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24 results on '"Cauet, Stéphane"'

1. Einkorn genomics sheds light on history of the oldest domesticated wheat

Author

Ahmed, Hanin Ibrahim, Heuberger, Matthias, Schoen, Adam, Koo, Dal-Hoe, Quiroz-Chavez, Jesus, Adhikari, Laxman, Raupp, John, Cauet, Stéphane, Rodde, Nathalie, Cravero, Charlotte, Callot, Caroline, Lazo, Gerard R., Kathiresan, Nagarajan, Sharma, Parva K., Moot, Ian, Yadav, Inderjit Singh, Singh, Lovepreet, Saripalli, Gautam, Rawat, Nidhi, Datla, Raju, Athiyannan, Naveenkumar, Ramirez-Gonzalez, Ricardo H., Uauy, Cristobal, Wicker, Thomas, Tiwari, Vijay K., Abrouk, Michael, Poland, Jesse, and Krattinger, Simon G.

Published
2023
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4. Population genomics of apricots unravels domestication history and adaptive events

Author

Groppi, Alexis, Liu, Shuo, Cornille, Amandine, Decroocq, Stéphane, Bui, Quynh Trang, Tricon, David, Cruaud, Corinne, Arribat, Sandrine, Belser, Caroline, Marande, William, Salse, Jérôme, Huneau, Cécile, Rodde, Nathalie, Rhalloussi, Wassim, Cauet, Stéphane, Istace, Benjamin, Denis, Erwan, Carrère, Sébastien, Audergon, Jean-Marc, Roch, Guillaume, Lambert, Patrick, Zhebentyayeva, Tetyana, Liu, Wei-Sheng, Bouchez, Olivier, Lopez-Roques, Céline, Serre, Rémy-Félix, Debuchy, Robert, Tran, Joseph, Wincker, Patrick, Chen, Xilong, Pétriacq, Pierre, Barre, Aurélien, Nikolski, Macha, Aury, Jean-Marc, Abbott, Albert Glenn, Giraud, Tatiana, and Decroocq, Véronique

Published
2021
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5. A receptor-like kinase enhances sunflower resistance to Orobanche cumana

Author

Duriez, Pauline, Vautrin, Sonia, Auriac, Marie-Christine, Bazerque, Julia, Boniface, Marie-Claude, Callot, Caroline, Carrère, Sébastien, Cauet, Stéphane, Chabaud, Mireille, Gentou, Fabienne, Lopez-Sendon, Marta, Paris, Clémence, Pegot-Espagnet, Prune, Rousseaux, Jean-Christophe, Pérez-Vich, Begoña, Velasco, Leonardo, Bergès, Hélène, Piquemal, Joël, and Muños, Stéphane

Published
2019
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6. Whole-genome landscape of Medicago truncatula symbiotic genes

Author

Pecrix, Yann, Staton, S. Evan, Sallet, Erika, Lelandais-Brière, Christine, Moreau, Sandra, Carrère, Sébastien, Blein, Thomas, Jardinaud, Marie-Françoise, Latrasse, David, Zouine, Mohamed, Zahm, Margot, Kreplak, Jonathan, Mayjonade, Baptiste, Satgé, Carine, Perez, Magali, Cauet, Stéphane, Marande, William, Chantry-Darmon, Céline, Lopez-Roques, Céline, Bouchez, Olivier, Bérard, Aurélie, Debellé, Frédéric, Muños, Stéphane, Bendahmane, Abdelhafid, Bergès, Hélène, Niebel, Andreas, Buitink, Julia, Frugier, Florian, Benhamed, Moussa, Crespi, Martin, Gouzy, Jérôme, and Gamas, Pascal

Published
2018
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7. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author

Abrouk, Michael, Ahmed, Hanin Ibrahim, Cubry, Philippe, Šimoníková, Denisa, Cauet, Stéphane, Pailles, Yveline, Bettgenhaeuser, Jan, Gapa, Liubov, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leila, Kathiresan, Nagarajan, Čížková, Jana, Hřibová, Eva, Doležel, Jaroslav, Arribat, Sandrine, Bergès, Hélène, Wieringa, Jan J., Gueye, Mathieu, Kane, Ndjido A., Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas, Vigouroux, Yves, Barnaud, Adeline, and Krattinger, Simon G.

