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The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes

Rickarlos Bezandry , Mathilde Dupeyron , Laura Natalia Gonzalez-Garcia , Artemis Anest , Perla Hamon et al.
Article dans une revue hal-04448243 v1
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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

J. Salojaervi , A. Rambani , Z. Yu , Romain Guyot , S. Strickler et al.
Nature Genetics, 2024, 56 (4), pp.721-731. ⟨10.1038/s41588-024-01695-w⟩
Article dans une revue hal-04611385 v1
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How genomics can help biodiversity conservation

Kathrin Theissinger , Carlos Fernandes , Giulio Formenti , Iliana Bista , Paul Berg et al.
Trends in Genetics, 2023, ⟨10.1016/j.tig.2023.01.005⟩
Article dans une revue hal-04082874 v1
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The era of reference genomes in conservation genomics

Giulio Formenti , Kathrin Theissinger , Carlos Fernandes , Iliana Bista , Aureliano Bombarely et al.
Trends in Ecology & Evolution, 2022, 37 (3), pp.197-202. ⟨10.1016/j.tree.2021.11.008⟩
Article dans une revue hal-03854324 v1
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Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis

Maria Camila Buitrago Acosta , Rommel Montúfar , Romain Guyot , Cédric Mariac , Timothy J. Tranbarger et al.
Mitochondrial DNA Part B Resources, 2022, 7 (8), pp.1540-1544. ⟨10.1080/23802359.2022.2109437⟩
Article dans une revue ird-04119645 v1

The era of reference genomes in conservation genomics

Florian Maumus , Giulio Formenti , Kathrin Theissinger , Carlos Fernandes , Iliana Bista et al.
Trends in Ecology & Evolution, 2022, 37 (3), pp.197-202. ⟨10.1016/j.tree.2021.11.008⟩
Article dans une revue hal-03717473 v1

High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Bárbara Hufnagel , André Marques , Alexandre Soriano , Laurence Marquès , Fanchon Divol et al.
Nature Communications, 2020, 11 (1), pp.492. ⟨10.1038/s41467-019-14197-9⟩
Article dans une revue hal-04721448 v1
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Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee)

Jean-Claude Charr , Andrea Garavito , Christophe Guyeux , Dominique Crouzillat , Patrick Descombes et al.
Molecular Phylogenetics and Evolution, 2020, 151, ⟨10.1016/j.ympev.2020.106906⟩
Article dans une revue hal-02934893 v1
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High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Barbara Hufnagel , André Marques , Alexandre Soriano , Laurence Marquès , Fanchon Divol et al.
Nature Communications, 2020, 11 (1), pp.492. ⟨10.1038/s41467-019-14197-9⟩
Article dans une revue hal-02460008 v1
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WCSdb: a database of wild <i>Coffea</i> species

Romain Guyot , Perla Hamon , Emmanuel Couturon , Nathalie Raharimalala , Jean-Jacques Rakotomalala et al.
Database - The journal of Biological Databases and Curation, 2020, 2020, ⟨10.1093/database/baaa069⟩
Article dans une revue (data paper) hal-04182535 v1
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Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis

Shuangyang Wu , Romain Guyot , Stéphanie Bocs , Gaëtan Droc , Fetrina Oktavia et al.
International Journal of Molecular Sciences, 2020, 21 (12), pp.4220. ⟨10.3390/ijms21124220⟩
Article dans une revue hal-02923368 v1
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Phenotypic diversity assessment wihin a major ex situ collection of coffees in Madagascar

Aurore Rimlinger , Nathalie Raharimalala , Véronique Letort , Jean-Jacques Rakotomalala , Dominique Crouzillat et al.
Annals of Botany, 2020, 126 (5), pp.849-863. ⟨10.1093/aob/mcaa073⟩
Article dans une revue hal-03167205 v1

Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species

Christophe Guyeux , Jean Charr , Hue T Tran , Agnelo Furtado , Robert J Henry et al.
PLoS ONE, 2019, 14 (6), pp.e0216347. ⟨10.1371/journal.pone.0216347⟩
Article dans une revue hal-02370722 v1

An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Tiago Benedito dos Santos , João Danillo Moura Soares , Joni Esrom Lima , Juliana Christiny Silva , Suzana Tiemi Ivamoto et al.
Functional and Integrative Genomics, 2019, 19 (1), pp.151-169. ⟨10.1007/s10142-018-0634-8⟩
Article dans une revue hal-03469108 v1

CRISPR/Cas9-mediated efficient targeted mutagenesis has the potential to accelerate the domestication of Coffea canephora

Jean-Christophe Breitler , Eveline Dechamp , Claudine Campa , Leonardo Augusto Zebral Rodrigues , Romain Guyot et al.
Plant Cell, Tissue and Organ Culture, 2018, 134 (3), pp.383-394. ⟨10.1007/s11240-018-1429-2⟩
Article dans une revue hal-03432730 v1
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Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions

