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Montfort J, Hervas-Sotomayor F, Le Cam A, Murat F. FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes. Nucleic Acids Res 2024:gkae264. [PMID: 38587202 DOI: 10.1093/nar/gkae264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/09/2024] Open
Abstract
Teleost fish represent one of the largest and most diverse clades of vertebrates, which makes them great models in various research areas such as ecology and evolution. Recent sequencing endeavors provided high-quality genomes for species covering the main fish evolutionary lineages, opening up large-scale comparative genomics studies. However, transcriptomic data across fish species and organs are heterogenous and have not been integrated with newly sequenced genomes making gene expression quantification and comparative analyses particularly challenging. Thus, resources integrating genomic and transcriptomic data across fish species and organs are still lacking. Here, we present FEVER, a web-based resource allowing evolutionary transcriptomics across species and tissues. First, based on query genes FEVER reconstructs gene trees providing orthologous and paralogous relationships as well as their evolutionary dynamics across 13 species covering the major fish lineages, and 4 model species as evolutionary outgroups. Second, it provides unbiased gene expression across 11 tissues using up-to-date fish genomes. Finally, genomic and transcriptomic data are combined together allowing the exploration of gene expression evolution following speciation and duplication events. FEVER is freely accessible at https://fever.sk8.inrae.fr/.
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Sepp M, Leiss K, Murat F, Okonechnikov K, Joshi P, Leushkin E, Spänig L, Mbengue N, Schneider C, Schmidt J, Trost N, Schauer M, Khaitovich P, Lisgo S, Palkovits M, Giere P, Kutscher LM, Anders S, Cardoso-Moreira M, Sarropoulos I, Pfister SM, Kaessmann H. Cellular development and evolution of the mammalian cerebellum. Nature 2024; 625:788-796. [PMID: 38029793 PMCID: PMC10808058 DOI: 10.1038/s41586-023-06884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
The expansion of the neocortex, a hallmark of mammalian evolution1,2, was accompanied by an increase in cerebellar neuron numbers3. However, little is known about the evolution of the cellular programmes underlying the development of the cerebellum in mammals. In this study we generated single-nucleus RNA-sequencing data for around 400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse and the marsupial opossum. We established a consensus classification of the cellular diversity in the developing mammalian cerebellum and validated it by spatial mapping in the fetal human cerebellum. Our cross-species analyses revealed largely conserved developmental dynamics of cell-type generation, except for Purkinje cells, for which we observed an expansion of early-born subtypes in the human lineage. Global transcriptome profiles, conserved cell-state markers and gene-expression trajectories across neuronal differentiation show that cerebellar cell-type-defining programmes have been overall preserved for at least 160 million years. However, we also identified many orthologous genes that gained or lost expression in cerebellar neural cell types in one of the species or evolved new expression trajectories during neuronal differentiation, indicating widespread gene repurposing at the cell-type level. In sum, our study unveils shared and lineage-specific gene-expression programmes governing the development of cerebellar cells and expands our understanding of mammalian brain evolution.
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Affiliation(s)
- Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Piyush Joshi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Lisa Spänig
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Noe Mbengue
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Céline Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Nils Trost
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Maria Schauer
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Philipp Khaitovich
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Miklós Palkovits
- Human Brain Tissue Bank, Semmelweis University, Budapest, Hungary
| | - Peter Giere
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- BioQuant, Heidelberg University, Heidelberg, Germany
| | | | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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3
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Okonechnikov K, Joshi P, Sepp M, Leiss K, Sarropoulos I, Murat F, Sill M, Beck P, Chan KCH, Korshunov A, Sah F, Deng MY, Sturm D, DeSisto J, Donson AM, Foreman NK, Green AL, Robinson G, Orr BA, Gao Q, Darrow E, Hadley JL, Northcott PA, Gojo J, Kawauchi D, Hovestadt V, Filbin MG, von Deimling A, Zuckermann M, Pajtler KW, Kool M, Jones DTW, Jäger N, Kutscher LM, Kaessmann H, Pfister SM. Mapping pediatric brain tumors to their origins in the developing cerebellum. Neuro Oncol 2023; 25:1895-1909. [PMID: 37534924 PMCID: PMC10547518 DOI: 10.1093/neuonc/noad124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas. METHODS We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques. RESULTS We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study. CONCLUSION Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Piyush Joshi
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mari Sepp
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | | | - Pengbo Beck
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kenneth Chun-Ho Chan
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sah
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Maximilian Y Deng
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - John DeSisto
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Giles Robinson
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Emily Darrow
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jennifer L Hadley
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Johannes Gojo
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Andreas von Deimling
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Zuckermann
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - David T W Jones
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lena M Kutscher
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Lamanna F, Hervas-Sotomayor F, Oel AP, Jandzik D, Sobrido-Cameán D, Santos-Durán GN, Martik ML, Stundl J, Green SA, Brüning T, Mößinger K, Schmidt J, Schneider C, Sepp M, Murat F, Smith JJ, Bronner ME, Rodicio MC, Barreiro-Iglesias A, Medeiros DM, Arendt D, Kaessmann H. Publisher Correction: A lamprey neural cell type atlas illuminates the origins of the vertebrate brain. Nat Ecol Evol 2023; 7:1741. [PMID: 37749404 PMCID: PMC10555831 DOI: 10.1038/s41559-023-02227-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Affiliation(s)
- Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | | | - A Phillip Oel
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
- Department of Zoology, Comenius University, Bratislava, Slovakia
| | - Daniel Sobrido-Cameán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gabriel N Santos-Durán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Megan L Martik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jan Stundl
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen A Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - María Celina Rodicio
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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5
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Lamanna F, Hervas-Sotomayor F, Oel AP, Jandzik D, Sobrido-Cameán D, Santos-Durán GN, Martik ML, Stundl J, Green SA, Brüning T, Mößinger K, Schmidt J, Schneider C, Sepp M, Murat F, Smith JJ, Bronner ME, Rodicio MC, Barreiro-Iglesias A, Medeiros DM, Arendt D, Kaessmann H. A lamprey neural cell type atlas illuminates the origins of the vertebrate brain. Nat Ecol Evol 2023; 7:1714-1728. [PMID: 37710042 PMCID: PMC10555824 DOI: 10.1038/s41559-023-02170-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The vertebrate brain emerged more than ~500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey-a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits-based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of cell types, tissue structures and gene expression programs of the ancestral vertebrate brain. However, our analyses also revealed key tissues and cell types that arose later in evolution. For example, the ancestral brain was probably devoid of cerebellar cell types and oligodendrocytes (myelinating cells); our data suggest that the latter emerged from astrocyte-like evolutionary precursors in the jawed vertebrate lineage. Altogether, our work illuminates the cellular and molecular architecture of the ancestral vertebrate brain and provides a foundation for exploring its diversification during evolution.
