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406 results on '"Rombauts, Stephane"'

1. Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Author

Ma, Xiao, Vanneste, Steffen, Chang, Jiyang, Ambrosino, Luca, Barry, Kerrie, Bayer, Till, Bobrov, Alexander A, Boston, LoriBeth, Campbell, Justin E, Chen, Hengchi, Chiusano, Maria Luisa, Dattolo, Emanuela, Grimwood, Jane, He, Guifen, Jenkins, Jerry, Khachaturyan, Marina, Marín-Guirao, Lázaro, Mesterházy, Attila, Muhd, Danish-Daniel, Pazzaglia, Jessica, Plott, Chris, Rajasekar, Shanmugam, Rombauts, Stephane, Ruocco, Miriam, Scott, Alison, Tan, Min Pau, Van de Velde, Jozefien, Vanholme, Bartel, Webber, Jenell, Wong, Li Lian, Yan, Mi, Sung, Yeong Yik, Novikova, Polina, Schmutz, Jeremy, Reusch, Thorsten BH, Procaccini, Gabriele, Olsen, Jeanine L, and Van de Peer, Yves

Subjects
Genetics, Life Below Water, Climate Action, Alismatales, Zosteraceae, Ecosystem, Plant Biology, Crop and Pasture Production, Ecology, Plant biology
Abstract

We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.

Published
2024

2. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Published
2024
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3. ‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)

Author

Maestri, Simone, Gambino, Giorgio, Lopatriello, Giulia, Minio, Andrea, Perrone, Irene, Cosentino, Emanuela, Giovannone, Barbara, Marcolungo, Luca, Alfano, Massimiliano, Rombauts, Stephane, Cantu, Dario, Rossato, Marzia, Delledonne, Massimo, and Calderón, Luciano

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Genomic Structural Variation, Italy, Vitis, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

Background'Nebbiolo' is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection.ResultsWe employed a multiple platform approach to produce long-range genomic data for two different 'Nebbiolo' clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar 'Nebbiolo' (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines' reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between 'Nebbiolo' and 'Cabernet Sauvignon' assemblies and iii) between clones CVT 71 and CVT 185, representing different 'Nebbiolo' biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes.ConclusionsOur results suggest that SVs accumulation rate and their functional implications in 'Nebbiolo' genome are highly-dependent on the organizational level under study. SVs are abundant when comparing 'Nebbiolo' to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.

Published
2022

5. The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments

Author

De Vos, Stephanie, Rombauts, Stephane, Coussement, Louis, Dermauw, Wannes, Vuylsteke, Marnik, Sorgeloos, Patrick, Clegg, James S, Nambu, Ziro, Van Nieuwerburgh, Filip, Norouzitallab, Parisa, Van Leeuwen, Thomas, De Meyer, Tim, Van Stappen, Gilbert, Van de Peer, Yves, and Bossier, Peter

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Generic health relevance, Animals, Artemia, Extreme Environments, Extremophiles, Heat-Shock Proteins, Salinity, Arthropod, Genome, Transcriptome, Assembly, Annotation, Extremophile, Anoxia, Brine shrimp, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundBrine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors.Results and discussionHere, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions.ConclusionsA relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.

Published
2021

7. The genome‐wide response of Dermatophagoides pteronyssinus to cystatin A, a peptidase inhibitor from human skin, sheds light on its digestive physiology and allergenicity.

Author

Vidal‐Quist, José Cristian, Ortego, Félix, Rombauts, Stephane, and Hernández‐Crespo, Pedro

Subjects
HOUSE dust mites, HORIZONTAL gene transfer, ANGIOTENSIN converting enzyme, DIGESTIVE enzymes, DERMATOPHAGOIDES pteronyssinus, PEPTIDASE
Abstract