Published
2020
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8. The genomics of linkage drag in inbred lines of sunflower

Author

Huang, Kaichi, primary, Jahani, Mojtaba, additional, Gouzy, Jérôme, additional, Legendre, Alexandra, additional, Carrere, Sébastien, additional, Lázaro-Guevara, José Miguel, additional, González Segovia, Eric Gerardo, additional, Todesco, Marco, additional, Mayjonade, Baptiste, additional, Rodde, Nathalie, additional, Cauet, Stéphane, additional, Dufau, Isabelle, additional, Staton, S. Evan, additional, Pouilly, Nicolas, additional, Boniface, Marie-Claude, additional, Tapy, Camille, additional, Mangin, Brigitte, additional, Duhnen, Alexandra, additional, Gautier, Véronique, additional, Poncet, Charles, additional, Donnadieu, Cécile, additional, Mandel, Tali, additional, Hübner, Sariel, additional, Burke, John M., additional, Vautrin, Sonia, additional, Bellec, Arnaud, additional, Owens, Gregory L., additional, Langlade, Nicolas, additional, Muños, Stéphane, additional, and Rieseberg, Loren H., additional

Published
2023
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9. Unravelling the structure of endogenous badnaviruses of african yam shed light on the origin and diversity of yam caulimoviridae insertions

Author

Umber, Marie, Bellec, Arnaud, Cauet, Stéphane, Theron, Anthony, Dalphrase, Stessy, Gautier, Véronique, Pailler, Vincent, Belmonte, Elodie, Teycheney, Pierre-Yves, Umber, Marie, Bellec, Arnaud, Cauet, Stéphane, Theron, Anthony, Dalphrase, Stessy, Gautier, Véronique, Pailler, Vincent, Belmonte, Elodie, and Teycheney, Pierre-Yves

Abstract

Endogenous viral elements (EVEs) of four distinct badnavirus species were previously partially characterized in the genome of African yam (Dioscorea cayenensis and D. rotundata), using molecular approaches. In order to fully elucidate the structure of badnaviral EVEs in African yams, the genomes of accessions 'Ti Guinée' (D. cayenensis) and 'Msg 5' (D. rotundata) were sequenced using HiFi PacBio high-throughput sequencing (HTS) and searched for badnavirus EVEs. Large contigs of up to 50 Mbp were assembled and combined with optical maps produced by Saphyr system (Bionano), resulting in two high-quality reference sequences for Dioscorea. Twelve and six contigs originating from the genomes of 'Ti Guinée' and 'Mgs 5', respectively, contained badnaviral EVEs ranging in size between 124.4 and 17.7 kbp. All badnaviral EVEs were highly rearranged, especially those of D. cayenensis, which were also larger, and most contained interspersed sequences originating from distinct badnavirus species or from viruses in different Caulimoviridae genera. One EVE from accession 'Ti Guinée' contained badnaviral sequences surrounded by putative Geminiviridae sequences. Several EVEs from 'Ti Guinée' contained sequences of a yet unreported Caulimoviridae closely related to but distinct from Dioscorea nummularia-associated virus (DNUaV; Dioscovirus). Several EVEs originating from either species contained more-than-length copies of badnaviral genomes that may be replication competent and infectious.

Published
2023

10. An online database for einkorn wheat to aid in gene discovery and functional genomics studies

Author

Sharma, Parva Kumar, Ahmed, Hanin Ibrahim, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus, Adhikari, Laxman, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte, Callot, Caroline, Yadav, Inderjit Singh, Kathiresan, Nagarajan, Athiyannan, Naveenkumar, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Abrouk, Michael, Gu, Yong Q, Poland, Jesse, Krattinger, Simon G, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, Tiwari, Vijay K, Sharma, Parva Kumar, Ahmed, Hanin Ibrahim, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus, Adhikari, Laxman, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte, Callot, Caroline, Yadav, Inderjit Singh, Kathiresan, Nagarajan, Athiyannan, Naveenkumar, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Abrouk, Michael, Gu, Yong Q, Poland, Jesse, Krattinger, Simon G, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, and Tiwari, Vijay K

Abstract

Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.