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Affiliation(s)
- Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | | | - A Phillip Oel
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
- Department of Zoology, Comenius University, Bratislava, Slovakia
| | - Daniel Sobrido-Cameán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gabriel N Santos-Durán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Megan L Martik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jan Stundl
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen A Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - María Celina Rodicio
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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6
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Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. The molecular evolution of spermatogenesis across mammals. Nature 2023; 613:308-316. [PMID: 36544022 PMCID: PMC9834047 DOI: 10.1038/s41586-022-05547-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.
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Affiliation(s)
- Florent Murat
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany. .,INRAE, LPGP, Rennes, France.
| | - Noe Mbengue
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
| | - Sofia Boeg Winge
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Timo Trefzer
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Julia Schmidt
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Thoomke Brüning
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Francesco Lamanna
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Christian Conrad
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Rüdiger Behr
- German Primate Center (DPZ), Platform Degenerative Diseases, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Miquel Crusafont Catalan Institute of Paleontology, Autonomous University of Barcelona, Barcelona, Spain
| | - Frank Grützner
- The Robinson Research Institute, School of Biological Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Kaessmann
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
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7
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Merdrignac C, Clément AE, Montfort J, Murat F, Bobe J. auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication. Cells 2022; 11:2694. [PMID: 36078102 PMCID: PMC9454499 DOI: 10.3390/cells11172694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
The AUTS2 gene plays major roles during brain development and is associated with various neuropathologies including autism. Data in non-mammalian species are scarce, and the aim of our study was to provide a comprehensive analysis of auts2 evolution in teleost fish, which are widely used for in vivo functional analysis and biomedical purposes. Comparative genomics in 78 species showed that auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD). auts2a, which is highly similar to human AUTS2, was almost systematically retained following TGD. In contrast, auts2b, which encodes for a shorter protein similar to a short human AUTS2 isoform, was lost more frequently and independently during evolution. RNA-seq analysis in 10 species revealed a highly conserved profile with predominant expression of both genes in the embryo, brain, and gonads. Based on protein length, conserved domains, and expression profiles, we speculate that the long human isoform functions were retained by auts2a, while the short isoform functions were retained by auts2a and/or auts2b, depending on the lineage/species. auts2a showed a burst in expression during medaka brain formation, where it was expressed in areas of the brain associated with neurodevelopmental disorders. Together, our data suggest a strong conservation of auts2 functions in vertebrates despite different evolutionary scenarios in teleosts.
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Affiliation(s)
| | | | | | | | - Julien Bobe
- INRAE, LPGP UR1037, Fish Physiology and Genomics, Campus de Beaulieu, F-35000 Rennes, France
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8
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Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. Nat Plants 2018; 4:440-452. [PMID: 29915331 PMCID: PMC6086335 DOI: 10.1038/s41477-018-0172-3] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/08/2018] [Indexed: 05/18/2023]
Abstract
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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Affiliation(s)
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Sébastien Faye
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Isabelle Lesur
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
- HelixVenture, Mérignac, France
| | | | | | | | | | - Nathalie Chantret
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jun Chen
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne Diévart
- CIRAD, UMR AGAP, Montpellier, France
- Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | - Marie-Lara Bouffaud
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | | | | | - David Cohen
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Carole Dossat
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | | | - Arnaud Hecker
- IAM, INRA, Université de Lorraine, Champenoux, France
| | - Sylvie Herrmann
- German Centre for Integrative Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Irène Hummel
- UMR Silva, INRA, Université de Lorraine, AgroPariTech, Nancy, France
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eric Lasserre
- Université de Perpignan, UMR 5096, Perpignan, France
| | - Arnaud Lemainque
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Mohammed-Amin Madoui
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France
| | | | | | | | | | - Olivier Rué
- Plateforme bioinformatique Toulouse Midi-Pyrénées, INRA, Auzeville Castanet-Tolosan, France
| | | | - Franck Salin
- BIOGECO, INRA, Université de Bordeaux, Cestas, France
| | - Marçal Soler
- Université de Toulouse, CNRS, UMR 5546, LRSV, Castanet-Tolosan, France
- Laboratori del Suro, University of Girona, Girona, Spain
| | - Mika Tarkka
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - Amandine Velt
- SVQV, Université de Strasbourg, INRA, Colmar, France
| | - Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
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9
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Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GKS, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant J 2018; 93:515-533. [PMID: 29237241 DOI: 10.1111/tpj.13801] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 05/18/2023]
Abstract
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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Affiliation(s)
- Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Florent Murat
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, D-06466, Stadt Seeland, Germany
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Mathieu Piednoel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829, Cologne, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Michiel Van Bel
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Cristina Vives
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | | | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Omar Saleh
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Guillaume Blanc
- Structural and Genomic Information Laboratory (IGS), Aix-Marseille Université, CNRS, UMR 7256 (IMM FR 3479), Marseille, France
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Anders Larsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | | | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Daniel S Rokshar
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - Shengqiang Shu
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Fritz Thümmler
- Vertis Biotechnologie AG, Lise-Meitner-Str. 30, 85354, Freising, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Thomas Widiez
- Department of Plant Biology, University of Geneva, Sciences III, Geneva 4, CH-1211, Switzerland
- Department of Plant Biology & Pathology Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Ann Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Yong Zhang
- Shenzhen Huahan Gene Life Technology Co. Ltd, Shenzhen, China
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralph S Quatrano
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany
- WZW, Technical University Munich, Munich, Germany
| | | | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Jérome Salse
- INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63100, Clermont-Ferrand, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany
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10
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El Baidouri M, Murat F, Veyssiere M, Molinier M, Flores R, Burlot L, Alaux M, Quesneville H, Pont C, Salse J. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytol 2017; 213:1477-1486. [PMID: 27551821 DOI: 10.1111/nph.14113] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/18/2016] [Indexed: 05/26/2023]
Abstract
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.
