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Bellec A, Sow MD, Pont C, Civan P, Mardoc E, Duchemin W, Armisen D, Huneau C, Thévenin J, Vernoud V, Depège-Fargeix N, Maunas L, Escale B, Dubreucq B, Rogowsky P, Bergès H, Salse J. Tracing 100 million years of grass genome evolutionary plasticity. Plant J 2023. [PMID: 36919199 DOI: 10.1111/tpj.16185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/29/2023] [Accepted: 02/24/2023] [Indexed: 05/17/2023]
Abstract
Grasses derive from a family of monocotyledonous plants that includes crops of major economic importance such as wheat, rice, sorghum and barley, sharing a common ancestor some 100 million years ago. The genomic attributes of plant adaptation remain obscure and the consequences of recurrent whole genome duplications (WGD) or polyploidization events, a major force in plant evolution, remain largely speculative. We conducted a comparative analysis of omics data from ten grass species to unveil structural (inversions, fusions, fissions, duplications, substitutions) and regulatory (expression and methylation) basis of genome plasticity, as possible attributes of plant long lasting evolution and adaptation. The present study demonstrates that diverged polyploid lineages sharing a common WGD event often present the same patterns of structural changes and evolutionary dynamics, but these patterns are difficult to generalize across independent WGD events as a result of non-WGD factors such as selection and domestication of crops. Polyploidy is unequivocally linked to the evolutionary success of grasses during the past 100 million years, although it remains difficult to attribute this success to particular genomic consequences of polyploidization, suggesting that polyploids harness the potential of genome duplication, at least partially, in lineage-specific ways. Overall, the present study clearly demonstrates that post-polyploidization reprogramming is more complex than traditionally reported in investigating single species and calls for a critical and comprehensive comparison across independently polyploidized lineages.
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Affiliation(s)
- Arnaud Bellec
- INRAE/CNRGV US 1258, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Mamadou Dia Sow
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Caroline Pont
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Peter Civan
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Emile Mardoc
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | | | - David Armisen
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Cécile Huneau
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Johanne Thévenin
- INRAE/AgroParisTech-UMR 1318. Bat 2. Centre INRA de Versailles, route de Saint Cyr, 78026, Versailles CEDEX, France
| | - Vanessa Vernoud
- INRAE/CNRS/ENS/Univ. Lyon-UMR 879, 46 allée d'Italie, 69364, Lyon Cedex 07, France
| | | | - Laurent Maunas
- Arvalis-Institut du végétal, 21 chemin de Pau, 64121 Montardon, France
| | - Brigitte Escale
- Arvalis-Institut du végétal, 21 chemin de Pau, 64121 Montardon, France
- Direction de l'agriculture de Polynésie française, Route de l'Hippodrome, 98713, Papeete, France
| | - Bertrand Dubreucq
- INRAE/AgroParisTech-UMR 1318. Bat 2. Centre INRA de Versailles, route de Saint Cyr, 78026, Versailles CEDEX, France
| | - Peter Rogowsky
- INRAE/CNRS/ENS/Univ. Lyon-UMR 879, 46 allée d'Italie, 69364, Lyon Cedex 07, France
| | - Hélène Bergès
- INRAE/CNRGV US 1258, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Jerome Salse
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
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Cauz-Santos LA, da Costa ZP, Callot C, Cauet S, Zucchi MI, Bergès H, van den Berg C, Vieira MLC. A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes. Genome Biol Evol 2021; 12:1841-1857. [PMID: 32722748 PMCID: PMC7586853 DOI: 10.1093/gbe/evaa155] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with ∼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in Passiflora capsularis and Passiflora costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.
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Affiliation(s)
- Luiz Augusto Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Maria Imaculada Zucchi
- Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, SP, Brazil
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Cássio van den Berg
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, BA, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
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3
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Blary A, Gonzalo A, Eber F, Bérard A, Bergès H, Bessoltane N, Charif D, Charpentier C, Cromer L, Fourment J, Genevriez C, Le Paslier MC, Lodé M, Lucas MO, Nesi N, Lloyd A, Chèvre AM, Jenczewski E. Corrigendum: FANCM Limits Meiotic Crossovers in Brassica Crops. Front Plant Sci 2020; 11:604728. [PMID: 33343604 PMCID: PMC7747853 DOI: 10.3389/fpls.2020.604728] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2018.00368.].
