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11 results on '"Smahane, Chalabi"'

1. MYLK*FLNB and DOCK1*LAMA2 gene–gene interactions associated with rheumatoid arthritis in the focal adhesion pathway

Author

Maëva Veyssiere, Maria del Pilar Rodriguez Ordonez, Smahane Chalabi, Laetitia Michou, François Cornelis, Anne Boland, Robert Olaso, Jean-François Deleuze, Elisabeth Petit-Teixeira, and Valérie Chaudru

Subjects
rare variants, pathway enrichment analysis, gene–gene interaction, rheumatoid arthritis, familial sample, Genetics, QH426-470
Abstract

Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease caused by a combination of genetic and environmental factors. Rare variants with low predicted effects in genes participating in the same biological function might be involved in developing complex diseases such as RA. From whole-exome sequencing (WES) data, we identified genes containing rare non-neutral variants with complete penetrance and no phenocopy in at least one of nine French multiplex families. Further enrichment analysis highlighted focal adhesion as the most significant pathway. We then tested if interactions between the genes participating in this function would increase or decrease the risk of developing RA disease. The model-based multifactor dimensionality reduction (MB-MDR) approach was used to detect epistasis in a discovery sample (19 RA cases and 11 healthy individuals from 9 families and 98 unrelated CEU controls from the International Genome Sample Resource). We identified 9 significant interactions involving 11 genes (MYLK, FLNB, DOCK1, LAMA2, RELN, PIP5K1C, TNC, PRKCA, VEGFB, ITGB5, and FLT1). One interaction (MYLK*FLNB) increasing RA risk and one interaction decreasing RA risk (DOCK1*LAMA2) were confirmed in a replication sample (200 unrelated RA cases and 91 GBR unrelated controls). Functional and genomic data in RA samples or relevant cell types argue the key role of these genes in RA.

Published
2024
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2. Region-specific expression of young small-scale duplications in the human central nervous system

Author

Solène Brohard-Julien, Vincent Frouin, Vincent Meyer, Smahane Chalabi, Jean-François Deleuze, Edith Le Floch, and Christophe Battail

Subjects
Paralog, Small scale duplication, Brain region-specific expression, Human central nervous system, Gene co-expression network, Ecology, QH540-549.5, Evolution, QH359-425
Abstract

Abstract Background The duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional specialization of the adult human central nervous system has not yet been well described. Results Our work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue Expression (GTEx) consortium. Interestingly, we found that paralogs were associated with region-specific expression in CNS, suggesting their involvement in the differentiation of these territories. Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs. Indeed, we found that small scale duplicated genes (SSDs) and in particular ySSDs (SSDs younger than the 2 rounds of whole genome duplications) were more CNS region-specific than other paralogs. Next, by studying the two paralogs of ySSD pairs, we observed that when they were region-specific, they tend to be specific to the same region more often than for other paralogs, showing the high co-expression of ySSD pairs. The extension of this analysis to families of paralogs showed that the families with co-expressed gene members (i.e. homogeneous families) were enriched in ySSDs. Furthermore, these homogeneous families tended to be region-specific families, where the majority of their gene members were specifically expressed in the same region. Conclusions Overall, our study suggests the involvement of ySSDs in the differentiation of human central nervous system territories. Therefore, we show the relevance of exploring region-specific expression of paralogs at the intra-organ level.

Published
2021
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3. Co-Transplantation of Barcoded Lymphoid-Primed Multipotent (LMPP) and Common Lymphocyte (CLP) Progenitors Reveals a Major Contribution of LMPP to the Lymphoid Lineage

Author

Victoria Michaels, Smahane Chalabi, Agnes Legrand, Julie Renard, Emmanuel Tejerina, Marina Daouya, Sylvie Fabrega, Jérôme Megret, Robert Olaso, Anne Boland, Jean-François Deleuze, Christophe Battail, Diana Tronik-Le Roux, Sophie Ezine, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Service de Recherche en Hémato-Immunologie (SRHI - UMR_E 05), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Immunologie humaine, physiopathologie & immunothérapie (HIPI (UMR_S_976 / U976)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Plateforme Vecteurs Viraux et Transfert de Gènes [SFR Necker] (VVTG), Structure Fédérative de Recherche Necker (SFR Necker - UMS 3633 / US24), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire Biosciences et bioingénierie pour la santé (BGE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)