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Affiliation(s)
- Moaine El Baidouri
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Maeva Veyssiere
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Mélanie Molinier
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Raphael Flores
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Laura Burlot
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Michael Alaux
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Hadi Quesneville
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Caroline Pont
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
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11
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Murat F, Louis A, Maumus F, Armero A, Cook R, Quesneville H, Roest Crollius H, Salse J. Erratum to: Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biol 2016; 17:64. [PMID: 27044591 PMCID: PMC4820912 DOI: 10.1186/s13059-016-0887-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 12/02/2022] Open
Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Alexandra Louis
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France.,Inserm, U1024, Paris, F-75005, France.,CNRS, UMR 8197, Paris, F-75005, France
| | - Florian Maumus
- INRA UMR 1164 URGI Route de Saint Cyr, Versailles, 78026, France
| | - Alex Armero
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Richard Cook
- CNRS/UPVD UMR 5096 LGDP, 58 avenue P. Alduy, Perpignan, 66860, Cedex, France
| | - Hadi Quesneville
- INRA UMR 1164 URGI Route de Saint Cyr, Versailles, 78026, France
| | - Hugues Roest Crollius
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France.,Inserm, U1024, Paris, F-75005, France.,CNRS, UMR 8197, Paris, F-75005, France
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France.
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12
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Murat F, Louis A, Maumus F, Armero A, Cooke R, Quesneville H, Roest Crollius H, Salse J. Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biol 2015; 16:262. [PMID: 26653025 PMCID: PMC4675067 DOI: 10.1186/s13059-015-0814-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/27/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed. RESULTS We reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula. The ancestral Brassicaceae karyotype (Brassicaceae lineages I and II) is composed of eight protochromosomes and 20,037 ordered and oriented protogenes. After speciation, it evolved into the ancestral Camelineae karyotype (eight protochromosomes and 22,085 ordered protogenes) and the proto-Calepineae karyotype (seven protochromosomes and 21,035 ordered protogenes) genomes. CONCLUSIONS The three inferred ancestral karyotype genomes are shown here to be powerful tools to unravel the reticulated evolutionary history of extant Brassicaceae genomes regarding the fate of ancestral genes and genomic compartments, particularly centromeres and evolutionary breakpoints. This new resource should accelerate research in comparative genomics and translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France
| | - Alexandra Louis
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France.,Inserm, U1024, Paris, F-75005, France.,CNRS, UMR 8197, Paris, F-75005, France
| | - Florian Maumus
- INRA UMR 1164 URGI Route de Saint Cyr, Versailles, 78026, France
| | - Alix Armero
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France
| | - Richard Cooke
- CNRS/UPVD UMR 5096 LGDP, 58 avenue P. Alduy, 66860, Perpignan, Cedex, France
| | - Hadi Quesneville
- INRA UMR 1164 URGI Route de Saint Cyr, Versailles, 78026, France
| | - Hugues Roest Crollius
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005, France.,Inserm, U1024, Paris, F-75005, France.,CNRS, UMR 8197, Paris, F-75005, France
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France.
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13
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de Miguel M, Bartholomé J, Ehrenmann F, Murat F, Moriguchi Y, Uchiyama K, Ueno S, Tsumura Y, Lagraulet H, de Maria N, Cabezas JA, Cervera MT, Gion JM, Salse J, Plomion C. Evidence of intense chromosomal shuffling during conifer evolution. Genome Biol Evol 2015; 7:2799-2809. [PMID: 26400405 PMCID: PMC4684699 DOI: 10.1093/gbe/evv185] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkage mapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma: Pinaceae and Cupressaceae. We propose for the first time a model based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n = 12) and Cupressaceae (with n = 11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes.
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Affiliation(s)
- Marina de Miguel
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Jérôme Bartholomé
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - François Ehrenmann
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Yoshinari Moriguchi
- Niigata University, Graduate School of Science and Technology, 8050, Igarashi 2-Nocho, Nishi-ku, Niigata 950-2181, Japan
| | - Kentaro Uchiyama
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Yoshihiko Tsumura
- University of Tsukuba, Faculty of Life & Environmental Sciences, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hélène Lagraulet
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Nuria de Maria
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - José-Antonio Cabezas
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Maria-Teresa Cervera
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Jean Marc Gion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France CIRAD, UMR AGAP, F-33612 Cestas, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Christophe Plomion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
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14
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Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour 2015; 16:254-65. [PMID: 25944057 DOI: 10.1111/1755-0998.12425] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022]
Abstract
The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
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Affiliation(s)
- Christophe Plomion
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Joëlle Amselem
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Tina Alaeitabar
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Catherine Bodénès
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Christophe Boury
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Sébastien Duplessis
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - François Ehrenmann
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Barbara Estrada-Mairey
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Stéphanie Fouteau
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | | | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, Orléans, F-45075, France
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Thibault Leroy
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Isabelle Lesur
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Francis Martin
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Célia Michotey
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Franck Salin
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Delphine Steinbach
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | | | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.,Université d'Evry Val d'Essone, UMR 8030, Evry, CP5706, France.,Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, CP5706, France
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Hadi Quesneville
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
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15
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Lesur I, Le Provost G, Bento P, Da Silva C, Leplé JC, Murat F, Ueno S, Bartholomé J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Léger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 2015; 16:112. [PMID: 25765701 PMCID: PMC4350297 DOI: 10.1186/s12864-015-1331-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 02/09/2015] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. RESULTS The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. CONCLUSION In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
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Affiliation(s)
- Isabelle Lesur
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- HelixVenture, F-33700, Mérignac, France.