Published
2023

11. Einkorn genomics sheds light on history of the oldest domesticated wheat

Author

Ahmed, Hanin Ibrahim; https://orcid.org/0000-0001-9078-183X, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Schoen, Adam, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus; https://orcid.org/0000-0001-5935-2578, Adhikari, Laxman; https://orcid.org/0000-0001-9507-5117, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte; https://orcid.org/0009-0005-1461-1894, Callot, Caroline, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, Kathiresan, Nagarajan; https://orcid.org/0000-0002-5558-6331, Sharma, Parva K; https://orcid.org/0000-0002-0393-6432, Moot, Ian, Yadav, Inderjit Singh, Singh, Lovepreet, Saripalli, Gautam, Rawat, Nidhi, Datla, Raju; https://orcid.org/0000-0003-0790-5569, Athiyannan, Naveenkumar; https://orcid.org/0000-0002-9232-4680, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Tiwari, Vijay K; https://orcid.org/0000-0001-7297-4048, Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Poland, Jesse; https://orcid.org/0000-0002-7856-1399, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Ahmed, Hanin Ibrahim; https://orcid.org/0000-0001-9078-183X, Heuberger, Matthias; https://orcid.org/0000-0003-3283-9233, Schoen, Adam, Koo, Dal-Hoe; https://orcid.org/0000-0003-4578-8519, Quiroz-Chavez, Jesus; https://orcid.org/0000-0001-5935-2578, Adhikari, Laxman; https://orcid.org/0000-0001-9507-5117, Raupp, John; https://orcid.org/0000-0002-0135-3911, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Rodde, Nathalie; https://orcid.org/0000-0003-3361-4730, Cravero, Charlotte; https://orcid.org/0009-0005-1461-1894, Callot, Caroline, Lazo, Gerard R; https://orcid.org/0000-0002-9160-2052, Kathiresan, Nagarajan; https://orcid.org/0000-0002-5558-6331, Sharma, Parva K; https://orcid.org/0000-0002-0393-6432, Moot, Ian, Yadav, Inderjit Singh, Singh, Lovepreet, Saripalli, Gautam, Rawat, Nidhi, Datla, Raju; https://orcid.org/0000-0003-0790-5569, Athiyannan, Naveenkumar; https://orcid.org/0000-0002-9232-4680, Ramirez-Gonzalez, Ricardo H, Uauy, Cristobal; https://orcid.org/0000-0002-9814-1770, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Tiwari, Vijay K; https://orcid.org/0000-0001-7297-4048, Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Poland, Jesse; https://orcid.org/0000-0002-7856-1399, and Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411

Abstract

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago$^{1,2}$. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

Published
2023

12. An online database for einkorn wheat to aid in gene discovery and functional genomics studies

Author

Sharma, Parva Kumar, primary, Ahmed, Hanin Ibrahim, additional, Heuberger, Matthias, additional, Koo, Dal-Hoe, additional, Quiroz-Chavez, Jesus, additional, Adhikari, Laxman, additional, Raupp, John, additional, Cauet, Stéphane, additional, Rodde, Nathalie, additional, Cravero, Charlotte, additional, Callot, Caroline, additional, Yadav, Inderjit Singh, additional, Kathiresan, Nagarajan, additional, Athiyannan, Naveenkumar, additional, Ramirez-Gonzalez, Ricardo H, additional, Uauy, Cristobal, additional, Wicker, Thomas, additional, Abrouk, Michael, additional, Gu, Yong Q, additional, Poland, Jesse, additional, Krattinger, Simon G, additional, Lazo, Gerard R, additional, and Tiwari, Vijay K, additional

Published
2023
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13. Comparative phylotranscriptomics reveals a 110 million years-old symbiotic program

Author

Libourel, Cyril, primary, Keller, Jean, additional, Brichet, Lukas, additional, Cazalé, Anne-Claire, additional, Carrère, Sébastien, additional, Vernié, Tatiana, additional, Couzigou, Jean-Malo, additional, Callot, Caroline, additional, Dufau, Isabelle, additional, Cauet, Stéphane, additional, Marande, William, additional, Bulach, Tabatha, additional, Suin, Amandine, additional, Masson-Boivin, Catherine, additional, Remigi, Philippe, additional, Delaux, Pierre-Marc, additional, and Capela, Delphine, additional

Published
2022
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15. The genomics of linkage drag in sunflower

