Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate.

Abstract:

:Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

journal_name

Nat Commun

journal_title

Nature communications

authors

Abrouk M,Ahmed HI,Cubry P,Šimoníková D,Cauet S,Pailles Y,Bettgenhaeuser J,Gapa L,Scarcelli N,Couderc M,Zekraoui L,Kathiresan N,Čížková J,Hřibová E,Doležel J,Arribat S,Bergès H,Wieringa JJ,Gueye M,Kane NA,Leclerc C

doi

10.1038/s41467-020-18329-4

subject

Has Abstract

pub_date

2020-09-08 00:00:00

pages

4488

issue

1

issn

2041-1723

pii

10.1038/s41467-020-18329-4

journal_volume

11

pub_type

杂志文章
  • Biomimetic superelastic graphene-based cellular monoliths.

    abstract::Many applications proposed for graphene require multiple sheets be assembled into a monolithic structure. The ability to maintain structural integrity upon large deformation is essential to ensure a macroscopic material which functions reliably. However, it has remained a great challenge to achieve high elasticity in ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2251

    authors: Qiu L,Liu JZ,Chang SL,Wu Y,Li D

    更新日期:2012-01-01 00:00:00

  • Disruption of TBP-2 ameliorates insulin sensitivity and secretion without affecting obesity.

    abstract::Type 2 diabetes mellitus (T2DM) is characterized by defects in both insulin sensitivity and glucose-stimulated insulin secretion (GSIS) and is often accompanied by obesity. In this study, we show that disruption of thioredoxin binding protein-2 (TBP-2, also called Txnip) in obese mice (ob/ob) dramatically improves hyp...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1127

    authors: Yoshihara E,Fujimoto S,Inagaki N,Okawa K,Masaki S,Yodoi J,Masutani H

    更新日期:2010-11-23 00:00:00

  • Release of SOS2 kinase from sequestration with GIGANTEA determines salt tolerance in Arabidopsis.

    abstract::Environmental challenges to plants typically entail retardation of vegetative growth and delay or cessation of flowering. Here we report a link between the flowering time regulator, GIGANTEA (GI), and adaptation to salt stress that is mechanistically based on GI degradation under saline conditions, thus retarding flow...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2357

    authors: Kim WY,Ali Z,Park HJ,Park SJ,Cha JY,Perez-Hormaeche J,Quintero FJ,Shin G,Kim MR,Qiang Z,Ning L,Park HC,Lee SY,Bressan RA,Pardo JM,Bohnert HJ,Yun DJ

    更新日期:2013-01-01 00:00:00

  • Methane seep carbonates yield clumped isotope signatures out of equilibrium with formation temperatures.

    abstract::Methane cold seep systems typically exhibit extensive buildups of authigenic carbonate minerals, resulting from local increases in alkalinity driven by methane oxidation. Here, we demonstrate that modern seep authigenic carbonates exhibit anomalously low clumped isotope values (Δ47), as much as ∼0.2‰ lower than expect...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12274

    authors: Loyd SJ,Sample J,Tripati RE,Defliese WF,Brooks K,Hovland M,Torres M,Marlow J,Hancock LG,Martin R,Lyons T,Tripati AE

    更新日期:2016-07-22 00:00:00

  • Microglia are an essential component of the neuroprotective scar that forms after spinal cord injury.

    abstract::The role of microglia in spinal cord injury (SCI) remains poorly understood and is often confused with the response of macrophages. Here, we use specific transgenic mouse lines and depleting agents to understand the response of microglia after SCI. We find that microglia are highly dynamic and proliferate extensively ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-08446-0

    authors: Bellver-Landete V,Bretheau F,Mailhot B,Vallières N,Lessard M,Janelle ME,Vernoux N,Tremblay MÈ,Fuehrmann T,Shoichet MS,Lacroix S

    更新日期:2019-01-31 00:00:00

  • Disposable ultrasound-sensing chronic cranial window by soft nanoimprinting lithography.

    abstract::Chronic cranial window (CCW) is an essential tool in enabling longitudinal imaging and manipulation of various brain activities in live animals. However, an active CCW capable of sensing the concealed in vivo environment while simultaneously providing longitudinal optical access to the brain is not currently available...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-12178-6

    authors: Li H,Dong B,Zhang X,Shu X,Chen X,Hai R,Czaplewski DA,Zhang HF,Sun C

    更新日期:2019-09-19 00:00:00

  • Percolation transition of cooperative mutational effects in colorectal tumorigenesis.