The digestive physiology of house dust mites (HDMs) is particularly relevant for their allergenicity since many of their allergens participate in digestion and are excreted into faecal pellets, a main source of exposure for allergic subjects. To gain insight into the mite dietary digestion, the genome of the HDM Dermatophagoides pteronyssinus was screened for genes encoding peptidases (n = 320), glycosylases (n = 77), lipases and esterases (n = 320), peptidase inhibitors (n = 65) and allergen‐related proteins (n = 52). Basal gene expression and transcriptional responses of mites to dietary cystatin A, a cysteine endopeptidase inhibitor with previously shown antinutritional effect on mites, were analysed by RNAseq. The ingestion of cystatin A resulted in significant regulation of different cysteine endopeptidase and glycosylase genes. One Der p 1‐like and two cathepsin B‐like cysteine endopeptidase genes of high basal expression were induced, which suggests their prominent role in proteolytic digestion together with major allergen Der p 1. A number of genes putatively participating in the interaction of mites with their microbiota and acquired by horizontal gene transfer were repressed, including genes encoding the peptidase Der p 38, two 1,3‐beta‐glucanases, a lysozyme and a GH19 chitinase. Finally, the disruption of mite digestion resulted in the regulation of up to 17 allergen and isoallergen genes. Altogether, our results shed light on the putative role of specific genes in digestion and illustrate the connection between the digestive physiology of HDM and allergy. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing.

Author

Rijk, Peter De, Watzeels, Tijs, Küçükali, Fahri, Dongen, Jasper Van, Faura, Júlia, Willems, Patrick, Deyn, Lara De, Duchateau, Lena, Grones, Carolin, Eekhout, Thomas, Pooter, Tim De, Joris, Geert, Rombauts, Stephane, Rybel, Bert De, Rademakers, Rosa, Breusegem, Frank Van, Strazisar, Mojca, Sleegers, Kristel, and Coster, Wouter De

Subjects
STATISTICAL correlation, QUALITY control, DEMULTIPLEXING, DATA analysis, CELL lines
Abstract

Motivation Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes. Results We introduce scywalker , an innovative and scalable package developed to comprehensively analyze long-read sequencing data of full-length single-cell or single-nuclei cDNA. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package. Scywalker streamlines the entire analysis process, from sequenced fragments in FASTQ format to demultiplexed pseudobulk isoform counts, into a single command suitable for execution on either server or cluster. Scywalker includes data quality control, cell type identification, and an interactive report. Assessment of datasets from the human brain, Arabidopsis leaves, and previously benchmarked data from mixed cell lines demonstrate excellent correlation with short-read analyses at both the cell-barcoding and gene quantification levels. At the isoform level, we show that scywalker facilitates the direct identification of cell-type-specific expression of novel isoforms. Availability and implementation Scywalker is available on github.com/derijkp/scywalker under the GNU General Public License (GPL) and at https://zenodo.org/records/13359438/files/scywalker-0.108.0-Linux-x86_64.tar.gz. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Author

Farhat, Sarah, Le, Phuong, Kayal, Ehsan, Noel, Benjamin, Bigeard, Estelle, Corre, Erwan, Maumus, Florian, Florent, Isabelle, Alberti, Adriana, Aury, Jean-Marc, Barbeyron, Tristan, Cai, Ruibo, Da Silva, Corinne, Istace, Benjamin, Labadie, Karine, Marie, Dominique, Mercier, Jonathan, Rukwavu, Tsinda, Szymczak, Jeremy, Tonon, Thierry, Alves-de-Souza, Catharina, Rouzé, Pierre, Van de Peer, Yves, Wincker, Patrick, Rombauts, Stephane, Porcel, Betina M., and Guillou, Laure

Published
2021
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13. The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Author

Raharimalala, Nathalie, Rombauts, Stephane, McCarthy, Andrew, Garavito, Andréa, Orozco-Arias, Simon, Bellanger, Laurence, Morales-Correa, Alexa Yadira, Froger, Solène, Michaux, Stéphane, Berry, Victoria, Metairon, Sylviane, Fournier, Coralie, Lepelley, Maud, Mueller, Lukas, Couturon, Emmanuel, Hamon, Perla, Rakotomalala, Jean-Jacques, Descombes, Patrick, Guyot, Romain, and Crouzillat, Dominique

Published
2021
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14. Author Correction to: Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Author