Author

Huang, Kaichi, primary, Jahani, Mojtaba, additional, Gouzy, Jérôme, additional, Legendre, Alexandra, additional, Carrere, Sebastien, additional, Lázaro-Guevara, José Miguel, additional, González Segovia, Eric Gerardo, additional, Todesco, Marco, additional, Mayjonade, Baptiste, additional, Rodde, Nathalie, additional, Cauet, Stéphane, additional, Dufau, Isabelle, additional, Staton, S Evan, additional, Pouilly, Nicolas, additional, Boniface, Marie-Claude, additional, Tapy, Camille, additional, Mangin, Brigitte, additional, Duhnen, Alexandra, additional, Gautier, Véronique, additional, Poncet, Charles, additional, Donnadieu, Cécile, additional, Mandel, Tali, additional, Hübner, Sariel, additional, Burke, John M., additional, Vautrin, Sonia, additional, Bellec, Arnaud, additional, Owens, Gregory L., additional, Langlade, Nicolas, additional, Muños, Stéphane, additional, and Rieseberg, Loren H., additional

Published
2022
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16. Biodiversity analysis in plant genomes: An innovative capture approach to characterize targeted region of interest

Author

Callot, Caroline, Satge, Carine, Fustier, Margaux-Alison, Cauet, Stéphane, Marande, William, Bacilieri, Roberto, Chabannes, Matthieu, Guichemerre, Audrey, Callot, Caroline, Satge, Carine, Fustier, Margaux-Alison, Cauet, Stéphane, Marande, William, Bacilieri, Roberto, Chabannes, Matthieu, and Guichemerre, Audrey

Abstract

In a context of climate change, population growth and limited energy resources, plant genomes knowledge is essential for a better understanding of mechanisms driving plant adaptation and evolution. Deciphering plant genomes is one of the strategic approaches. However, this remains challenging due to the high level of complexity of plant genomes in terms of size, polyploidy levels and repetitive elements contents. Moreover, due to high intra-species variability, a single reference genome is not enough to understand complex biological processes, such as resistance to biotic or abiotic stresses. Understanding the link between a genomic region and a phenotype of interest requires a reliable sequence information from the specific cultivar carrying this trait of interest. Due to the evolution of Long-Read Sequencing technology (Pacific Biosciences or Oxford Nanopore Technology) in term of chemistry and cost, genome information become more accessible. However, the cost of whole genome sequencing can remain high due to the complexity of plants, especially to study multiple genotypes at once. Focusing on a genomic region of interest is an alternative solution for diversity analysis. Here we present an update of an innovative sequence capture approach aiming at targeting large DNA fragments in eukaryote genomes. This strategy is adapted from the CRISPR-Cap method (Cas9-Assisted Targeting of Chromosomal segments) described by Lee and al. in 2018. CNRGV adapted this protocol by using a Cas9 enzyme deprived of its endonuclease function coupled to a cluster of gRNA specific to the region of interest to be captured. We present the efficiency of this strategy to: (i) characterize complex viruses' insertions in banana genome and (ii) identify the sex locus in grapevine.

Published
2022

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

Author

Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Ahmed, Hanin Ibrahim, Cubry, Philippe; https://orcid.org/0000-0003-1561-8949, Šimoníková, Denisa, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Pailles, Yveline, Bettgenhaeuser, Jan; https://orcid.org/0000-0002-6901-1774, Gapa, Liubov; https://orcid.org/0000-0002-2744-9858, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leila, Kathiresan, Nagarajan, Čížková, Jana, Hřibová, Eva, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Arribat, Sandrine, Bergès, Hélène, Wieringa, Jan J; https://orcid.org/0000-0003-0566-372X, Gueye, Mathieu, Kane, Ndjido A; https://orcid.org/0000-0002-1879-019X, Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Vigouroux, Yves; https://orcid.org/0000-0002-8361-6040, Barnaud, Adeline; https://orcid.org/0000-0001-9896-1210, Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411, Abrouk, Michael; https://orcid.org/0000-0001-9082-1432, Ahmed, Hanin Ibrahim, Cubry, Philippe; https://orcid.org/0000-0003-1561-8949, Šimoníková, Denisa, Cauet, Stéphane; https://orcid.org/0000-0003-4985-8940, Pailles, Yveline, Bettgenhaeuser, Jan; https://orcid.org/0000-0002-6901-1774, Gapa, Liubov; https://orcid.org/0000-0002-2744-9858, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leila, Kathiresan, Nagarajan, Čížková, Jana, Hřibová, Eva, Doležel, Jaroslav; https://orcid.org/0000-0002-6263-0492, Arribat, Sandrine, Bergès, Hélène, Wieringa, Jan J; https://orcid.org/0000-0003-0566-372X, Gueye, Mathieu, Kane, Ndjido A; https://orcid.org/0000-0002-1879-019X, Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas; https://orcid.org/0000-0002-6777-7135, Vigouroux, Yves; https://orcid.org/0000-0002-8361-6040, Barnaud, Adeline; https://orcid.org/0000-0001-9896-1210, and Krattinger, Simon G; https://orcid.org/0000-0001-6912-7411