    abstract::Cancer is caused by the accumulation of multiple genetic mutations, but their cooperative effects are poorly understood. Using a genome-wide analysis of all the somatic mutations in colorectal cancer patients in a large-scale molecular interaction network, here we find that a giant cluster of mutation-propagating modu...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01171-6

    authors: Shin D,Lee J,Gong JR,Cho KH

    更新日期:2017-11-02 00:00:00

  • Superplume mantle tracked isotopically the length of Africa from the Indian Ocean to the Red Sea.

    abstract::Seismological findings show a complex scenario of plume upwellings from a deep thermo-chemical anomaly (superplume) beneath the East African Rift System (EARS). It is unclear if these geophysical observations represent a true picture of the superplume and its influence on magmatism along the EARS. Thus, it is essentia...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13181-7

    authors: O'Connor JM,Jokat W,Regelous M,Kuiper KF,Miggins DP,Koppers AAP

    更新日期:2019-12-02 00:00:00

  • An atlas of DNA methylomes in porcine adipose and muscle tissues.

    abstract::It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct ske...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1854

    authors: Li M,Wu H,Luo Z,Xia Y,Guan J,Wang T,Gu Y,Chen L,Zhang K,Ma J,Liu Y,Zhong Z,Nie J,Zhou S,Mu Z,Wang X,Qu J,Jing L,Wang H,Huang S,Yi N,Wang Z,Xi D,Wang J,Yin G,Wang L,Li N,Jiang Z,Lang Q,Xiao H,Ji

    更新日期:2012-05-22 00:00:00

  • Power laws in pressure-induced structural change of glasses.

    abstract::Many glasses exhibit fractional power law (FPL) between the mean atomic volume va and the first diffraction peak position q1, i.e. [Formula: see text] with d ≃ 2.5 deviating from the space dimension D = 3, under compression or composition change. What structural change causes such FPL and whether the FPL and d are uni...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15583-4

    authors: Zhang H,Qiao K,Han Y

    更新日期:2020-04-24 00:00:00

  • Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona.

    abstract::Large-scale, unbiased proteomics studies are constrained by the complexity of the plasma proteome. Here we report a highly parallel protein quantitation platform integrating nanoparticle (NP) protein coronas with liquid chromatography-mass spectrometry for efficient proteomic profiling. A protein corona is a protein l...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17033-7

    authors: Blume JE,Manning WC,Troiano G,Hornburg D,Figa M,Hesterberg L,Platt TL,Zhao X,Cuaresma RA,Everley PA,Ko M,Liou H,Mahoney M,Ferdosi S,Elgierari EM,Stolarczyk C,Tangeysh B,Xia H,Benz R,Siddiqui A,Carr SA,Ma P,Lan

    更新日期:2020-07-22 00:00:00

  • TALEN outperforms Cas9 in editing heterochromatin target sites.

    abstract::Genome editing critically relies on selective recognition of target sites. However, despite recent progress, the underlying search mechanism of genome-editing proteins is not fully understood in the context of cellular chromatin environments. Here, we use single-molecule imaging in live cells to directly study the beh...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20672-5

    authors: Jain S,Shukla S,Yang C,Zhang M,Fatma Z,Lingamaneni M,Abesteh S,Lane ST,Xiong X,Wang Y,Schroeder CM,Selvin PR,Zhao H

    更新日期:2021-01-27 00:00:00

  • Structural decoding of netrin-4 reveals a regulatory function towards mature basement membranes.

    abstract::Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s. However, mainly based on shared homologies wi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13515

    authors: Reuten R,Patel TR,McDougall M,Rama N,Nikodemus D,Gibert B,Delcros JG,Prein C,Meier M,Metzger S,Zhou Z,Kaltenberg J,McKee KK,Bald T,Tüting T,Zigrino P,Djonov V,Bloch W,Clausen-Schaumann H,Poschl E,Yurchenco PD,Eh

    更新日期:2016-11-30 00:00:00

  • A spin torque meter with magnetic facet domains.

    abstract::Current-induced magnetic domain wall (DW) motion is an important operating principle of spintronic devices. Injected current generates spin torques (STs) on the DWs in two ways. One is the spin transfer from magnetic domains to the walls by the current flowing in the magnet. Current flow in attached heavy metals also ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06223-z

    authors: Moon KW,Kim C,Yoon J,Choi JW,Kim DO,Song KM,Kim D,Chun BS,Hwang C

    更新日期:2018-09-17 00:00:00

  • A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping.