Subjects
[SDV]Life Sciences [q-bio], Organic Chemistry, high-throughput DNA-sequencing, bone marrow graft, General Medicine, differentiation, cytometry, Catalysis, Computer Science Applications, Inorganic Chemistry, lymphoid progenitors, thymus, lentivirus, genome barcoding, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, cell labeling
Abstract

International audience; T cells have the potential to maintain immunological memory and self-tolerance by recognizing antigens from pathogens or tumors. In pathological situations, failure to generate de novo T cells causes immunodeficiency resulting in acute infections and complications. Hematopoietic stem cells (HSC) transplantation constitutes a valuable option to restore proper immune function. However, delayed T cell reconstitution is observed compared to other lineages. To overcome this difficulty, we developed a new approach to identify populations with efficient lymphoid reconstitution properties. To this end, we use a DNA barcoding strategy based on the insertion into a cell chromosome of a lentivirus (LV) carrying a non-coding DNA fragment named barcode (BC). These will segregate through cell divisions and be present in cells' progeny. The remarkable characteristic of the method is that different cell types can be tracked simultaneously in the same mouse. Thus, we in vivo barcoded LMPP and CLP progenitors to test their ability to reconstitute the lymphoid lineage. Barcoded progenitors were co-grafted in immuno-compromised mice and their fate analyzed by evaluating the BC composition in transplanted mice. The results highlight the predominant role of LMPP progenitors for lymphoid generation and reveal valuable novel insights to be reconsidered in clinical transplantation assays.

Published
2023
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4. Temporal Gene Expression Profiles Reflect the Dynamics of Lymphoid Differentiation

Author

Smahane Chalabi, Agnes Legrand, Victoria Michaels, Marie-Ange Palomares, Robert Olaso, Anne Boland, Jean-François Deleuze, Sophie Ezine, Christophe Battail, and Diana Tronik-Le Roux

Subjects
Genetic Markers, Male, QH301-705.5, Catalysis, Inorganic Chemistry, Mice, lymphopoiesis, hematopoietic differentiation, RNAseq, long non-coding RNA, transcriptome, gene networks, Animals, Gene Regulatory Networks, Physical and Theoretical Chemistry, Biology (General), Molecular Biology, QD1-999, Spectroscopy, Cells, Cultured, Sequence Analysis, RNA, Gene Expression Profiling, Organic Chemistry, High-Throughput Nucleotide Sequencing, General Medicine, Lymphoid Progenitor Cells, Computer Science Applications, Hematopoiesis, Chemistry, Gene Expression Regulation, Female, RNA, Long Noncoding
Abstract

Understanding the emergence of lymphoid committed cells from multipotent progenitors (MPP) is a great challenge in hematopoiesis. To gain deeper insight into the dynamic expression changes associated with these transitions, we report the quantitative transcriptome of two MPP subsets and the common lymphoid progenitor (CLP). While the transcriptome is rather stable between MPP2 and MPP3, expression changes increase with differentiation. Among those, we found that pioneer lymphoid genes such as Rag1, Mpeg1, and Dntt are expressed continuously from MPP2. Others, such as CD93, are CLP specific, suggesting their potential use as new markers to improve purification of lymphoid populations. Notably, a six-transcription factor network orchestrates the lymphoid differentiation program. Additionally, we pinpointed 24 long intergenic-non-coding RNA (lincRNA) differentially expressed through commitment and further identified seven novel forms. Collectively, our approach provides a comprehensive landscape of coding and non-coding transcriptomes expressed during lymphoid commitment.