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.

Published
2020

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

Author

Abrouk, Michael, primary, Ahmed, Hanin Ibrahim, additional, Cubry, Philippe, additional, Šimoníková, Denisa, additional, Cauet, Stéphane, additional, Bettgenhaeuser, Jan, additional, Gapa, Liubov, additional, Pailles, Yveline, additional, Scarcelli, Nora, additional, Couderc, Marie, additional, Zekraoui, Leila, additional, Kathiresan, Nagarajan, additional, Čížková, Jana, additional, Hřibová, Eva, additional, Doležel, Jaroslav, additional, Arribat, Sandrine, additional, Bergès, Hélène, additional, Wieringa, Jan J., additional, Gueye, Mathieu, additional, Kane, Ndjido A., additional, Leclerc, Christian, additional, Causse, Sandrine, additional, Vancoppenolle, Sylvie, additional, Billot, Claire, additional, Wicker, Thomas, additional, Vigouroux, Yves, additional, Barnaud, Adeline, additional, and Krattinger, Simon G., additional

Published
2020
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20. Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. ‘Nure’ and expression analysis

Author

Mareri, Lavinia, primary, Milc, Justyna, additional, Laviano, Luca, additional, Buti, Matteo, additional, Vautrin, Sonia, additional, Cauet, Stéphane, additional, Mascagni, Flavia, additional, Natali, Lucia, additional, Cavallini, Andrea, additional, Bergès, Hélène, additional, Pecchioni, Nicola, additional, and Francia, Enrico, additional

Published
2020
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21. A receptor-like kinase enhances sunflower resistance to Orobanche cumana

Author

Syngenta, Institut National de la Recherche Agronomique (France), Duriez, Pauline, Vautrin, Sonia, Auriac, Marie-Christine, Bazerque, Julia, Boniface, Marie-Claude, Callot, Caroline, Carrère, Sébastien, Cauet, Stéphane, Chabaud, Mireille, Gentou, Fabienne, López-Sendón, Marta, Paris, Clémence, Pegot-Espagnet, Prune, Rousseaux, Jean-Chrstophe, Pérez-Vich, Begoña, Velasco Varo, Leonardo, Bergès, Hélène, Piquemal, Joël, Muños, Stéphane, Syngenta, Institut National de la Recherche Agronomique (France), Duriez, Pauline, Vautrin, Sonia, Auriac, Marie-Christine, Bazerque, Julia, Boniface, Marie-Claude, Callot, Caroline, Carrère, Sébastien, Cauet, Stéphane, Chabaud, Mireille, Gentou, Fabienne, López-Sendón, Marta, Paris, Clémence, Pegot-Espagnet, Prune, Rousseaux, Jean-Chrstophe, Pérez-Vich, Begoña, Velasco Varo, Leonardo, Bergès, Hélène, Piquemal, Joël, and Muños, Stéphane

Abstract

Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that infects sunflower roots, causing yield losses. Here, by using a map-based cloning strategy, we identified HaOr7—a gene that confers resistance to O. cumana race F—which was found to encode a leucine-rich repeat receptor-like kinase. The complete HAOR7 protein is present in resistant lines of sunflower and prevents O. cumana from connecting to the vascular system of sunflower roots, whereas susceptible lines encode a truncated protein that lacks transmembrane and kinase domains.