    abstract::Long-read sequencing technologies have greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer are combined with Bionano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sor...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07271-1

    authors: Deschamps S,Zhang Y,Llaca V,Ye L,Sanyal A,King M,May G,Lin H

    更新日期:2018-11-19 00:00:00

  • Tenomodulin promotes human adipocyte differentiation and beneficial visceral adipose tissue expansion.

    abstract::Proper regulation of energy storage in adipose tissue is crucial for maintaining insulin sensitivity and molecules contributing to this process have not been fully revealed. Here we show that type II transmembrane protein tenomodulin (TNMD) is upregulated in adipose tissue of insulin-resistant versus insulin-sensitive...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10686

    authors: Senol-Cosar O,Flach RJ,DiStefano M,Chawla A,Nicoloro S,Straubhaar J,Hardy OT,Noh HL,Kim JK,Wabitsch M,Scherer PE,Czech MP

    更新日期:2016-02-16 00:00:00

  • NK1.1+ CD8+ T cells escape TGF-β control and contribute to early microbial pathogen response.

    abstract::Following microbial pathogen invasion, one of the main challenges for the host is to rapidly control pathogen spreading to avoid vital tissue damage. Here we report that an effector CD8(+) T-cell population that expresses the marker NK1.1 undergoes delayed contraction and sustains early anti-microbial protection. NK1....

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6150

    authors: Ruiz AL,Soudja SM,Deceneux C,Lauvau G,Marie JC

    更新日期:2014-10-06 00:00:00

  • Multiscale real time and high sensitivity ion detection with complementary organic electrochemical transistors amplifier.

    abstract::Ions are ubiquitous biological regulators playing a key role for vital processes in animals and plants. The combined detection of ion concentration and real-time monitoring of small variations with respect to the resting conditions is a multiscale functionality providing important information on health states. This mu...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17547-0

    authors: Romele P,Gkoupidenis P,Koutsouras DA,Lieberth K,Kovács-Vajna ZM,Blom PWM,Torricelli F

    更新日期:2020-07-27 00:00:00

  • Long-term hepatitis B infection in a scalable hepatic co-culture system.

    abstract::Hepatitis B virus causes chronic infections in 250 million people worldwide. Chronic hepatitis B virus carriers are at risk of developing fibrosis, cirrhosis, and hepatocellular carcinoma. A prophylactic vaccine exists and currently available antivirals can suppress but rarely cure chronic infections. The study of hep...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00200-8

    authors: Winer BY,Huang TS,Pludwinski E,Heller B,Wojcik F,Lipkowitz GE,Parekh A,Cho C,Shrirao A,Muir TW,Novik E,Ploss A

    更新日期:2017-07-25 00:00:00

  • Coupled microbial bloom and oxygenation decline recorded by magnetofossils during the Palaeocene-Eocene Thermal Maximum.

    abstract::Understanding marine environmental change and associated biological turnover across the Palaeocene-Eocene Thermal Maximum (PETM; ~56 Ma)-the most pronounced Cenozoic short-term global warming event-is important because of the potential role of the ocean in atmospheric CO2 drawdown, yet proxies for tracing marine produ...

    journal_title:Nature communications

    pub_type: 历史文章,杂志文章

    doi:10.1038/s41467-018-06472-y

    authors: Chang L,Harrison RJ,Zeng F,Berndt TA,Roberts AP,Heslop D,Zhao X

    更新日期:2018-10-01 00:00:00

  • Phosphorylation of ULK1 affects autophagosome fusion and links chaperone-mediated autophagy to macroautophagy.

    abstract::The Unc-51 like autophagy activating kinase 1 (ULK1) complex plays a central role in the initiation stage of autophagy. However, the function of ULK1 in the late stage of autophagy is unknown. Here, we report that ULK1, a central kinase of the ULK1 complex involved in autophagy initiation, promotes autophagosome-lysos...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05449-1

    authors: Wang C,Wang H,Zhang D,Luo W,Liu R,Xu D,Diao L,Liao L,Liu Z

    更新日期:2018-08-28 00:00:00

  • Protease-degradable electrospun fibrous hydrogels.