Farhat, Sarah, Le, Phuong, Kayal, Ehsan, Noel, Benjamin, Bigeard, Estelle, Corre, Erwan, Maumus, Florian, Florent, Isabelle, Alberti, Adriana, Aury, Jean-Marc, Barbeyron, Tristan, Cai, Ruibo, Da Silva, Corinne, Istace, Benjamin, Labadie, Karine, Marie, Dominique, Mercier, Jonathan, Rukwavu, Tsinda, Szymczak, Jeremy, Tonon, Thierry, Alves-de-Souza, Catharina, Rouzé, Pierre, Van de Peer, Yves, Wincker, Patrick, Rombauts, Stephane, Porcel, Betina M., and Guillou, Laure

Published
2021
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15. The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization

Author

Nishiyama, Tomoaki, Sakayama, Hidetoshi, de Vries, Jan, Buschmann, Henrik, Saint-Marcoux, Denis, Ullrich, Kristian K., Haas, Fabian B., Vanderstraeten, Lisa, Becker, Dirk, Lang, Daniel, Vosolsobě, Stanislav, Rombauts, Stephane, Wilhelmsson, Per K.I., Janitza, Philipp, Kern, Ramona, Heyl, Alexander, Rümpler, Florian, Villalobos, Luz Irina A. Calderón, Clay, John M., Skokan, Roman, Toyoda, Atsushi, Suzuki, Yutaka, Kagoshima, Hiroshi, Schijlen, Elio, Tajeshwar, Navindra, Catarino, Bruno, Hetherington, Alexander J., Saltykova, Assia, Bonnot, Clemence, Breuninger, Holger, Symeonidi, Aikaterini, Radhakrishnan, Guru V., Van Nieuwerburgh, Filip, Deforce, Dieter, Chang, Caren, Karol, Kenneth G., Hedrich, Rainer, Ulvskov, Peter, Glöckner, Gernot, Delwiche, Charles F., Petrášek, Jan, Van de Peer, Yves, Friml, Jiri, Beilby, Mary, Dolan, Liam, Kohara, Yuji, Sugano, Sumio, Fujiyama, Asao, Delaux, Pierre-Marc, Quint, Marcel, Theißen, Günter, Hagemann, Martin, Harholt, Jesper, Dunand, Christophe, Zachgo, Sabine, Langdale, Jane, Maumus, Florian, Van Der Straeten, Dominique, Gould, Sven B., and Rensing, Stefan A.

Published
2018
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19. A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locusCMD2in cassava

Author

Luc, Cornet, primary, Zaidi, Syed Shan-e-Ali, additional, Li, Jia, additional, Yvan, Ngapout, additional, Shakir, Sara, additional, Loic, Meunier, additional, Callot, Caroline, additional, Marande, William, additional, Marc, Hanikenne, additional, Rombauts, Stephane, additional, Van de Peer, Yves, additional, and Vanderschuren, Hervé, additional