Renata de Castro Nunes , Simon Orozco-Arias , Dominique Crouzillat , Lukas Mueller , Suzy Strickler et al.
Frontiers in Plant Science, 2018, 9, pp.175. ⟨10.3389/fpls.2018.00175⟩
Article dans une revue hal-03421885 v1
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Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

Gustavo C. Sant’ana , Luiz Pereira , David Pot , Suzana Tiemi Ivamoto , Douglas Domingues et al.
Scientific Reports, 2018, 8 (1), ⟨10.1038/s41598-017-18800-1⟩
Article dans une revue hal-02546614 v1
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Inpactor, Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons and Its Application for Pineapple LTR Retrotransposons Diversity and Dynamics

Simon Orozco-Arias , Juan Liu , Reinel Tabares-Soto , Diego Ceballos , Douglas Silva Domingues et al.
Biology, 2018, 7 (2), pp.32. ⟨10.3390/biology7020032⟩
Article dans une revue hal-03472296 v1

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species

Perla Hamon , Corrinne Grover , Aaron Davis , Jean-Jacques Rakotomalala , Nathalie Raharimalala et al.
Molecular Phylogenetics and Evolution, 2017, 109, pp.351-361. ⟨10.1016/j.ympev.2017.02.009⟩
Article dans une revue hal-03422451 v1

Methylcytosine dioxygenase TET3 interacts with thyroid hormone nuclear receptors and stabilizes their association to chromatin

Wenyue Guan , Romain Guyot , Jacques Samarut , Frederic Flamant , Jiemin Wong et al.
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (31), pp.8229-8234. ⟨10.1073/pnas.1702192114⟩
Article dans une revue hal-03278385 v1

Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons

Mathilde Dupeyron , Rogerio Fernandes de Souza , Perla Hamon , Alexandre de Kochko , Dominique Crouzillat et al.
Molecular Genetics and Genomics, 2017, 292 (4), pp.741-754. ⟨10.1007/s00438-017-1308-2⟩
Article dans une revue hal-03423453 v1

Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories

Romain Guyot , Thibaud Darré , Mathilde Dupeyron , Alexandre de Kochko , Serge Hamon et al.
Molecular Genetics and Genomics, 2016, 291 (5), pp.1979-1990. ⟨10.1007/s00438-016-1235-7⟩
Article dans une revue hal-03430588 v1

Pineapple Genome: A Reference for Monocots and CAM Photosynthesis

Ray Ming , Ching Man Wai , Romain Guyot
Trends in Genetics, 2016, 32 (11), pp.690-696. ⟨10.1016/j.tig.2016.08.008⟩
Article dans une revue hal-03477103 v1

Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species

Julissa Roncal , Romain Guyot , Perla Hamon , Dominique Crouzillat , Michel Rigoreau et al.
Molecular Genetics and Genomics, 2016, 291 (1), pp.155-168. ⟨10.1007/s00438-015-1098-3⟩
Article dans une revue hal-03431261 v1
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Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico

Andrea Garavito , Christophe Montagnon , Romain Guyot , Benoît Bertrand
BMC Plant Biology, 2016, 16 (1), pp.242. ⟨10.1186/s12870-016-0933-y⟩
Article dans une revue hal-03443157 v1
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Developmental programmed cell death during asymmetric microsporogenesis in holocentric species of Rhynchospora (Cyperaceae)

Danilo Rocha , André Marques , Celia G.T.J. Andrade , Romain Guyot , Srinivasa Chaluvadi et al.
Journal of Experimental Botany, 2016, 67 (18), pp.5391-5401. ⟨10.1093/jxb/erw300⟩
Article dans une revue hal-03477144 v1
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Are Genetic and Epigenetic Instabilities of Plant Embryogenic Cells a Fatality? The Experience of Coffee Somatic Embryogenesis

Herve Etienne , Benoit Bertrand , Eveline Dechamp , Patrick Maurel , Frédéric Georget et al.
Human Genetics & Embryology, 2016, 06 (01), pp.136. ⟨10.4172/2161-0436.1000136⟩
Article dans une revue hal-03476825 v1
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Origin and domestication of papaya Y-h chromosome

Robert Vanburen , Fanchang Zeng , Cuixia Chen , Jisen Zhang , Ching Man Wai et al.
Genome Research, 2015, 25 (4), pp.524-533. ⟨10.1101/gr.183905.114⟩
Article dans une revue hal-03479048 v1
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Large distribution and high sequence identity of a Copia&#8209;type retrotransposon in angiosperm families

