Jerome Salse

Jerome Salse

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Jerome Salse

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Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.

Genome Biol 2019 02 11;20(1):29. Epub 2019 Feb 11.

INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1627-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369560PMC
February 2019

Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements.

Plant J 2018 05 15;94(4):721-734. Epub 2018 Apr 15.

State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, China.

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http://dx.doi.org/10.1111/tpj.13894DOI Listing
May 2018

Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat ( L.).

Front Plant Sci 2017 14;8:1843. Epub 2017 Nov 14.

Institut National de la Recherche Agronomique, Université Clermont Auvergne, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France.

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http://journal.frontiersin.org/article/10.3389/fpls.2017.018
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http://dx.doi.org/10.3389/fpls.2017.01843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694560PMC
November 2017

Wheat paleohistory created asymmetrical genomic evolution.

Curr Opin Plant Biol 2017 04 7;36:29-37. Epub 2017 Feb 7.

INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France(*). Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2017.01.001DOI Listing
April 2017

Reconstructing the genome of the most recent common ancestor of flowering plants.

Nat Genet 2017 Apr 13;49(4):490-496. Epub 2017 Mar 13.

INRA/UCA UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Group PaleoEVO 'Paleogenomics and Evolution', Clermont Ferrand, France.

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http://dx.doi.org/10.1038/ng.3813DOI Listing
April 2017

Reconciling the evolutionary origin of bread wheat (Triticum aestivum).

New Phytol 2017 Feb 23;213(3):1477-1486. Epub 2016 Aug 23.

INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France.

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https://www.researchgate.net/profile/Moaine_El_Baidouri/publ
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http://dx.doi.org/10.1111/nph.14113DOI Listing
February 2017

Deciphering the evolutionary interplay between subgenomes following polyploidy: A paleogenomics approach in grasses.

Authors:
Jérôme Salse

Am J Bot 2016 07 17;103(7):1167-74. Epub 2016 Jul 17.

INRA/UBP UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Laboratory of Paleogenomics & Evolution, 5 chemin de Beaulieu 63100 Clermont Ferrand, France

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http://dx.doi.org/10.3732/ajb.1500459DOI Listing
July 2016

Ancestors of modern plant crops.

Authors:
Jérôme Salse

Curr Opin Plant Biol 2016 04 14;30:134-42. Epub 2016 Mar 14.

INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Laboratory PaleoEVO 'Paleogenomics & Evolution', 5 chemin de Beaulieu, 63100 Clermont Ferrand, France(1). Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2016.02.005DOI Listing
April 2016

Erratum to: Understanding Brassicaceae evolution through ancestral genome reconstruction.

Genome Biol 2016 Apr 4;17:64. Epub 2016 Apr 4.

INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France.

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http://dx.doi.org/10.1186/s13059-016-0887-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820912PMC
April 2016

Understanding Brassicaceae evolution through ancestral genome reconstruction.

Genome Biol 2015 Dec 10;16:262. Epub 2015 Dec 10.

INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France.

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http://dx.doi.org/10.1186/s13059-015-0814-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675067PMC
December 2015

FRIZZY PANICLE drives supernumerary spikelets in bread wheat.

Plant Physiol 2015 Jan 14;167(1):189-99. Epub 2014 Nov 14.

Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)

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http://www.plantphysiol.org/content/167/1/189.full.pdf+html
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http://www.plantphysiol.org/content/early/2014/11/14/pp.114.
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http://www.plantphysiol.org/content/167/1/189.full.pdf
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http://www.plantphysiol.org/lookup/doi/10.1104/pp.114.250043
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http://dx.doi.org/10.1104/pp.114.250043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281007PMC
January 2015

GenomicusPlants: a web resource to study genome evolution in flowering plants.

Plant Cell Physiol 2015 Jan 27;56(1):e4. Epub 2014 Nov 27.

Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France CNRS, UMR 8197, Paris, F-75005 France Inserm, U1024, Paris, F-75005 France.

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http://dx.doi.org/10.1093/pcp/pcu177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301744PMC
January 2015

Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat.

Theor Appl Genet 2014 Jul 10;127(7):1463-89. Epub 2014 Jun 10.

Wheat Physiology, Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 56130, Mexico DF, Mexico,

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http://dx.doi.org/10.1007/s00122-014-2332-9DOI Listing
July 2014

The genome of Eucalyptus grandis.

Nature 2014 Jun 11;510(7505):356-62. Epub 2014 Jun 11.

1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.

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http://dx.doi.org/10.1038/nature13308DOI Listing
June 2014

Paleo-evolutionary plasticity of plant disease resistance genes.

BMC Genomics 2014 Mar 12;15:187. Epub 2014 Mar 12.

INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 chemin de Beaulieu, 63100 Clermont-Ferrand, France.

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http://dx.doi.org/10.1186/1471-2164-15-187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234491PMC
March 2014

Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication.

Plant Cell 2012 May 15;24(5):1776-92. Epub 2012 May 15.

Institut National de la Recherche Agronomique/Université Blaise Pascal, Unité Mixte de Recherche 1095, Génétique, Diversité et Ecophysiologie des Céréales, Clermont Ferrand, France.

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http://dx.doi.org/10.1105/tpc.112.095752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3442569PMC
May 2012

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution.

Authors:
Jérôme Salse

Curr Opin Plant Biol 2012 Apr 24;15(2):122-30. Epub 2012 Jan 24.

INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Group PPAV 'Paléogénomique des Plantes pour l'Amélioration Variétale', Domaine de Crouelle, 234 avenue du Brézet, 63100 Clermont Ferrand, France.

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http://dx.doi.org/10.1016/j.pbi.2012.01.001DOI Listing
April 2012

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).

Genome Biol 2011 Dec 2;12(12):R119. Epub 2011 Dec 2.

INRA, UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, 234 avenue du Brézet, Clermont-Ferrand, France.

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http://dx.doi.org/10.1186/gb-2011-12-12-r119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334614PMC
December 2011

Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.

Bioinformatics 2011 Jul;27(13):i257-65

Faculty of Natural Sciences, University of Sarajevo, Bosnia and Herzegovina.

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http://dx.doi.org/10.1093/bioinformatics/btr224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117370PMC
July 2011

Palaeogenomics in cereals: modeling of ancestors for modern species improvement.

C R Biol 2011 Mar 31;334(3):205-11. Epub 2011 Jan 31.

INRA/UBP UMR 1095 GDEC 'génétique, diversité et écophysiologie des céréales', Research group PPAV 'Paleogénomique des Plantes pour l'Amélioration Variétale', 234 avenue du Brézet, Clermont-Ferrand, France.

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https://linkinghub.elsevier.com/retrieve/pii/S16310691100030
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http://dx.doi.org/10.1016/j.crvi.2010.12.014DOI Listing
March 2011

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.

Genome Res 2010 Nov 28;20(11):1545-57. Epub 2010 Sep 28.

INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.109744.110
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http://dx.doi.org/10.1101/gr.109744.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2963818PMC
November 2010

Palaeogenomics of plants: synteny-based modelling of extinct ancestors.

Trends Plant Sci 2010 Sep 17;15(9):479-87. Epub 2010 Jul 17.

INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brézet, 63100 Clermont Ferrand, France.

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http://www.cell.com/trends/plant-science/pdf/S1360-1385(10)0
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http://linkinghub.elsevier.com/retrieve/pii/S136013851000132
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http://dx.doi.org/10.1016/j.tplants.2010.06.001DOI Listing
September 2010

Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection.

Funct Integr Genomics 2009 Nov 3;9(4):473-84. Epub 2009 Jul 3.

Génétique, Diversité et Ecophysiologie des Céréales (GDEC), UMR 1095 INRA/Université Blaise Pascal, Domaine de Crouelle, 234 avenue du Brézet, 63100, Clermont-Ferrand, France.

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http://dx.doi.org/10.1007/s10142-009-0129-8DOI Listing
November 2009

Improved criteria and comparative genomics tool provide new insights into grass paleogenomics.

Brief Bioinform 2009 Nov 31;10(6):619-30. Epub 2009 Aug 31.

INRA/Université Blaise Pascal UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, Domaine de Crouelle, 234 avenue du Brézet, 63100 Clermont-Ferrand, France.

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http://dx.doi.org/10.1093/bib/bbp037DOI Listing
November 2009

Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals.

Proc Natl Acad Sci U S A 2009 Sep 13;106(35):14908-13. Epub 2009 Aug 13.

Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1095, Génétique, Diversité et Ecophysiologie des Céréales, Université Blaise Pascal, 234 Avenue du Brézet, 63100 Clermont Ferrand, France.

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http://www.pnas.org/content/106/35/14908.full.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.0902350106
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http://dx.doi.org/10.1073/pnas.0902350106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736418PMC
September 2009

The 'inner circle' of the cereal genomes.

Curr Opin Plant Biol 2009 Apr 16;12(2):119-25. Epub 2008 Dec 16.

INRA/UBP UMR 1095, Domaine de Crouelle, 234 avenue du Brézet 63100 Clermont Ferrand, France.

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http://dx.doi.org/10.1016/j.pbi.2008.10.011DOI Listing
April 2009

Structure and expression analysis of rice paleo duplications.

Nucleic Acids Res 2009 Mar 9;37(4):1248-59. Epub 2009 Jan 9.

UMR 1095 INRA/UBP, Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Domaine de Crouelle, 234, 63100 Clermont Ferrand, France.

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http://dx.doi.org/10.1093/nar/gkn1048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651813PMC
March 2009

Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.

Funct Integr Genomics 2008 Feb 24;8(1):29-32. Epub 2007 Nov 24.

INRA, UMR 1095, ASP, 234, avenue du Brézet, 63100, Clermont-Ferrand, France.

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http://dx.doi.org/10.1007/s10142-007-0068-1DOI Listing
February 2008

Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution.

Plant Cell 2008 Jan 4;20(1):11-24. Epub 2008 Jan 4.

Institut National de la Recherche Agronomique/Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont-Ferrand, France.

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http://dx.doi.org/10.1105/tpc.107.056309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2254919PMC
January 2008

New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome.

Plant J 2004 May;38(3):396-409

Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan (Centre National de la Recherche Scientifique, UMR 5096), 66860 Perpignan Cedex, France.

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http://dx.doi.org/10.1111/j.1365-313X.2004.02058.xDOI Listing
May 2004

Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project.

Nucleic Acids Res 2002 Jun;30(11):2316-28

Laboratoire Génome et Développement des Plantes, Université de Perpignan (Centre National de la Recherche Scientifique, UMR 5096), 52 Avenue de Villeneuve, F-66860 Perpignan Cedex, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117207PMC
http://dx.doi.org/10.1093/nar/30.11.2316DOI Listing
June 2002