Published
2023
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20. The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, primary, Rambani, Aditi, additional, Yu, Zhe, additional, Guyot, Romain, additional, Strickler, Susan, additional, Lepelley, Maud, additional, Wang, Cui, additional, Rajaraman, Sitaram, additional, Rastas, Pasi, additional, Zheng, Chunfang, additional, Muñoz, Daniella Santos, additional, Meidanis, João, additional, Paschoal, Alexandre Rossi, additional, Bawin, Yves, additional, Krabbenhoft, Trevor, additional, Wang, Zhen Qin, additional, Fleck, Steven, additional, Aussel, Rudy, additional, Bellanger, Laurence, additional, Charpagne, Aline, additional, Fournier, Coralie, additional, Kassam, Mohamed, additional, Lefebvre, Gregory, additional, Métairon, Sylviane, additional, Moine, Déborah, additional, Rigoreau, Michel, additional, Stolte, Jens, additional, Hamon, Perla, additional, Couturon, Emmanuel, additional, Tranchant-Dubreuil, Christine, additional, Mukherjee, Minakshi, additional, Lan, Tianying, additional, Engelhardt, Jan, additional, Stadler, Peter, additional, De Lemos, Samara Mireza Correia, additional, Suzuki, Suzana Ivamoto, additional, Sumirat, Ucu, additional, Man, Wai Ching, additional, Dauchot, Nicolas, additional, Orozco-Arias, Simon, additional, Garavito, Andrea, additional, Kiwuka, Catherine, additional, Musoli, Pascal, additional, Nalukenge, Anne, additional, Guichoux, Erwan, additional, Reinout, Havinga, additional, Smit, Martin, additional, Carretero-Paulet, Lorenzo, additional, Filho, Oliveiro Guerreiro, additional, Braghini, Masako Toma, additional, Padilha, Lilian, additional, Sera, Gustavo Hiroshi, additional, Ruttink, Tom, additional, Henry, Robert, additional, Marraccini, Pierre, additional, Van de Peer, Yves, additional, Andrade, Alan, additional, Domingues, Douglas, additional, Giuliano, Giovanni, additional, Mueller, Lukas, additional, Pereira, Luiz Filipe, additional, Plaisance, Stephane, additional, Poncet, Valerie, additional, Rombauts, Stephane, additional, Sankoff, David, additional, Albert, Victor A., additional, Crouzillat, Dominique, additional, de Kochko, Alexandre, additional, and Descombes, Patrick, additional

Published
2023
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22. Transcriptome Analysis during Cell Division in Plants

Author

Breyne, Peter, Dreesen, Rozemarijn, Vandepoele, Klaas, De Veylder, Lieven, Van Breusegem, Frank, Callewaert, Lindy, Rombauts, Stephane, Raes, Jeroen, Cannoot, Bernard, Engler, Gilbert, Inzé, Dirk, and Zabeau, Marc

Published
2002

24. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

Author

Rensing, Stefan A., Lang, Daniel, Zimmer, Andreas D., Terry, Astrid, Salamov, Asaf, Shapiro, Harris, Nishiyama, Tomaoki, Perroud, Pierre-Francois, Lindquist, Erika A., Kamisugi, Yasuko, Tanahashi, Takako, Sakakibara, Keiko, Fujita, Tomomichi, Oishi, Kazuko, Shin, Tadasu, Kuroki, Yoko, Toyoda, Atsushi, Suzuki, Yutaka, Hashimoto, Shin-ichi, Yamaguchi, Kazuo, Sugano, Sumio, Kohara, Yuji, Fujiyama, Asao, Anterola, Aldwin, Aoki, Setsuyuki, Ashton, Neil, Barbazuk, W. Brad, Barker, Elizabeth, Bennetzen, Jeffrey L., Blankenship, Robert, Cho, Sung Hyun, Dutcher, Susan K., Estelle, Mark, Fawcett, Jeffrey A., Gundlach, Heidrum, Hanada, Kousuke, Melkozernov, Alexander, Murata, Takashi, Nelson, David R., Pils, Birgit, Prigge, Michael, Reiss, Bernd, Renner, Tanya, Rombauts, Stephane, Rushton, Paul J., Sanderfoot, Anton, Schween, Gabriele, Shiu, Shin-Han, Stueber, Kurt, Theodoulou, Frederica L., Tu, Hank, Peer, Yves Van de, Verrier, Paul J., Waters, Elizabeth, Wood, Andrew, Yang, Lixing, Cove, David, Cuming, Andrew C., Hasebe, Mitsayasu, Lucas, Susan, Mishler, Brent D., Reski, Ralf, Grigoriev, Igor V., Quatrano, Rakph S., and Boore, Jeffrey L.