Published
2022

6. Region-specific expression of young small-scale duplications in the human central nervous system

Author

Vincent Meyer, Christophe Battail, Solène Brohard-Julien, Jean-François Deleuze, Vincent Frouin, Edith Le Floch, Smahane Chalabi, Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Fondation Jean Dausset - Centre d’Etudes du Polymorphisme Humain [Paris] (CEPH), Unité Analyse et Traitement de l'Information (UNATI), Service NEUROSPIN (NEUROSPIN), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA))

Subjects
Central Nervous System, Scale (anatomy), Gene co-expression network, Evolution, [SDV]Life Sciences [q-bio], Central nervous system, Biology, Genome, Transcriptome, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Genes, Duplicate, Gene Duplication, Gene duplication, Gene expression, medicine, QH359-425, Humans, Brain region-specific expression, Gene, QH540-549.5, 030304 developmental biology, Small scale duplication, 0303 health sciences, Ecology, Human central nervous system, Paralog, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], medicine.anatomical_structure, Expression (architecture), [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Evolutionary biology, 030217 neurology & neurosurgery, Research Article
Abstract

BackgroundThe duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional specialization of the adult human central nervous system has not yet been well described.ResultsOur work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue Expression (GTEx) consortium. Interestingly, we found that paralogs were associated with region-specific expression in CNS, suggesting their involvement in the differentiation of these territories. Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs. Indeed, we found that small scale duplicated genes (SSDs) and in particular ySSDs (SSDs younger than the 2 rounds of whole genome duplications) were more CNS region-specific than other paralogs. Next, by studying the two paralogs of ySSD pairs, we observed that when they were region-specific, they tend to be specific to the same region more often than for other paralogs, showing the high co-expression of ySSD pairs. Extension of this analysis to families of paralogs showed that the families with co-expressed gene members (i.e. homogeneous families) were enriched in ySSDs. Furthermore, these homogeneous families tended to be region-specific families, where the majority of their gene members were specifically expressed in the same region.ConclusionsOverall, our study suggests the major involvement of ySSDs in the differentiation of human central nervous system territories. Therefore, we show the relevance of exploring region-specific expression of paralogs at the intra-organ level.

Published
2020
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7. Combining bottom-up and top-down systems biology methods to obtain an integrative, global RA-specific network

Author

Quentin, MIAGOUX, Dereck, De MEZQUITA, Vidisha, SING, Smahane, CHALABI, Elisabeth, PETIT-TEIXEIRA, and Anna, NIARAKIS

Subjects
Rheumatoid arthritis molecular map, Rheumatoid arthritis specific variants, Machine learning, Rheumatoid arthritis, Network inference, co-regulatory network
Abstract

Rheumatoid arthritis (RA) is a multifactorial autoimmune disease that causes chronic inflammation of the joints, with an aetiology still unclear. RA is a complex inflammatory disease that involves an interconnected array of genetic, environmental, and epigenetic factors. Recently, systems biology and network-based approaches have been proposed to study such complex diseases. Combining multiple data types allows us to discover new knowledge as integration can help compensate for missing or unreliable information. Moreover, if multiple sources of evidence point to the same outcome then it is less likely to obtain false positives. Among computational approaches, machine learning stands out as a promising field in bioinformatics, as it allows for integration of multi-omic biomedical datasets. In this work, we present our efforts to integrate different layers of biological data in the form of networks in order to obtain a global view of the disease. To do so, we make use of publicly available transcriptomic datasets (peripheral blood) relative to RA and a variety of bioinformatics analyses such as statistical analysis, differential expression analysis, and machine learning network inference (Nicolle et al., 2015) to infer an RA-specific TF co-regulatory network. The TF cooperativity network is subsequently enriched in signalling cascades and upstream regulators using the state of the art RA map based on the functional overlaps between the two networks (Singh et al., 2020). Lastly, a list of RA specific variants available in DisGeNET (Piñero et al., 2020) will be used as an overlap to highlight key genes associated with known disease mutations. We combine three different biological layers (gene expression, signalling cascades, mutations), obtained by bottom-up prior knowledge-based (DisGenNET, RA map) and top-down data-driven (CoRegNet) methods to build an integrative, disease-specific network. The goal behind this endeavor is to unravel mechanisms governing the regulation of key genes identified as mutation carriers in RA and also derive patient-specific models to gain more insights into the disease heterogeneity., Please open the .m4v file with VLC in order to get the sound of the video