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Pascal Bento
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Corinne Da Silva
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075, Orléans, France.
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France.
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Jerôme Bartholomé
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- CIRAD, UMR AGAP, F-34398, Montpellier, France.
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - François Ehrenmann
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Céline Noirot
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France.
| | - Christian Burban
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Valérie Léger
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Joelle Amselem
- INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France.
| | - Caroline Belser
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Hadi Quesneville
- INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France.
| | | | - Silvia Fluch
- AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Str 24, 3430, Tulln, Austria.
| | - Lasse Feldhahn
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
| | - Mika Tarkka
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
| | - Sylvie Herrmann
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
- Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, 06120, Halle/Saale, Germany.
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France.
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France.
| | - Jean-Marc Aury
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Christophe Plomion
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
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16
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Murat F, Zhang R, Guizard S, Gavranović H, Flores R, Steinbach D, Quesneville H, Tannier E, Salse J. Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. Genome Biol Evol 2015; 7:735-49. [PMID: 25637221 PMCID: PMC5322550 DOI: 10.1093/gbe/evv014] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, “DicotSyntenyViewer” (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France
| | - Rongzhi Zhang
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France
| | - Sébastien Guizard
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France
| | - Haris Gavranović
- Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Raphael Flores
- INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France
| | - Delphine Steinbach
- INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France
| | - Hadi Quesneville
- INRA 'Unité de Recherche en Génomique et Informatique', Centre INRA de Versailles, Versailles, France
| | - Eric Tannier
- INRIA Rhône-Alpes, Université de Lyon 1, CNRS UMR5558, Laboratoire Biométrie et Biologie Évolutive, Villeurbanne Cedex, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', Clermont Ferrand, France
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17
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Abstract
Comparative genomics combined with phylogenetic reconstructions are powerful approaches to study the evolution of genes and genomes. However, the current rapid expansion of the volume of genomic information makes it increasingly difficult to interrogate, integrate and synthesize comparative genome data while taking into account the maximum breadth of information available. GenomicusPlants (http://www.genomicus.biologie.ens.fr/genomicus-plants) is an extension of the Genomicus webserver that addresses this issue by allowing users to explore flowering plant genomes in an intuitive way, across the broadest evolutionary scales. Extant genomes of 26 flowering plants can be analyzed, as well as 23 ancestral reconstructed genomes. Ancestral gene order provides a long-term chronological view of gene order evolution, greatly facilitating comparative genomics and evolutionary studies. Four main interfaces ('views') are available where: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes; (ii) AlignView projects loci of interest against all other genomes to visualize its topological conservation; (iii) MatrixView compares two genomes in a classical dotplot representation; and (iv) Karyoview visualizes chromosome karyotypes 'painted' with colours of another genome of interest. All four views are interconnected and benefit from many customizable features.
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Affiliation(s)
- Alexandra Louis
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France CNRS, UMR 8197, Paris, F-75005 France Inserm, U1024, Paris, F-75005 France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC (Génétique, Diversité et Ecophysiologie des Céréales), Clermont Ferrand, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC (Génétique, Diversité et Ecophysiologie des Céréales), Clermont Ferrand, France
| | - Hugues Roest Crollius
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, F-75005 France CNRS, UMR 8197, Paris, F-75005 France Inserm, U1024, Paris, F-75005 France
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Dobrovolskaya O, Pont C, Sibout R, Martinek P, Badaeva E, Murat F, Chosson A, Watanabe N, Prat E, Gautier N, Gautier V, Poncet C, Orlov YL, Krasnikov AA, Bergès H, Salina E, Laikova L, Salse J. FRIZZY PANICLE drives supernumerary spikelets in bread wheat. Plant Physiol 2015; 167:189-99. [PMID: 25398545 PMCID: PMC4281007 DOI: 10.1104/pp.114.250043] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Bread wheat (Triticum aestivum) inflorescences, or spikes, are characteristically unbranched and normally bear one spikelet per rachis node. Wheat mutants on which supernumerary spikelets (SSs) develop are particularly useful resources for work towards understanding the genetic mechanisms underlying wheat inflorescence architecture and, ultimately, yield components. Here, we report the characterization of genetically unrelated mutants leading to the identification of the wheat FRIZZY PANICLE (FZP) gene, encoding a member of the APETALA2/Ethylene Response Factor transcription factor family, which drives the SS trait in bread wheat. Structural and functional characterization of the three wheat FZP homoeologous genes (WFZP) revealed that coding mutations of WFZP-D cause the SS phenotype, with the most severe effect when WFZP-D lesions are combined with a frameshift mutation in WFZP-A. We provide WFZP-based resources that may be useful for genetic manipulations with the aim of improving bread wheat yield by increasing grain number.
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Affiliation(s)
- Oxana Dobrovolskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Caroline Pont
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Richard Sibout
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Petr Martinek
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Ekaterina Badaeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Florent Murat
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Audrey Chosson
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Nobuyoshi Watanabe
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Elisa Prat
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Nadine Gautier
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Véronique Gautier
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Charles Poncet
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Yuriy L Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Alexander A Krasnikov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Hélène Bergès
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Elena Salina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Lyudmila Laikova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
| | - Jerome Salse
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (O.D., Y.L.O., E.S., L.L.);Institut National de la Recherche Agronomique-Université Blaise Pascal Unité Mixte de Recherche-1095, 63100 Clermont-Ferrand cedex 2, France (Ca.P., F.M., A.C., V.G., Ch.P., J.S.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche-1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France (R.S.); AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France (R.S.);Agrotest Fyto, Ltd., 767 01 Kromeriz, Czech Republic (P.M.);Vavilov Institute of General Genetics, Russian Academy of Sciences, 3119333 Moscow, Russia (E.B.);College of Agriculture, Ibaraki University, 3-21-1 Chuuo, Ami, Inashiki, Ibaraki 300-0393, Japan (N.W.);Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques Végétales, 31326 Castanet Tolosan cedex, France (E.P., N.G., H.B.);Novosibirsk State University, 630090 Novosibirsk, Russia (Y.O.); andCentral Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.)