Abstract

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

Published
2007

25. Annotation of the Tomato Genome

Author

Rombauts, Stephane, Kole, Chittaranjan, Series editor, Causse, Mathilde, editor, Giovannoni, Jim, editor, Bouzayen, Mondher, editor, and Zouine, Mohamed, editor

Published
2016
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26. Identification and characterization of CYP71 subclade cytochrome P450 enzymes involved in the biosynthesis of bitterness compounds in Cichorium intybus

Author

De Bruyn, Charlotte, primary, Ruttink, Tom, additional, Lacchini, Elia, additional, Rombauts, Stephane, additional, Haegeman, Annelies, additional, De Keyser, Ellen, additional, Van Poucke, Christof, additional, Desmet, Sandrien, additional, Jacobs, Thomas B., additional, Eeckhaut, Tom, additional, Goossens, Alain, additional, and Van Laere, Katrijn, additional

Published
2023
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27. Industrial chicory genome gives insights into the molecular timetable of anther development and male sterility

Author

Waegneer, Evelien, primary, Rombauts, Stephane, additional, Baert, Joost, additional, Dauchot, Nicolas, additional, De Keyser, Annick, additional, Eeckhaut, Tom, additional, Haegeman, Annelies, additional, Liu, Chang, additional, Maudoux, Olivier, additional, Notté, Christine, additional, Staelens, Ariane, additional, Van der Veken, Jeroen, additional, Van Laere, Katrijn, additional, and Ruttink, Tom, additional

Published
2023
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28. The genome and population genomics of allopolyploid Coffea arabicareveal the diversification history of modern coffee cultivars

Author

Salojärvi, Jarkko, Rambani, Aditi, Yu, Zhe, Guyot, Romain, Strickler, Susan, Lepelley, Maud, Wang, Cui, Rajaraman, Sitaram, Rastas, Pasi, Zheng, Chunfang, Muñoz, Daniella Santos, Meidanis, João, Paschoal, Alexandre Rossi, Bawin, Yves, Krabbenhoft, Trevor J., Wang, Zhen Qin, Fleck, Steven J., Aussel, Rudy, Bellanger, Laurence, Charpagne, Aline, Fournier, Coralie, Kassam, Mohamed, Lefebvre, Gregory, Métairon, Sylviane, Moine, Déborah, Rigoreau, Michel, Stolte, Jens, Hamon, Perla, Couturon, Emmanuel, Tranchant-Dubreuil, Christine, Mukherjee, Minakshi, Lan, Tianying, Engelhardt, Jan, Stadler, Peter, Correia De Lemos, Samara Mireza, Suzuki, Suzana Ivamoto, Sumirat, Ucu, Wai, Ching Man, Dauchot, Nicolas, Orozco-Arias, Simon, Garavito, Andrea, Kiwuka, Catherine, Musoli, Pascal, Nalukenge, Anne, Guichoux, Erwan, Reinout, Havinga, Smit, Martin, Carretero-Paulet, Lorenzo, Filho, Oliveiro Guerreiro, Braghini, Masako Toma, Padilha, Lilian, Sera, Gustavo Hiroshi, Ruttink, Tom, Henry, Robert, Marraccini, Pierre, Van de Peer, Yves, Andrade, Alan, Domingues, Douglas, Giuliano, Giovanni, Mueller, Lukas, Pereira, Luiz Filipe, Plaisance, Stephane, Poncet, Valerie, Rombauts, Stephane, Sankoff, David, Albert, Victor A., Crouzillat, Dominique, de Kochko, Alexandre, and Descombes, Patrick

Abstract

Coffea arabica, an allotetraploid hybrid of Coffea eugenioidesand Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabicaaccession and modern representatives of its diploid progenitors, C. eugenioidesand C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

Published
2024
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31. Seagrass genomes reveal a hexaploid ancestry facilitating adaptation to the marine environment

Author

Ma, Xiao, primary, Vanneste, Steffen, additional, Chang, Jiyang, additional, Ambrosino, Luca, additional, Barry, Kerrie, additional, Bayer, Till, additional, Bobrov, Alexander A., additional, Boston, LoriBeth, additional, Campbell, Justin E, additional, Chen, Hengchi, additional, Chiusano, Maria Luisa, additional, Dattolo, Emanuela, additional, Grimwood, Jane, additional, He, Guifen, additional, Jenkins, Jerry, additional, Khachaturyan, Marina, additional, Marín-Guirao, Lázaro, additional, Mesterházy, Attila, additional, Muhd, Danish-Daniel, additional, Pazzaglia, Jessica, additional, Plott, Chris, additional, Rajasekar, Shanmugam, additional, Rombauts, Stephane, additional, Ruocco, Miriam, additional, Scott, Alison, additional, Tan, Min Pau, additional, Van de Velde, Jozefien, additional, Vanholme, Bartel, additional, Webber, Jenell, additional, Wong, Li Lian, additional, Yan, Mi, additional, Sung, Yeong Yik, additional, Novikova, Polina, additional, Schmutz, Jeremy, additional, Reusch, Thorsten, additional, Procaccini, Gabriele, additional, Olsen, Jeanine, additional, and Van de Peer, Yves, additional