Published
2020
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8. Erratum for the Report: 'Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome' by B. Chalhoub, F. Denoeud, S. Liu, I. A. P. Parkin, H. Tang, X. Wang, J. Chiquet, H. Belcram, C. Tong, B. Samans, M. Corréa, C. Da Silva, J. Just, C. Falentin, C. S. Koh, I. Le Clainche, M. Bernard, P. Bento, B. Noel, K. Labadie, A. Alberti, M. Charles, D. Arnaud, H. Guo, C. Daviaud, S. Alamery, K. Jabbari, M. Zhao, P. P. Edger, H. Chelaifa, D. Tack, G. Lassalle, I. Mestiri, N. Schnel, M.-C. Le Paslier, G. Fan, V. Renault, P. E. Bayer, A. A. Golicz, S. Manoli, T.-H. Lee, V. Ha Dinh Thi, S. Chalabi, Q. Hu, C. Fan, R. Tollenaere, Y. Lu, C. Battail, J. Shen, C. H. D. Sidebottom, X. Wang, A. Canaguier, A. Chauveau, A. Bérard, G. Deniot, M. Guan, Z. Liu, F. Sun, Y. P. Lim, E. Lyons, C. D. Town, I. Bancroft, X. Wang, J. Meng, J. Ma, J. C. Pires, G. J. King, D. Brunel, R. Delourme, M. Renard, J.-M. Aury, K. L. Adams, J. Batley, R. J. Snowdon, J. Tost, D. Edwards, Y. Zhou, W. Hua, A. G. Sharpe, A. H. Paterson, C. Guan, P. Wincker

Author

Aurélie Canaguier, Christophe Battail, Jean-Marc Aury, Christopher D. Town, Christian Daviaud, David C. Tack, Wei Hua, Christine Sidebottom, Shengyi Liu, Reece Tollenaere, Sahana Manoli, Graham J.W. King, Fengming Sun, J. Shen, Victor Renault, Philipp E. Bayer, I. Le Clainche, Jacqueline Batley, Ian Bancroft, Nicolas Schnel, M. C. Le Paslier, Dominique Arnaud, Karine Labadie, Agnieszka A. Golicz, Dominique Brunel, Smahane Chalabi, Hui Guo, Yongming Zhou, Eric Lyons, Pascal Bento, Gilles Lassalle, Chunyun Guan, Yong Pyo Lim, Imen Mestiri, J. C. Pires, Guangyi Fan, Houda Chelaifa, Mei Guan, Tae-Ho Lee, Harry Belcram, Qiong Hu, F. Denoeud, Aurélie Chauveau, Andrew G. Sharpe, Bernard Noël, Boulos Chalhoub, Chaobo Tong, Adriana Alberti, Patrick Wincker, Jinling Meng, Birgit Samans, Patrick P. Edger, C. Da Silva, Margot Correa, Jianxin Ma, Régine Delourme, Keith L. Adams, Meixia Zhao, Haibao Tang, David Edwards, Andrew H. Paterson, Cyril Falentin, Zhongsong Liu, Julien Chiquet, Y. Lu, Xinfa Wang, Jérémy Just, V. Ha Dinh Thi, Kamel Jabbari, Chuchuan Fan, G. Deniot, Rod J. Snowdon, Jörg Tost, Aurélie Bérard, Mathieu Charles, Michel Renard, Salman Alamery, Maria Bernard, Isobel A. P. Parkin, and Chu Shin Koh

Subjects
Multidisciplinary, Botany, Brassica, Biology, biology.organism_classification, Genome
Published
2014
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9. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Author