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Murat F, Zhang R, Guizard S, Flores R, Armero A, Pont C, Steinbach D, Quesneville H, Cooke R, Salse J. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome Biol Evol 2014; 6:12-33. [PMID: 24317974 PMCID: PMC3914691 DOI: 10.1093/gbe/evt200] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC (Génétique, Diversité et Ecophysiologie des Céréales), Clermont Ferrand, France
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20
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Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 2014; 32:656-62. [PMID: 24908277 PMCID: PMC4113729 DOI: 10.1038/nbt.2906] [Citation(s) in RCA: 320] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
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Affiliation(s)
- G. Albert Wu
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Simon Prochnik
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France
| | - Uffe Hellsten
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Javier Terol
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Kamel Jabbari
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | | | | | - Andrea Zuccolo
- Istituto di Genomica Applicata, Udine, Italy
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jarrod Chapman
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Francisco R. Tadeo
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Leandro H. Estornell
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Juan V. Muñoz-Sanz
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Victoria Ibanez
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Amparo Herrero-Ortega
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Pablo Aleza
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | | | | | - Dominique Brunel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- INRA, US EPGV_1279, Evry, France
| | | | - Chunxian Chen
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Brian Desany
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Chinnappa Kodira
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Mohammed Mohiuddin
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Tim Harkins
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Karin Fredrikson
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Paul Burns
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark Borodovsky
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Giuseppe Reforgiato
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy
| | - Juliana Freitas-Astúa
- Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil
- Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil
| | - Francis Quetier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | - Mikeal Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | - Jeremy Schmutz
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy
| | | | - Manuel Talon
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Olivier Jaillon
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | | | - Frederick Gmitter
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - Daniel Rokhsar
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA
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Zhang R, Murat F, Pont C, Langin T, Salse J. Paleo-evolutionary plasticity of plant disease resistance genes. BMC Genomics 2014; 15:187. [PMID: 24617999 PMCID: PMC4234491 DOI: 10.1186/1471-2164-15-187] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 02/25/2014] [Indexed: 01/28/2023] Open
Abstract
Background The recent access to a large set of genome sequences, combined with a robust evolutionary scenario of modern monocot (i.e. grasses) and eudicot (i.e. rosids) species from their founder ancestors, offered the opportunity to gain insights into disease resistance genes (R-genes) evolutionary plasticity. Results We unravel in the current article (i) a R-genes repertoire consisting in 7883 for monocots and 15758 for eudicots, (ii) a contrasted R-genes conservation with 23.8% for monocots and 6.6% for dicots, (iii) a minimal ancestral founder pool of 384 R-genes for the monocots and 150 R-genes for the eudicots, (iv) a general pattern of organization in clusters accounting for more than 60% of mapped R-genes, (v) a biased deletion of ancestral duplicated R-genes between paralogous blocks possibly compensated by clusterization, (vi) a bias in R-genes clusterization where Leucine-Rich Repeats act as a ‘glue’ for domain association, (vii) a R-genes/miRNAs interome enriched toward duplicated R-genes. Conclusions Together, our data may suggest that R-genes family plasticity operated during plant evolution (i) at the structural level through massive duplicates loss counterbalanced by massive clusterization following polyploidization; as well as at (ii) the regulation level through microRNA/R-gene interactions acting as a possible source of functional diploidization of structurally retained R-genes duplicates. Such evolutionary shuffling events leaded to CNVs (i.e. Copy Number Variation) and PAVs (i.e. Presence Absence Variation) between related species operating in the decay of R-genes colinearity between plant species.
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Affiliation(s)
| | | | | | | | - Jerome Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 chemin de Beaulieu, 63100 Clermont-Ferrand, France.
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22
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Pont C, Murat F, Guizard S, Flores R, Foucrier S, Bidet Y, Quraishi UM, Alaux M, Doležel J, Fahima T, Budak H, Keller B, Salvi S, Maccaferri M, Steinbach D, Feuillet C, Quesneville H, Salse J. Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J 2013; 76:1030-1044. [PMID: 24164652 DOI: 10.1111/tpj.12366] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/01/2013] [Accepted: 10/08/2013] [Indexed: 05/27/2023]
Abstract
Bread wheat derives from a grass ancestor structured in seven protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing conserved orthologous set (COS) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supra-dominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat.
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Affiliation(s)
- Caroline Pont
- INRA/UBP UMR 1095, Centre de Clermont Ferrand-Theix, 5 Chemin de Beaulieu, 63100, Clermont Ferrand, France
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23
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Bodénès C, Chancerel E, Gailing O, Vendramin GG, Bagnoli F, Durand J, Goicoechea PG, Soliani C, Villani F, Mattioni C, Koelewijn HP, Murat F, Salse J, Roussel G, Boury C, Alberto F, Kremer A, Plomion C. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC Plant Biol 2012; 12:153. [PMID: 22931513 PMCID: PMC3493355 DOI: 10.1186/1471-2229-12-153] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 08/22/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. RESULTS We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. CONCLUSIONS This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
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Affiliation(s)
- Catherine Bodénès
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Emilie Chancerel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology Göttingen University, Büsgenweg 2, 37077, Göttingen, Germany
- New address: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Giovanni G Vendramin
- Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Jerome Durand
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Pablo G Goicoechea
- NEIKER-Tecnalia, Dpto Biotecnologia, PO Box 46, Vitoria-Gasteiz, 01080, Spain
| | - Carolina Soliani
- Unidad de Genética Ecológica y Mejoramiento Forestal, INTA EEA Bariloche, Bariloche, CC277 8400, Argentina
| | - Fiorella Villani
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | - Claudia Mattioni
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | | | - Florent Murat
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Jerome Salse
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Guy Roussel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Florian Alberto
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Antoine Kremer
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
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Abstract
Continuing advances in genome sequencing technologies and computational methods for comparative genomics currently allow inferring the evolutionary history of entire plant and animal genomes. Based on the comparison of the plant and animal genome paleohistory, major differences are unveiled in 1) evolutionary mechanisms (i.e., polyploidization versus diploidization processes), 2) genome conservation (i.e., coding versus noncoding sequence maintenance), and 3) modern genome architecture (i.e., genome organization including repeats expansion versus contraction phenomena). This article discusses how extant animal and plant genomes are the result of inherently different rates and modes of genome evolution resulting in relatively stable animal and much more dynamic and plastic plant genomes.