Published
2023
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38. AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling

Author

Rehrauer, Hubert, Aquino, Catharine, Gruissem, Wilhelm, Henz, Stefan R., Hilson, Pierre, Laubinger, Sascha, Naouar, Naira, Patrignani, Andrea, Rombauts, Stephane, Shu, Huan, Van de Peer, Yves, Vuylsteke, Marnik, Weigel, Detlef, Zeller, Georg, and Hennig, Lars

Published
2010

40. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Author

Worden, Alexandra Z., Lee, Jae-Hyeok, Mock, Thomas, Rouzé, Pierre, Simmons, Melinda P., Aerts, Andrea L., Allen, Andrew E., Cuvelier, Marie L., Derelle, Evelyne, Everett, Meredith V., Foulon, Elodie, Grimwood, Jane, Gundlach, Heidrun, Henrissat, Bernard, Napoli, Carolyn, McDonald, Sarah M., Parker, Micaela S., Rombauts, Stephane, Salamov, Aasf, Von Dassow, Peter, Badger, Jonathan H., Coutinho, Pedro M., Demir, Elif, Dubchak, Inna, Gentemann, Chelle, Eikrem, Wenche, Gready, Jill E., John, Uwe, Lanier, William, Lindquist, Erika A., Lucas, Susan, Mayer, Klaus F. X., Moreau, Herve, Not, Fabrice, Otillar, Robert, Panaud, Olivier, Pangilinan, Jasmyn, Paulsen, Ian, Piegu, Benoit, Poliakov, Aaron, Robbens, Steven, Schmutz, Jeremy, Toulza, Eve, Wyss, Tania, Zelensky, Alexander, Zhou, Kemin, Armbrust, E. Virginia, Bhattacharya, Debashish, Goodenough, Ursula W., Van de Peer, Yves, and Grigoriev, Igor V.

Published
2009
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42. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Author

Rensing, Stefan A., Lang, Daniel, Zimmer, Andreas D., Terry, Astrid, Salamov, Asaf, Shapiro, Harris, Nishiyama, Tomoaki, Perroud, Pierre-François, Lindquist, Erika A., Kamisugi, Yasuko, Tanahashi, Takako, Sakakibara, Keiko, Fujita, Tomomichi, Oishi, Kazuko, Shin-I, Tadasu, Kuroki, Yoko, Toyoda, Atsushi, Suzuki, Yutaka, Hashimoto, Shin-ichi, Yamaguchi, Kazuo, Sugano, Sumio, Kohara, Yuji, Fujiyama, Asao, Anterola, Aldwin, Aoki, Setsuyuki, Ashton, Neil, Barbazuk, W. Brad, Barker, Elizabeth, Bennetzen, Jeffrey L., Blankenship, Robert, Cho, Sung Hyun, Dutcher, Susan K., Estelle, Mark, Fawcett, Jeffrey A., Gundlach, Heidrun, Hanada, Kousuke, Heyl, Alexander, Hicks, Karen A., Hughes, Jon, Lohr, Martin, Mayer, Klaus, Melkozernov, Alexander, Murata, Takashi, Nelson, David R., Pils, Birgit, Prigge, Michael, Reiss, Bernd, Renner, Tanya, Rombauts, Stephane, Rushton, Paul J., Sanderfoot, Anton, Schween, Gabriele, Shiu, Shin-Han, Stueber, Kurt, Theodoulou, Frederica L., Tu, Hank, Van de Peer, Yves, Verrier, Paul J., Waters, Elizabeth, Wood, Andrew, Yang, Lixing, Cove, David, Cuming, Andrew C., Hasebe, Mitsuyasu, Lucas, Susan, Mishler, Brent D., Reski, Ralf, Grigoriev, Igor V., Quatrano, Ralph S., and Boore, Jeffrey L.