Boulos, Chalhoub, France, Denoeud, Shengyi, Liu, Isobel A P, Parkin, Haibao, Tang, Xiyin, Wang, Julien, Chiquet, Harry, Belcram, Chaobo, Tong, Birgit, Samans, Margot, Corréa, Corinne, Da Silva, Jérémy, Just, Cyril, Falentin, Chu Shin, Koh, Isabelle, Le Clainche, Maria, Bernard, Pascal, Bento, Benjamin, Noel, Karine, Labadie, Adriana, Alberti, Mathieu, Charles, Dominique, Arnaud, Hui, Guo, Christian, Daviaud, Salman, Alamery, Kamel, Jabbari, Meixia, Zhao, Patrick P, Edger, Houda, Chelaifa, David, Tack, Gilles, Lassalle, Imen, Mestiri, Nicolas, Schnel, Marie-Christine, Le Paslier, Guangyi, Fan, Victor, Renault, Philippe E, Bayer, Agnieszka A, Golicz, Sahana, Manoli, Tae-Ho, Lee, Vinh Ha Dinh, Thi, Smahane, Chalabi, Qiong, Hu, Chuchuan, Fan, Reece, Tollenaere, Yunhai, Lu, Christophe, Battail, Jinxiong, Shen, Christine H D, Sidebottom, Xinfa, Wang, Aurélie, Canaguier, Aurélie, Chauveau, Aurélie, Bérard, Gwenaëlle, Deniot, Mei, Guan, Zhongsong, Liu, Fengming, Sun, Yong Pyo, Lim, Eric, Lyons, Christopher D, Town, Ian, Bancroft, Xiaowu, Wang, Jinling, Meng, Jianxin, Ma, J Chris, Pires, Graham J, King, Dominique, Brunel, Régine, Delourme, Michel, Renard, Jean-Marc, Aury, Keith L, Adams, Jacqueline, Batley, Rod J, Snowdon, Jorg, Tost, David, Edwards, Yongming, Zhou, Wei, Hua, Andrew G, Sharpe, Andrew H, Paterson, Chunyun, Guan, and Patrick, Wincker

Subjects
Evolution, Molecular, Polyploidy, Brassica napus, Chromosome Duplication, Seeds, Genome, Plant
Abstract

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Published
2014

10. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

Author

Patrick Wincker, Pascal Bento, Sahana Manoli, Agnieszka A. Golicz, G. Deniot, Shengyi Liu, Christine Sidebottom, Chu Shin Koh, Ian Bancroft, Christian Daviaud, David C. Tack, Rod J. Snowdon, Jörg Tost, Guangyi Fan, Hui Guo, Smahane Chalabi, Boulos Chalhoub, Xinfa Wang, Harry Belcram, Aurélie Chauveau, Gilles Lassalle, Jean-Marc Aury, Tae-Ho Lee, Houda Chelaifa, Jinling Meng, Christopher D. Town, Haibao Tang, Zhongsong Liu, Julien Chiquet, Andrew G. Sharpe, Salman Alamery, Chunyun Guan, Mathieu Charles, Qiong Hu, Xiyin Wang, Xiaowu Wang, Jianxin Ma, Régine Delourme, Mei Guan, Eric Lyons, Chaobo Tong, Margot Correa, Adriana Alberti, Keith L. Adams, Patrick P. Edger, Marie-Christine Le Paslier, Yunhai Lu, Corinne Da Silva, Christophe Battail, Andrew H. Paterson, Isabelle Le Clainche, Benjamin Noel, Jérémy Just, Jacqueline Batley, Jinxiong Shen, Fengming Sun, Kamel Jabbari, Karine Labadie, Michel Renard, Maria Bernard, Birgit Samans, Aurélie Canaguier, Isobel A. P. Parkin, Yong Pyo Lim, Vinh Ha Dinh Thi, Victor Renault, Meixia Zhao, David Edwards, Graham J.W. King, Nicolas Schnel, Dominique Brunel, Cyril Falentin, Reece Tollenaere, Aurélie Bérard, Yongming Zhou, Dominique Arnaud, Imen Mestiri, Philippe E. Bayer, Chuchuan Fan, Wei Hua, J. Chris Pires, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Agriculture and Agri-Food (AAFC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University (FAFU), University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Research Center for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, National Research Council of Canada (NRC), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Genotypage, Plant Genome Mapping Laboratory, Laboratoire épigénétique et environnement, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Cologne Center for Genomics, University of Cologne, Department of Agronomy, Purdue University [West Lafayette], Department of Plant and Microbial Biology, University of California (UC), Department of Botany [Vancouver] (UBC Botany), University of British Columbia (UBC), National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), Beijing Genome Institute, Fondation Jean Dausset - Centre d’Étude du Polymorphisme Humain, College of Agronomy, Hunan Agricultural University [Changsha], Department of Horticulture, Molecular Genetics and Genomics Laboratory, Chungnam National University (CNU), School of Plant Sciences, iPlant Collaborative, University of Arizona, Department of Biology, University of York [York, UK], Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Division of Biological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Southern Cross Plant Science, Southern Cross University (SCU), School of Plant Biology, The University of Western Australia (UWA), Laboratory for Epigenetics and Environment, Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire de Mathématiques et Modélisation d'Evry, Justus-Liebig-Universität Gießen (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of California, Huazhong Agricultural University, Euralis Semences, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), BIOGEMMA, Unité de Recherches Zootechniques (URZ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Limagrain, J. Craig Venter Institute, Fujian Agriculture and Forestry University, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Botany, University of Missouri [Columbia], Southern Cross University, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1165 Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique ( INRA ) -Université d'Evry Val d'Essonne, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ministry of Agriculture-Chinese Academy of Agricultural Sciences ( CAAS ), Agriculture and Agri-Food [Ottawa] ( AAFC ), University of Georgia, Laboratoire de Mathématiques et Modélisation d'Evry ( LaMME ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -ENSIIE-Centre National de la Recherche Scientifique ( CNRS ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Justus Liebig University Giessen, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, National Research Council of Canada ( NRC ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), University of British Columbia ( UBC ), National Key Laboratory of Crop Genetic Improvement, Chungnam National University, Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), University of Missouri ( Saisissez le sigle en majuscules sans points ), The University of Western Australia ( UWA ), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], Brassica, rapeseed, Biology, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, chemistry.chemical_compound, Gene duplication, genetics, Epigenetics, Domestication, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], molecular evolution, Brassica napus, chromosome duplication, food and beverages, plant seed, biology.organism_classification, chemistry, Glucosinolate, Seeds, cytology, Genome, Plant, 010606 plant biology & botany
Abstract