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Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC ‘Génétique, Diversité et Ecophysiologie des Céréales’, Clermont Ferrand, France
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC ‘Génétique, Diversité et Ecophysiologie des Céréales’, Clermont Ferrand, France
- *Corresponding author: E-mail:
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Dibari B, Murat F, Chosson A, Gautier V, Poncet C, Lecomte P, Mercier I, Bergès H, Pont C, Blanco A, Salse J. Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. BMC Genomics 2012; 13:221. [PMID: 22672222 PMCID: PMC3413518 DOI: 10.1186/1471-2164-13-221] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/06/2012] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY) plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules, the first committed step in carotenogenesis. PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY1-3) that have been widely characterized in rice, maize and sorghum. RESULTS In wheat, for which yellow pigment content is extremely important for flour colour, only PSY1 has been extensively studied because of its association with QTLs reported for yellow pigment whereas PSY2 has been partially characterized. Here, we report the isolation of bread wheat PSY3 genes from a Renan BAC library using Brachypodium as a model genome for the Triticeae to develop Conserved Orthologous Set markers prior to gene cloning and sequencing. Wheat PSY3 homoeologous genes were sequenced and annotated, unravelling their novel structure associated with intron-loss events and consequent exonic fusions. A wheat PSY3 promoter region was also investigated for the presence of cis-acting elements involved in the response to abscisic acid (ABA), since carotenoids also play an important role as precursors of signalling molecules devoted to plant development and biotic/abiotic stress responses. Expression of wheat PSYs in leaves and roots was investigated during ABA treatment to confirm the up-regulation of PSY3 during abiotic stress. CONCLUSIONS We investigated the structural and functional determinisms of PSY genes in wheat. More generally, among eudicots and monocots, the PSY gene family was found to be associated with differences in gene copy numbers, allowing us to propose an evolutionary model for the entire PSY gene family in Grasses.
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Affiliation(s)
- Bianca Dibari
- INRA-UMR 1095 Génétique Diversité Ecophysiologie des Céréales (GDEC), Clermont-Ferrand, France
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Abrouk M, Zhang R, Murat F, Li A, Pont C, Mao L, Salse J. Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication. Plant Cell 2012; 24:1776-92. [PMID: 22589464 PMCID: PMC3442569 DOI: 10.1105/tpc.112.095752] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 03/29/2012] [Accepted: 04/10/2012] [Indexed: 05/21/2023]
Abstract
The recent availability of plant genome sequences, combined with a robust evolutionary scenario of the modern monocot and eudicot karyotypes from their diploid ancestors, offers an opportunity to gain insights into microRNA (miRNA) gene paleohistory in plants. Characterization and comparison of miRNAs and associated protein-coding targets in plants allowed us to unravel (1) contrasted genome conservation patterns of miRNAs in monocots and eudicots after whole-genome duplication (WGD), (2) an ancestral miRNA founder pool in the monocot genomes dating back to 100 million years ago, (3) miRNA subgenome dominance during the post-WGD diploidization process with selective miRNA deletion complemented with possible transposable element-mediated return flows, and (4) the miRNA/target interaction-directed differential loss/retention of miRNAs following the gene dosage balance rule. Together, our data suggest that overretained miRNAs in grass genomes may be implicated in connected gene regulations for stress responses, which is essential for plant adaptation and useful for crop variety innovation.
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Affiliation(s)
- Michael Abrouk
- Institut National de la Recherche Agronomique/Université Blaise Pascal, Unité Mixte de Recherche 1095, Génétique, Diversité et Ecophysiologie des Céréales, Laboratory Paléogénomique des Plantes pour l’Amélioration Variétale, 63100 Clermont Ferrand, France
| | - Rongzhi Zhang
- Institut National de la Recherche Agronomique/Université Blaise Pascal, Unité Mixte de Recherche 1095, Génétique, Diversité et Ecophysiologie des Céréales, Laboratory Paléogénomique des Plantes pour l’Amélioration Variétale, 63100 Clermont Ferrand, France
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Florent Murat
- Institut National de la Recherche Agronomique/Université Blaise Pascal, Unité Mixte de Recherche 1095, Génétique, Diversité et Ecophysiologie des Céréales, Laboratory Paléogénomique des Plantes pour l’Amélioration Variétale, 63100 Clermont Ferrand, France
| | - Aili Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caroline Pont
- Institut National de la Recherche Agronomique/Université Blaise Pascal, Unité Mixte de Recherche 1095, Génétique, Diversité et Ecophysiologie des Céréales, Laboratory Paléogénomique des Plantes pour l’Amélioration Variétale, 63100 Clermont Ferrand, France
| | - Long Mao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jérôme Salse
- Institut National de la Recherche Agronomique/Université Blaise Pascal, Unité Mixte de Recherche 1095, Génétique, Diversité et Ecophysiologie des Céréales, Laboratory Paléogénomique des Plantes pour l’Amélioration Variétale, 63100 Clermont Ferrand, France
- Address correspondence to
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Bordat A, Savois V, Nicolas M, Salse J, Chauveau A, Bourgeois M, Potier J, Houtin H, Rond C, Murat F, Marget P, Aubert G, Burstin J. Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L. G3 (Bethesda) 2011; 1:93-103. [PMID: 22384322 PMCID: PMC3276132 DOI: 10.1534/g3.111.000349] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 05/06/2011] [Indexed: 12/31/2022]
Abstract
To identify genes involved in phenotypic traits, translational genomics from highly characterized model plants to poorly characterized crop plants provides a valuable source of markers to saturate a zone of interest as well as functionally characterized candidate genes. In this paper, an integrated view of the pea genetic map was developed. A series of gene markers were mapped and their best reciprocal homologs were identified on M. truncatula, L. japonicus, soybean, and poplar pseudomolecules. Based on the syntenic relationships uncovered between pea and M. truncatula, 5460 pea Unigenes were tentatively placed on the consensus map. A new bioinformatics tool, http://www.thelegumeportal.net/pea_mtr_translational_toolkit, was developed that allows, for any gene sequence, to search its putative position on the pea consensus map and hence to search for candidate genes among neighboring Unigenes. As an example, a promising candidate gene for the hypernodulation mutation nod3 in pea was proposed based on the map position of the likely homolog of Pub1, a M. truncatula gene involved in nodulation regulation. A broader view of pea genome evolution was obtained by revealing syntenic relationships between pea and sequenced genomes. Blocks of synteny were identified which gave new insights into the evolution of chromosome structure in Papillionoids and Eudicots. The power of the translational genomics approach was underlined.
