A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice.

Computational Biology / methods DNA, Plant / genetics Databases, Genetic Genome, Plant / genetics High-Throughput Nucleotide Sequencing / methods Open Reading Frames / genetics Oryza / genetics Protein Interaction Mapping / methods Protein Interaction Maps / genetics Sequence Analysis, DNA / methods
ORFeome networks next-generation sequencing protein–protein interaction rice

Journal

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876

Informations de publication

Date de publication:
26 05 2020
Historique:
pubmed: 14 5 2020
medline: 19 8 2020
entrez: 14 5 2020
Statut: ppublish

Résumé

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop

Identifiants

DOI: 10.1073/pnas.1918068117 PMID: 32398372 PMC: PMC7260977
pubmed: 32398372
pii: 1918068117
doi: 10.1073/pnas.1918068117
pmc: PMC7260977
doi:

Substances chimiques

DNA, Plant 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

11836-11842

Subventions

Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK115398
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM125639
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM122968
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM124559
Pays : United States

Déclaration de conflit d'intérêts

The authors declare no competing interest.

Références

Cell. 2020 Apr 16;181(2):460-474.e14
pubmed: 32191846
Nucleic Acids Res. 2000 Sep 15;28(18):3442-4
pubmed: 10982861
Science. 2003 Jul 18;301(5631):376-9
pubmed: 12869764
Science. 2002 Apr 5;296(5565):92-100
pubmed: 11935018
Cell. 2005 Sep 23;122(6):957-68
pubmed: 16169070
Plant J. 2006 Apr;46(1):1-13
pubmed: 16553892
Database (Oxford). 2010 Oct 12;2010:baq023
pubmed: 20940177
Plant J. 2004 Apr;38(1):172-81
pubmed: 15053770
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613
pubmed: 30476243
Nucleic Acids Res. 2015 Jul 1;43(W1):W122-7
pubmed: 25813048
Nature. 2000 Dec 14;408(6814):796-815
pubmed: 11130711
Nat Struct Biol. 2003 Dec;10(12):980
pubmed: 14634627
Sci Signal. 2013 May 21;6(276):ra38
pubmed: 23695164
PLoS Genet. 2011 Apr;7(4):e1002020
pubmed: 21533176
Nat Rev Genet. 2011 Jan;12(1):56-68
pubmed: 21164525
Plant Physiol. 2004 Jun;135(2):773-82
pubmed: 15208423
Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63
pubmed: 24234451
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
pubmed: 16381927
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72
pubmed: 18988627
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18548-53
pubmed: 22042862
BMC Syst Biol. 2012 Jul 30;6:92
pubmed: 22846459
FEBS J. 2008 Jun;275(11):2942-55
pubmed: 18435761
Redox Biol. 2013 Dec 14;2:44-51
pubmed: 24396728
Nucleic Acids Res. 2000 Jan 1;28(1):289-91
pubmed: 10592249
Genome Res. 2003 Oct;13(10):2363-71
pubmed: 14525934
Nat Methods. 2011 Jun 26;8(8):659-61
pubmed: 21706014
Plant Cell Physiol. 2013 Feb;54(2):e6
pubmed: 23299411
Nature. 2007 Dec 13;450(7172):973-82
pubmed: 18075576
FEBS Lett. 2009 Dec 17;583(24):3891-4
pubmed: 19913537
Nature. 1998 Feb 12;391(6668):715-8
pubmed: 9490418
Science. 2008 Oct 3;322(5898):104-10
pubmed: 18719252
Cell. 2011 Mar 18;144(6):986-98
pubmed: 21414488
Plant Physiol. 2009 Mar;149(3):1478-92
pubmed: 19109415
Nucleic Acids Res. 2012 Jan;40(Database issue):D857-61
pubmed: 22096227
Cell. 2016 Jan 14;164(1-2):310-323
pubmed: 26771498
Science. 2011 Jul 29;333(6042):601-7
pubmed: 21798944
DNA Repair (Amst). 2009 Apr 5;8(4):449-60
pubmed: 19223247
BMC Bioinformatics. 2011 May 16;12:161
pubmed: 21575196
Nat Methods. 2008 Jul;5(7):597-600
pubmed: 18552854
Science. 2001 Feb 16;291(5507):1304-51
pubmed: 11181995
Bioinformatics. 2005 Mar;21(6):832-4
pubmed: 15531608
Plant Physiol. 2015 Sep;169(1):760-79
pubmed: 26175513
Genome Res. 2004 Oct;14(10B):2128-35
pubmed: 15489335
Plant Cell. 2010 Jan;22(1):124-42
pubmed: 20086187
Nat Biotechnol. 2006 Jul;24(7):841-7
pubmed: 16823372
Nature. 2005 Oct 20;437(7062):1173-8
pubmed: 16189514
Sci Rep. 2017 Dec 15;7(1):17668
pubmed: 29247210
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4945-50
pubmed: 12684538
Genes Dev. 2005 Dec 1;19(23):2816-26
pubmed: 16322557
Nat Genet. 2003 May;34(1):35-41
pubmed: 12679813

Auteurs

Shayne D Wierbowski (SD)

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853.
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0002-2595-2011

Tommy V Vo (TV)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.