Oilseed rape (Brassica napus L.) was formed ∼7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement., Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782

Published
2014
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11. Prevalence of gene expression additivity in genetically stable wheat allohexaploids

Author

Virginie Huteau, Denise Deffains, Harry Belcram, Smahane Chalabi, Julien Chiquet, Houda Chelaifa, Yun Hai Lu, Véronique Chagué, Joseph Jahier, Olivier Coriton, Jérémy Just, Dominique Arnaud, Imen Mestiri, Boulos Chalhoub, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Univ Evry Val dEssonne, Lab Stat & Genome, UMR 8071, CNRS,USC INRA, Institut National de la Recherche Agronomique (INRA), ANR (Agence Nationale pour la Recherche) [ANR-05-BDIV-015], Evry-Genopole postdoctoral fellowship, French Research Ministry (MENRT), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Laboratoire Statistique et Génome (SG), ANR-05-BDIV-0015,Polyploidie,Effet de la polyploïdie sur la biodiversité et l'évolution du génome des plantes (BioPPG)(2005), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Genome evolution, additivity, Physiology, [SDV]Life Sciences [q-bio], Plant Science, Biology, Genes, Plant, 01 natural sciences, Genome, AEGILOPS-TRITICUM GROUP, Genomic Instability, allopolyploidy, Polyploidy, 03 medical and health sciences, Gene Expression Regulation, Plant, wheat, Gene expression, evolution, Aegilops tauschii, POLYPLOWHEAT, LOW-COPY DNA, PLANT, Gene, Triticum, ELIMINATION, 030304 developmental biology, 2. Zero hunger, Regulation of gene expression, Genetics, 0303 health sciences, GENOME EVOLUTION, Gene Expression Profiling, food and beverages, biology.organism_classification, Gene expression profiling, gene expression, Hybrid speciation, ALLOPOLYPLOWHEAT, HEXAPLOWHEAT, Genome, Plant, HYBRIDIZATION, HYBRID SPECIATION, 010606 plant biology & botany
Abstract

International audience; The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents. In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted. Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34 820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploid Triticum turgidum as the genome progenitor. Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids.

Published
2012
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