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Mayer KF, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 2011; 23:1249-63. [PMID: 21467582 PMCID: PMC3101540 DOI: 10.1105/tpc.110.082537] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/10/2011] [Accepted: 03/18/2011] [Indexed: 05/18/2023]
Abstract
We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
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Affiliation(s)
- Klaus F.X. Mayer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Mihaela Martis
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Pete E. Hedley
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Hui Liu
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Jenny A. Morris
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Stefan Taudien
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Stephan Roessner
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Pavla Suchánková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Florent Murat
- Institut National de la Recherche Agronomique Clermont-Ferrand, Unité Mixte de Recherche, Institut National de la Recherche Agronomique, Université Blaise Pascal 1095, Amélioration et Santé des Plantes, Domaine de Crouelle, Clermont-Ferrand 63100, France
| | - Marius Felder
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Thomas Nussbaumer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Jerome Salse
- Institut National de la Recherche Agronomique Clermont-Ferrand, Unité Mixte de Recherche, Institut National de la Recherche Agronomique, Université Blaise Pascal 1095, Amélioration et Santé des Plantes, Domaine de Crouelle, Clermont-Ferrand 63100, France
| | - Takashi Endo
- Kyoto University, Laboratory of Plant Genetics, Kyoto 606-8502, Japan
| | - Hiroaki Sakai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Tsuyoshi Tanaka
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Kazuhiro Sato
- Okayama University, Institute of Plant Science and Resources, Kurashiki 710-0046, Japan
| | - Matthias Platzer
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Robbie Waugh
- Scottish Crop Research Institute, Invergowrie, Dundee, Scotland DD25DA, United Kingdom
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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Quraishi UM, Abrouk M, Murat F, Pont C, Foucrier S, Desmaizieres G, Confolent C, Rivière N, Charmet G, Paux E, Murigneux A, Guerreiro L, Lafarge S, Le Gouis J, Feuillet C, Salse J. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. Plant J 2011; 65:745-56. [PMID: 21251102 DOI: 10.1111/j.1365-313x.2010.04461.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.
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Affiliation(s)
- Umar Masood Quraishi
- INRA/Université Blaise Pascal UMR 1095 GDEC, Domaine de Crouelle, 234 Avenue du Brézet, 63100 Clermont-Ferrand, France
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Ueno S, Le Provost G, Léger V, Klopp C, Noirot C, Frigerio JM, Salin F, Salse J, Abrouk M, Murat F, Brendel O, Derory J, Abadie P, Léger P, Cabane C, Barré A, de Daruvar A, Couloux A, Wincker P, Reviron MP, Kremer A, Plomion C. Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 2010; 11:650. [PMID: 21092232 PMCID: PMC3017864 DOI: 10.1186/1471-2164-11-650] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 11/23/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity. RESULTS We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html. CONCLUSIONS This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.
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Affiliation(s)
- Saneyoshi Ueno
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | | | - Valérie Léger
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
| | - Christophe Klopp
- Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France
| | - Céline Noirot
- Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France
| | | | - Franck Salin
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brézet, 63100 Clermont Ferrand, France
| | - Michael Abrouk
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brézet, 63100 Clermont Ferrand, France
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brézet, 63100 Clermont Ferrand, France
| | - Oliver Brendel
- INRA, UMR1137 EEF "Ecologie et Ecophysiologie Forestières", F 54280 Champenoux, France
| | - Jérémy Derory
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
| | - Pierre Abadie
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
| | - Patrick Léger
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
| | - Cyril Cabane
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
- CNRS, UMR 5800, Laboratoire Bordelais de Recherche en Informatique, Talence, France
| | - Aurélien Barré
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
| | - Antoine de Daruvar
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
- CNRS, UMR 5800, Laboratoire Bordelais de Recherche en Informatique, Talence, France
| | - Arnaud Couloux
- CEA, DSV, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux CP5706 91057 Evry cedex, France
| | - Patrick Wincker
- CEA, DSV, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux CP5706 91057 Evry cedex, France
| | | | - Antoine Kremer
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
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Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, Pont C, Messing J, Salse J. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 2010; 20:1545-57. [PMID: 20876790 PMCID: PMC2963818 DOI: 10.1101/gr.109744.110] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 08/24/2010] [Indexed: 11/25/2022]
Abstract
The comparison of the chromosome numbers of today's species with common reconstructed paleo-ancestors has led to intense speculation of how chromosomes have been rearranged over time in mammals. However, similar studies in plants with respect to genome evolution as well as molecular mechanisms leading to mosaic synteny blocks have been lacking due to relevant examples of evolutionary zooms from genomic sequences. Such studies require genomes of species that belong to the same family but are diverged to fall into different subfamilies. Our most important crops belong to the family of the grasses, where a number of genomes have now been sequenced. Based on detailed paleogenomics, using inference from n = 5-12 grass ancestral karyotypes (AGKs) in terms of gene content and order, we delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice, maize, sorghum, and Brachypodium genomes, representing three different subfamilies and different polyploidization events. By focusing on these sequence intervals, we could show that the chromosome number variation/reduction from the n = 12 common paleo-ancestor was driven by nonrandom centric double-strand break repair events. It appeared that the centromeric/telomeric illegitimate recombination between nonhomologous chromosomes led to nested chromosome fusions (NCFs) and synteny break points (SBPs). When intervals comprising NCFs were compared in their structure, we concluded that SBPs (1) were meiotic recombination hotspots, (2) corresponded to high sequence turnover loci through repeat invasion, and (3) might be considered as hotspots of evolutionary novelty that could act as a reservoir for producing adaptive phenotypes.