Pascal Falter-Braun (P)

Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Munich, Germany.
Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität München, 80539 Munich, Germany.
ORCID: 0000-0003-2012-6746

Timothy O Jobe (TO)

Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany.
ORCID: 0000-0002-5729-4981

Lars H Kruse (LH)

Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0002-0449-092X

Xiaomu Wei (X)

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853.

Jin Liang (J)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.

Michael J Meyer (MJ)

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853.
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.

Nurten Akturk (N)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.

Christen A Rivera-Erick (CA)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.

Nicolas A Cordero (NA)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0002-6443-3089

Mauricio I Paramo (MI)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0002-9518-1881

Elnur E Shayhidin (EE)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.

Marta Bertolotti (M)

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.

Nathaniel D Tippens (ND)

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853.
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0003-4377-8691

Kazi Akther (K)

Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901.

Rita Sharma (R)

School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

Yuichi Katayose (Y)

Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8634, Japan.
ORCID: 0000-0002-4500-3964

Kourosh Salehi-Ashtiani (K)

Laboratory of Algal, Systems, and Synthetic Biology, Division of Science and Math, New York University Abu Dhabi, 129188, Abu Dhabi, United Arab Emirates.
Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215.
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115.
Center for Genomics and Systems Biology, New York University Abu Dhabi, 129188, Abu Dhabi, United Arab Emirates.
ORCID: 0000-0002-6521-5243

Tong Hao (T)

Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215.
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115.

Pamela C Ronald (PC)

Department of Plant Pathology, University of California, Davis, CA 95616.
The Genome Center, University of California, Davis, CA 95616.
Innovative Genomics Institute, Berkeley, CA 94704.
ORCID: 0000-0002-4107-1345

Joseph R Ecker (JR)

Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037.
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037.
ORCID: 0000-0001-5799-5895

Peter A Schweitzer (PA)

BRC Genomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0003-4525-7013

Shoshi Kikuchi (S)

Plant Genome Research Unit, Division of Genome and Biodiversity Research, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba 305-0856, Japan.

Hiroshi Mizuno (H)

Department of Molecular Biology, National Institute of Agrobiological Resources, Tsukuba 305-0856, Japan.

David E Hill (DE)

Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215.
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115.
ORCID: 0000-0001-5192-0921

Marc Vidal (M)

Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215.
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115.

Gaurav D Moghe (GD)

Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0002-8761-064X

Susan R McCouch (SR)

Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901; srm4@cornell.edu haiyuan.yu@cornell.edu.
ORCID: 0000-0001-9246-3106

Haiyuan Yu (H)

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853; srm4@cornell.edu haiyuan.yu@cornell.edu.
Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853.
ORCID: 0000-0001-7597-6049

Articles similaires

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Yue Zhang, Meifang Song, Deying Tang et al.
1.00
Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

Fasciola hepatica and Fasciola hybrid form co-existence in yak from Tibet of China: application of rDNA internal transcribed spacer.

Wenqiang Tang, Yule Zhou, Leyi Li et al.
1.00
Animals Cattle Tibet Fasciola Fascioliasis

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.

Arunmozhi Bharathi Achudhan, Lilly M Saleena
1.00
Coal Metagenome Phylogeny Bacteria Genome, Bacterial

Exploring the complexity of genome size reduction in angiosperms.

Akihiro Ezoe, Motoaki Seki
1.00
Genome Size Genome, Plant Magnoliopsida Evolution, Molecular Arabidopsis

Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › A massively parallel barcoded sequencing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › ADN des plantes › A massively parallel barcoded sequencing...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › A massively parallel barcoded sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › A massively parallel barcoded sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › A massively parallel barcoded sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Cadres ouverts de lecture › A massively parallel barcoded sequencing...
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Poaceae › Oryza › A massively parallel barcoded sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques de sonde moléculaire › Cartographie d'interactions entre protéines › A massively parallel barcoded sequencing...
questionsmedicales.fr › Métabolisme › Voies et réseaux métaboliques › Cartes d'interactions protéiques › A massively parallel barcoded sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › A massively parallel barcoded sequencing...