    abstract::Electrospun nanofibres are promising in biomedical applications to replicate features of the natural extracellular matrix (ECM). However, nearly all electrospun scaffolds are either non-degradable or degrade hydrolytically, whereas natural ECM degrades proteolytically, often through matrix metalloproteinases. Here we ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7639

    authors: Wade RJ,Bassin EJ,Rodell CB,Burdick JA

    更新日期:2015-03-23 00:00:00

  • Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny.

    abstract::Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbio...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07275-x

    authors: Pollock FJ,McMinds R,Smith S,Bourne DG,Willis BL,Medina M,Thurber RV,Zaneveld JR

    更新日期:2018-11-22 00:00:00

  • Partially coherent ultrafast spectrography.

    abstract::Modern ultrafast metrology relies on the postulate that the pulse to be measured is fully coherent, that is, that it can be completely described by its spectrum and spectral phase. However, synthesizing fully coherent pulses is not always possible in practice, especially in the domain of emerging ultrashort X-ray sour...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7465

    authors: Bourassin-Bouchet C,Couprie ME

    更新日期:2015-03-06 00:00:00

  • Boosting the catalysis of gold by O2 activation at Au-SiO2 interface.

    abstract::Supported gold (Au) nanocatalysts have attracted extensive interests in the past decades because of their unique catalytic properties for a number of key chemical reactions, especially in (selective) oxidations. The activation of O2 on Au nanocatalysts is crucial and remains a challenge because only small Au nanoparti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-14241-8

    authors: Zhang Y,Zhang J,Zhang B,Si R,Han B,Hong F,Niu Y,Sun L,Li L,Qiao B,Sun K,Huang J,Haruta M

    更新日期:2020-01-28 00:00:00

  • Direct observation of ultrafast coherent exciton dynamics in helical π-stacks of self-assembled perylene bisimides.

    abstract::Ever since the discovery of dye self-assemblies in nature, there have been tremendous efforts to exploit biomimetic supramolecular assemblies for tailored artificial photon processing materials. This feature necessarily has resulted in an increasing demand for understanding exciton dynamics in the dye self-assemblies....

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9646

    authors: Sung J,Kim P,Fimmel B,Würthner F,Kim D

    更新日期:2015-10-23 00:00:00

  • History-based action selection bias in posterior parietal cortex.

    abstract::Making decisions based on choice-outcome history is a crucial, adaptive ability in life. However, the neural circuit mechanisms underlying history-dependent decision-making are poorly understood. In particular, history-related signals have been found in many brain areas during various decision-making tasks, but the ca...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01356-z

    authors: Hwang EJ,Dahlen JE,Mukundan M,Komiyama T

    更新日期:2017-11-01 00:00:00

  • Programmed spatial organization of biomacromolecules into discrete, coacervate-based protocells.

    abstract::The cell cytosol is crowded with high concentrations of many different biomacromolecules, which is difficult to mimic in bottom-up synthetic cell research and limits the functionality of existing protocellular platforms. There is thus a clear need for a general, biocompatible, and accessible tool to more accurately em...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20124-0

    authors: Altenburg WJ,Yewdall NA,Vervoort DFM,van Stevendaal MHME,Mason AF,van Hest JCM

    更新日期:2020-12-08 00:00:00

  • SREBP1 drives Keratin-80-dependent cytoskeletal changes and invasive behavior in endocrine-resistant ERα breast cancer.

    abstract::Approximately 30% of ERα breast cancer patients relapse with metastatic disease following adjuvant endocrine therapies. The connection between acquisition of drug resistance and invasive potential is poorly understood. In this study, we demonstrate that the type II keratin topological associating domain undergoes epig...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09676-y

    authors: Perone Y,Farrugia AJ,Rodríguez-Meira A,Győrffy B,Ion C,Uggetti A,Chronopoulos A,Marrazzo P,Faronato M,Shousha S,Davies C,Steel JH,Patel N,Del Rio Hernandez A,Coombes C,Pruneri G,Lim A,Calvo F,Magnani L

    更新日期:2019-05-09 00:00:00

  • Simple non-fused electron acceptors for efficient and stable organic solar cells.

    abstract::The flexibility in structural design of organic semiconductors endows organic solar cells (OSCs) not only great function-tunabilities, but also high potential toward practical application. In this work, simple non-fused-ring electron acceptors are developed through two-step synthesis from single aromatic units for con...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10098-z

    authors: Yu ZP,Liu ZX,Chen FX,Qin R,Lau TK,Yin JL,Kong X,Lu X,Shi M,Li CZ,Chen H

    更新日期:2019-05-14 00:00:00