Elaine Silva Dias , Clémence Hatt , Perla Hamon , Serge Hamon , Michel Rigoreau et al.
Plant Molecular Biology, 2015, 89 (1-2), pp.83-97. ⟨10.1007/s11103-015-0352-8⟩
Article dans une revue ird-01225496 v1
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Terminal-repeat Retrotransposons with GAG domain (TR-GAG) in plant genomes: A new testimony on the complex world of transposable elements

Cristian Chaparro , Thomas Gayraud , Rogerio Fernandes de Souza , Douglas Silva Domingues , Sélastique Doffou Akaffou et al.
Genome Biology and Evolution, 2015, 7 (2), pp.493-504. ⟨10.1093/gbe/evv001⟩
Article dans une revue hal-01162666 v2
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Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Roberto Bobadilla Landey , Alberto Cenci , Romain Guyot , Benoît Bertrand , Frédéric Georget et al.
Plant Cell, Tissue and Organ Culture, 2015, 122 (3), pp.517-531. ⟨10.1007/s11240-015-0772-9⟩
Article dans une revue hal-03388147 v1
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The pineapple genome and the evolution of CAM photosynthesis

Ray Ming , Robert Vanburen , Ching Man Wai , Haibao Tang , Michael C. Schatz et al.
Nature Genetics, 2015, 47 (12), pp.1435-1442. ⟨10.1038/ng.3435⟩
Article dans une revue hal-03478898 v1

Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses

Fabíola Carvalho Santos , Romain Guyot , Cacilda Borges Do Valle , Lucimara Chiari , Vânia Helena Techio et al.
Chromosome Research, 2015, 23 (3), pp.571-582. ⟨10.1007/s10577-015-9492-6⟩
Article dans une revue hal-03478996 v1
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Genome-wide analysis of LTR-retrotransposons in oil palm

Thierry Beulé , Mawussé Dt Agbessi , Stephane Dussert , Estelle Jaligot , Romain Guyot
BMC Genomics, 2015, 16, pp.795. ⟨10.1186/s12864-015-2023-1⟩
Article dans une revue hal-03205781 v1
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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

France Denoeud , Lorenzo Carretero-Paulet , Alexis Dereeper , Gaëtan Droc , Romain Guyot et al.
Science, 2014, 345 (6201), pp.1181-1184. ⟨10.1126/science.1255274⟩
Article dans une revue hal-02641562 v1

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

Alexis Dereeper , Romain Guyot , Christine Tranchant-Dubreuil , François Anthony , Xavier Argout et al.
Plant Molecular Biology, 2013, 83, pp.177-189. ⟨10.1007/s11103-013-0077-5⟩
Article dans une revue istex cea-04667063 v1

A genetic model for the female sterility barrier between Asian and African cultivated rice species.

Andrea Garavito , Romain Guyot , Jaime Lozano , Frédérick F. Gavory , Sylvie Samain et al.
Genetics, 2010, 185 (4), pp.1425-40. ⟨10.1534/genetics.110.116772⟩
Article dans une revue hal-00787398 v1
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In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

Mauricio Soto-Suárez , Diana Bernal , Carolina González , Boris Szurek , Romain Guyot et al.
BMC Microbiology, 2010, 10, pp.170. ⟨10.1186/1471-2180-10-170⟩
Article dans une revue ird-01075143 v1
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Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.

Romain Guyot , Marion de La Mare , Véronique Viader , Perla Hamon , Olivier Coriton et al.
BMC Plant Biology, 2009, 9 (22), pp.22. ⟨10.1186/1471-2229-9-22⟩
Article dans une revue hal-00695701 v1

RetrOryza: a database of the rice LTR-retrotransposons.

Cristian Chaparro , Romain Guyot , Andrea Zuccolo , Benoit Piegu , Olivier Panaud
Nucleic Acids Research, 2007, 35 (Database issue), pp.D66-70. ⟨10.1093/nar/gkl780⟩
Article dans une revue hal-00164403 v1

Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice.

Benoit Piegu , Romain Guyot , Nathalie Picault , Anne Roulin , Abhijit Saniyal et al.
Genome Research, 2006, 16 (10), pp.1262-9. ⟨10.1101/gr.5290206⟩
Article dans une revue hal-00164404 v1

Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2'-O-methylation sites

Fredy Barneche , Christine Gaspin , Romain Guyot , Manuel Echeverria
Journal of Molecular Biology, 2001, 311 (1), pp.57-73. ⟨10.1006/jmbi.2001.4851⟩
Article dans une revue istex hal-02677526 v1

From Rice to Other Cereals: Comparative Genomics

Richard Cooke , Benoit Piegu , Olivier Panaud , Romain Guyot , Jérôme Salse et al.
Rice Functional Genomics, Springer New York, pp.429-479, 2007
Chapitre d'ouvrage hal-02114392 v1