Published
2008
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46. The Tiny Eukaryote Ostreococcus Provides Genomic Insights into the Paradox of Plankton Speciation

Author

Palenik, Brian, Grimwood, Jane, Aerts, Andrea, Rouzé, Pierre, Salamov, Asaf, Putnam, Nicholas, Dupont, Chris, Jorgensen, Richard, Derelle, Evelyne, Rombauts, Stephane, Zhou, Kemin, Otillar, Robert, Merchant, Sabeeha S., Podell, Sheila, Gaasterland, Terry, Napoli, Carolyn, Gendler, Karla, Manuell, Andrea, Tai, Vera, Vallon, Olivier, Piganeau, Gwenael, Jancek, Séverine, Heijde, Marc, Jabbari, Kamel, Bowler, Chris, Lohr, Martin, Robbens, Steven, Werner, Gregory, Dubchak, Inna, Pazour, Gregory J., Ren, Qinghu, Paulsen, Ian, Delwiche, Chuck, Schmutz, Jeremy, Rokhsar, Daniel, Van de Peer, Yves, Moreau, Hervé, and Grigoriev, Igor V.

Published
2007
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47. The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales

Author

Xu, Zhichao, primary, Li, Zhen, additional, Ren, Fengming, additional, Gao, Ranran, additional, Wang, Zhe, additional, Zhang, Jinlan, additional, Zhao, Tao, additional, Ma, Xiao, additional, Pu, Xiangdong, additional, Xin, Tianyi, additional, Rombauts, Stephane, additional, Sun, Wei, additional, Van de Peer, Yves, additional, Chen, Shilin, additional, and Song, Jingyuan, additional

Published
2022
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48. Additional file 1 of ���Nebbiolo��� genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)

Author

Maestri, Simone, Gambino, Giorgio, Lopatriello, Giulia, Minio, Andrea, Perrone, Irene, Cosentino, Emanuela, Giovannone, Barbara, Marcolungo, Luca, Alfano, Massimiliano, Rombauts, Stephane, Cantu, Dario, Rossato, Marzia, Delledonne, Massimo, and Calder��n, Luciano

Subjects
Data_FILES
Abstract

Additional file 1.

Published
2022
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49. Legume Genome Evolution Viewed through the Medicago truncatula and Lotus japonicus Genomes

Author

Cannon, Steven B., Sterck, Lieven, Rombauts, Stephane, Sato, Shusei, Cheung, Foo, Gouzy, Jérôme, Wang, Xiaohong, Mudge, Joann, Vasdewani, Jayprakash, Scheix, Thomas, Spannagl, Manuel, Monaghan, Erin, Nicholson, Christine, Humphray, Sean J., Schoof, Heiko, Mayer, Klaus F. X., Rogers, Jane, Quétier, Francis, Oldroyd, Giles E., Debellé, Frédéric, Cook, Douglas R., Retzel, Ernest F., Roe, Bruce A., Town, Christopher D., Tabata, Satoshi, van de Peer, Yves, and Young, Nevin D.

Published
2006
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50. Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus tauri Unveils Many Unique Features

Author

Derelle, Evelyne, Ferraz, Conchita, Rombauts, Stephane, Rouzé, Pierre, Worden, Alexandra Z., Robbens, Steven, Partensky, Frédéric, Degroeve, Sven, Echeynié, Sophie, Cooke, Richard, Saeys, Yvan, Wuyts, Jan, Jabbari, Kamel, Bowler, Chris, Panaud, Olivier, Piégu, Benoît, Ball, Steven G., Ral, Jean-Philippe, Bouget, François-Yves, Piganeau, Gwenael, De Baets, Bernard, Picard, André, Delseny, Michel, Demaille, Jacques, Van de Peer, Yves, and Moreau, Hervé

Published
2006
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