerevisiae and Escherichia coli networks were subject to both weight loss and node deletion, a combination of two types of perturbation, as opposed to weight loss only (as the labelling incorrectly indicated). The collapse in Fig. 3h was also obtained from this combin...

    journal_title:Nature

    pub_type: 已发布勘误

    doi:10.1038/s41586-019-1091-9

    authors: Gao J,Barzel B,Barabási AL

    更新日期:2019-04-01 00:00:00

  • The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3.

    abstract::A complex between HLA-DR3 and a fragment of invariant chain called CLIP was isolated from a human cell line defective in antigen presentation and its X-ray crystal structure determined. Previous data indicate that this complex is an intermediate in class II histocompatibility maturation, occurring between invariant ch...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/378457a0

    authors: Ghosh P,Amaya M,Mellins E,Wiley DC

    更新日期:1995-11-30 00:00:00

  • Predicting new molecular targets for known drugs.

    abstract::Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. Because many drug-target combinations exist, it would be useful to explore possible interactions computationally. Here we compared 3,665 US Food and Drug Administration (FDA)-approved...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature08506

    authors: Keiser MJ,Setola V,Irwin JJ,Laggner C,Abbas AI,Hufeisen SJ,Jensen NH,Kuijer MB,Matos RC,Tran TB,Whaley R,Glennon RA,Hert J,Thomas KL,Edwards DD,Shoichet BK,Roth BL

    更新日期:2009-11-12 00:00:00

  • Highly siderophile elements in Earth's mantle as a clock for the Moon-forming impact.

    abstract::According to the generally accepted scenario, the last giant impact on Earth formed the Moon and initiated the final phase of core formation by melting Earth's mantle. A key goal of geochemistry is to date this event, but different ages have been proposed. Some argue for an early Moon-forming event, approximately 30 m...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature13172

    authors: Jacobson SA,Morbidelli A,Raymond SN,O'Brien DP,Walsh KJ,Rubie DC

    更新日期:2014-04-03 00:00:00

  • A nucleotide regulatory site for somatostatin inhibition of adenylate cyclase in S49 lymphoma cells.

    abstract::The cyc- variants of S49 lymphoma cells have served as powerful tools for studying the components and mechanisms of hormone-induced adenylate cyclase stimulation, as these cells are deficient in the guanine nucleotide regulatory site (Ns) mediating hormone, guanine nucleotide, cholera toxin and fluoride-induced stimul...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/303177a0

    authors: Jakobs KH,Aktories K,Schultz G

    更新日期:1983-05-12 00:00:00

  • ATP is a mediator of chemosensory transduction in the central nervous system.

    abstract::Extracellular signalling by the purine nucleotide ATP has long been associated with sensory function. In the periphery, ATP mediates nociception, mechanosensitivity, thermal sensitivity and O2 chemosensitivity. These processes share a common mechanism that involves the release of ATP to excite afferent fibres via acti...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature03690

    authors: Gourine AV,Llaudet E,Dale N,Spyer KM

    更新日期:2005-07-07 00:00:00

  • Activation of stress-activated protein kinase by MEKK1 phosphorylation of its activator SEK1.

    abstract::A kinase distinct from the MEK activator Raf, termed MEK kinase-1 (MEKK), was originally identified by virtue of its homology to kinases involved in yeast mating signal cascades. Like Raf, MEKK is capable of activating MEK in vitro. High-level expression of MEKK in COS-7 cells or using vaccinia virus vectors also acti...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/372798a0

    authors: Yan M,Dai T,Deak JC,Kyriakis JM,Zon LI,Woodgett JR,Templeton DJ

    更新日期:1994-12-22 00:00:00

  • The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

    abstract::Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized c...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature11241

    authors: D'Hont A,Denoeud F,Aury JM,Baurens FC,Carreel F,Garsmeur O,Noel B,Bocs S,Droc G,Rouard M,Da Silva C,Jabbari K,Cardi C,Poulain J,Souquet M,Labadie K,Jourda C,Lengellé J,Rodier-Goud M,Alberti A,Bernard M,Correa M

    更新日期:2012-08-09 00:00:00

  • Three mutant insulins in man.

    abstract::We have previously identified a structurally abnormal insulin in the serum and pancreas of a middle-aged man with diabetes mellitus which arose from a leucine for phenylalanine substitution at position 24 or 25 of the insulin B chain; further analysis of the patient's leukocyte DNA showed that one of the patient's ins...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/302540a0

    authors: Shoelson S,Haneda M,Blix P,Nanjo A,Sanke T,Inouye K,Steiner D,Rubenstein A,Tager H

    更新日期:1983-04-07 00:00:00

  • Complex hybrid origin of genetic caste determination in harvester ants.

    abstract::Caste differentiation and division of labour are the hallmarks of insect societies and at the root of their ecological success. Kin selection predicts that caste determination should result from environmentally induced differences in gene expression, a prediction largely supported by empirical data. However, two excep...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature01744

    authors: Helms Cahan S,Keller L

    更新日期:2003-07-17 00:00:00

  • Author Correction: Autophagy maintains tumour growth through circulating arginine.

    abstract::In this Letter, 'released' should have been 'regulated' in the sentence starting: 'Deletion of Atg5 in the host similarly regulated circulating arginine and suppressed tumorigenesis...' This has been corrected online. ...

    journal_title:Nature

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41586-018-0815-6

    authors: Poillet-Perez L,Xie X,Zhan L,Yang Y,Sharp DW,Hu ZS,Su X,Maganti A,Jiang C,Lu W,Zheng H,Bosenberg MW,Mehnert JM,Guo JY,Lattime E,Rabinowitz JD,White E

    更新日期:2019-01-01 00:00:00

  • Hypothalamic programming of systemic ageing involving IKK-β, NF-κB and GnRH.

    abstract::Ageing is a result of gradual and overall functional deteriorations across the body; however, it is unknown whether an individual tissue primarily works to mediate the ageing progress and control lifespan. Here we show that the hypothalamus is important for the development of whole-body ageing in mice, and that the un...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature12143

    authors: Zhang G,Li J,Purkayastha S,Tang Y,Zhang H,Yin Y,Li B,Liu G,Cai D

    更新日期:2013-05-09 00:00:00