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Affiliation(s)
- Florent Murat
- INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France
| | - Jian-Hong Xu
- The Plant Genome Initiative at Rutgers (PGIR), Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Eric Tannier
- INRIA Rhône-Alpes, Université de Lyon 1, CNRS UMR5558, Laboratoire Biométrie et Biologie Évolutive, 69622 Villeurbanne Cedex, France
| | - Michael Abrouk
- INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France
| | - Nicolas Guilhot
- INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France
| | - Caroline Pont
- INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France
| | - Joachim Messing
- The Plant Genome Initiative at Rutgers (PGIR), Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Jérôme Salse
- INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France
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Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J. Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci 2010; 15:479-87. [PMID: 20638891 DOI: 10.1016/j.tplants.2010.06.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 05/28/2010] [Accepted: 06/16/2010] [Indexed: 05/03/2023]
Abstract
In the past ten years, international initiatives have led to the development of large sets of genomic resources that allow comparative genomic studies between plant genomes at a high level of resolution. Comparison of map-based genomic sequences revealed shared intra-genomic duplications, providing new insights into the evolution of flowering plant genomes from common ancestors. Plant genomes can be presented as concentric circles, providing a new reference for plant chromosome evolutionary relationships and an efficient tool for gene annotation and cross-genome markers development. Recent palaeogenomic data demonstrate that whole-genome duplications have provided a motor for the evolutionary success of flowering plants over the last 50-70 million years.
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Affiliation(s)
- Michael Abrouk
- INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brézet, 63100 Clermont Ferrand, France
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Quraishi UM, Murat F, Abrouk M, Pont C, Confolent C, Oury FX, Ward J, Boros D, Gebruers K, Delcour JA, Courtin CM, Bedo Z, Saulnier L, Guillon F, Balzergue S, Shewry PR, Feuillet C, Charmet G, Salse J. Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.). Funct Integr Genomics 2010; 11:71-83. [PMID: 20697765 DOI: 10.1007/s10142-010-0183-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/07/2010] [Accepted: 07/12/2010] [Indexed: 11/30/2022]
Abstract
Grain dietary fiber content in wheat not only affects its end use and technological properties including milling, baking and animal feed but is also of great importance for health benefits. In this study, integration of association genetics (seven detected loci on chromosomes 1B, 3A, 3D, 5B, 6B, 7A, 7B) and meta-QTL (three consensus QTL on chromosomes 1B, 3D and 6B) analyses allowed the identification of seven chromosomal regions underlying grain dietary fiber content in bread wheat. Based either on a diversity panel or on bi-parental populations, we clearly demonstrate that this trait is mainly driven by a major locus located on chromosome 1B associated with a log of p value >13 and a LOD score >8, respectively. In parallel, we identified 73 genes differentially expressed during the grain development and between genotypes with contrasting grain fiber contents. Integration of quantitative genetics and transcriptomic data allowed us to propose a short list of candidate genes that are conserved in the rice, sorghum and Brachypodium chromosome regions orthologous to the seven wheat grain fiber content QTL and that can be considered as major candidate genes for future improvement of the grain dietary fiber content in bread wheat breeding programs.
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Affiliation(s)
- Umar Masood Quraishi
- INRA-University Blaise Pascal, UMR1095 Génétique, Diversité et Ecophysiologie des Céréales, 234 Avenue du Brézet, 63100, Clermont-Ferrand, France
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Salse J, Abrouk M, Murat F, Quraishi UM, Feuillet C. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Brief Bioinform 2009; 10:619-30. [DOI: 10.1093/bib/bbp037] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
OBJECTIVE To analyse the relationship between obesity and prostate cancer, when compared with men with benign prostatic hyperplasia (BPH). PATIENTS AND METHODS The records were reviewed of consecutive patients with histologically confirmed prostate cancer admitted for prostate surgery between January 1993 and February 1999. Controls were selected from patients who were hospitalized at the same time for the surgical treatment of BPH. One control was matched to each case by age. Obesity was defined as a body mass index (BMI) of> 29 kg/m2. RESULTS The study included 194 cases and 194 controls; their median (range) age at operation was 69.5 (50-88) years in both groups, and the BMI 26.1 (16.6-38.1) kg/m2 in the cancer and 25.7 (15.1-36.8) kg/m2 in the BPH group. The difference between the groups was not significant (P = 0.06). Obesity was significantly associated with prostate cancer, with an odds ratio (95% confidence interval) of 2.47 (1.41-4.34). Cases with advanced disease had a higher BMI than those with localized disease, but when age was considered the difference was not significant. CONCLUSION In general the BMI was not significantly associated with prostate cancer when compared with men having BPH. However, obese men had 2.5 times the risk of having prostate cancer.
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Affiliation(s)
- J Irani
- Department of Urology, Centre Hospitalier Universitaire La Milétrie, Poitiers, France.
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Dubois R, Valvalle AF, Murat F, Dodat H. [Malformations of male internal genital organs originating from the Wolff mesonephrotic canal]. Prog Urol 2001; 11:733-40. [PMID: 11761702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- R Dubois
- Service de Chirurgie Pédiatrique, Unité d'Urologie, Hôpital Edouard-Herriot, Place d'Arsonval, 69437 Lyon
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Etaner R, Cevanşir B, Murat F. [Results obtained with thiethylperazine in vestibular tests]. Turk Tip Cemiy Mecm 1966; 32:707-10. [PMID: 5298620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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