Published
2019

22. The complete genome sequence of Orobanche cumana (sunflower broomrape)

Author

Gouzy, Jérôme, Pouill, Nicolas, Boniface, Marie-Claude, Bouchez, Olivier, Carrère, Sébastien, Catrice, Olivier, Cauet, Stéphane, Claudel, Clotilde, Cottret, Ludovic, Faure, Sébastien, Calderón González, Álvaro, Grand, Xavier, Hu, Luyang, Jéziorski, Céline, Lechat, Marc-Marie, Legrand, Ludovic, Louarn, Johann, Marnade, William, Ribière, Nicolas, Sallet, Erika, Simier, Philippe, Velasco Varo, Leonardo, Donnadieu, Cécile, Jestin, Christophe, Delavault, Philippe, Bergès, Hélène, Coque, Marie, Pérez-Vich, Begoña, and Muños, Stéphane

Abstract

Trabajo presentado en el 14th World Congress on Parasitic Plants (From genome to field), celebrado en Asilomar (California) el 24 y 25 de junio de 2017., Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that specifically infects sunflower (Helianthus annuus). It is one of the main limiting factors of sunflower crop in Eastern Europe, Spain and Asia. In 2007, the first infested fields have been reported in France. Breeding for resistance in sunflower was successful but new more virulent races of O. cumana often overcame the resistance genes. The first developmental stages of O. cumana occur underground. The germination of the seeds is first stimulated by sunflower root exudates before entering the host root through a haustorium. Without roots nor chlorophyll, O. cumana depends on sunflower for water and nutrients supply. It connects to the vascular system of the sunflower root and store metabolites in a tubercle before emerging a flowering shoot. The inactivation of these developmental stages is a key resistance mechanism in sunflower. A better understanding of the biology of O. cumana will help to identify new resistance processes and resistance genes in sunflower. In the frame of a collaborative project between French and Spanish research institutes, we have produced a first version of the 1.42 Gb genome sequence of O. cumana by combining PacBio sequencing, optical mapping and genetic map. More than twenty transcriptomic RNA-seq experiments from O. cumana were used for annotating the genome sequence. This first sequence assembly (622 scaffolds, 1.38Gb, N50=5.9Mb) and its annotation will be provided through a Web Genome Browser to the public research community. Our strategy to obtain and finalize the genome assembly as well as results on population diversity will be presented. The genome sequence of O. cumana will enable the characterization of its physiology and development. Avirulence genes should be identified more efficiently and, as putative interactor with sunflower proteins, should help in identifying new resistance genes in sunflower. This resource will help in understanding parasitic plants’ biology and evolution, like parasitism capacity acquisition.

Published
2017

23. Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep

Author

Demars, Julie, primary, Cano, Margarita, additional, Drouilhet, Laurence, additional, Plisson-Petit, Florence, additional, Bardou, Philippe, additional, Fabre, Stéphane, additional, Servin, Bertrand, additional, Sarry, Julien, additional, Woloszyn, Florent, additional, Mulsant, Philippe, additional, Foulquier, Didier, additional, Carrière, Fabien, additional, Aletru, Mathias, additional, Rodde, Nathalie, additional, Cauet, Stéphane, additional, Bouchez, Olivier, additional, Pirson, Maarten, additional, Tosser-Klopp, Gwenola, additional, and Allain, Daniel, additional

Published
2017
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24. Whole-genome landscape of Medicago truncatulasymbiotic genes

Author

Pecrix, Yann, Staton, S. Evan, Sallet, Erika, Lelandais-Brière, Christine, Moreau, Sandra, Carrère, Sébastien, Blein, Thomas, Jardinaud, Marie-Françoise, Latrasse, David, Zouine, Mohamed, Zahm, Margot, Kreplak, Jonathan, Mayjonade, Baptiste, Satgé, Carine, Perez, Magali, Cauet, Stéphane, Marande, William, Chantry-Darmon, Céline, Lopez-Roques, Céline, Bouchez, Olivier, Bérard, Aurélie, Debellé, Frédéric, Muños, Stéphane, Bendahmane, Abdelhafid, Bergès, Hélène, Niebel, Andreas, Buitink, Julia, Frugier, Florian, Benhamed, Moussa, Crespi, Martin, Gouzy, Jérôme, and Gamas, Pascal

Abstract

Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatulaA17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatulagenome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatulagenome.

Published
2018
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