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Affiliation(s)
- Aurélien Blary
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Adrián Gonzalo
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Frédérique Eber
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Aurélie Bérard
- EPGV US 1279, Institut National de la Recherche Agronomique, CEA-IG-CNG, Université Paris-Saclay, Evry, France
| | - Hélène Bergès
- Institut National de la Recherche Agronomique UPR 1258, Centre National des Ressources Génomiques Végétales, Castanet-Tolosan, France
| | - Nadia Bessoltane
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Delphine Charif
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Catherine Charpentier
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Laurence Cromer
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Joelle Fourment
- Institut National de la Recherche Agronomique UPR 1258, Centre National des Ressources Génomiques Végétales, Castanet-Tolosan, France
| | - Camille Genevriez
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Marie-Christine Le Paslier
- EPGV US 1279, Institut National de la Recherche Agronomique, CEA-IG-CNG, Université Paris-Saclay, Evry, France
| | - Maryse Lodé
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Marie-Odile Lucas
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Nathalie Nesi
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Andrew Lloyd
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Anne-Marie Chèvre
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Eric Jenczewski
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
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4
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Abrouk M, Ahmed HI, Cubry P, Šimoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun 2020; 11:4488. [PMID: 32901040 DOI: 10.1101/2020.04.11.037671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/13/2020] [Accepted: 08/16/2020] [Indexed: 05/28/2023] Open
Abstract
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
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Affiliation(s)
- Michael Abrouk
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Yveline Pailles
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jan Bettgenhaeuser
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Liubov Gapa
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | | | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Hélène Bergès
- CNRGV Plant Genomics Center, INRAE, Toulouse, France
- Inari Agriculture, One Kendall Square Building 600/700, Cambridge, MA, 02139, USA
| | | | - Mathieu Gueye
- Laboratoire de Botanique, Département de Botanique et Géologie, IFAN Ch. A. Diop/UCAD, Dakar, Senegal
| | - Ndjido A Kane
- Senegalese Agricultural Research Institute, Dakar, Senegal
- Laboratoire Mixte International LAPSE, Dakar, Senegal
| | - Christian Leclerc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Causse
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sylvie Vancoppenolle
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Claire Billot
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | | | - Adeline Barnaud
- DIADE, Univ Montpellier, IRD, Montpellier, France.
- Laboratoire Mixte International LAPSE, Dakar, Senegal.
| | - Simon G Krattinger
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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5
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Abrouk M, Ahmed HI, Cubry P, Šimoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun 2020; 11:4488. [PMID: 32901040 PMCID: PMC7479619 DOI: 10.1038/s41467-020-18329-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/16/2020] [Indexed: 01/24/2023] Open
Abstract
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
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Affiliation(s)
- Michael Abrouk
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Yveline Pailles
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jan Bettgenhaeuser
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Liubov Gapa
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | | | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Hélène Bergès
- CNRGV Plant Genomics Center, INRAE, Toulouse, France
- Inari Agriculture, One Kendall Square Building 600/700, Cambridge, MA, 02139, USA
| | | | - Mathieu Gueye
- Laboratoire de Botanique, Département de Botanique et Géologie, IFAN Ch. A. Diop/UCAD, Dakar, Senegal
| | - Ndjido A Kane
- Senegalese Agricultural Research Institute, Dakar, Senegal
- Laboratoire Mixte International LAPSE, Dakar, Senegal
| | - Christian Leclerc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Causse
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sylvie Vancoppenolle
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Claire Billot
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | | | - Adeline Barnaud
- DIADE, Univ Montpellier, IRD, Montpellier, France.
- Laboratoire Mixte International LAPSE, Dakar, Senegal.
| | - Simon G Krattinger
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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6
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Sader MA, Dias Y, Costa ZP, Munhoz C, Penha H, Bergès H, Vieira MLC, Pedrosa-Harand A. Correction to: Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH. Chromosome Res 2020; 29:237-238. [PMID: 32430859 DOI: 10.1007/s10577-020-09633-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- M A Sader
- Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, Centro de Biociências, Universidade Federal de Pernambuco, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-901, Brazil
| | - Y Dias
- Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, Centro de Biociências, Universidade Federal de Pernambuco, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-901, Brazil
| | - Z P Costa
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - C Munhoz
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - H Penha
- Department of Technology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - H Bergès
- French Plant Genomic Resources Center (CNRGV)/INRA, Toulouse, France
| | - M L C Vieira
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - A Pedrosa-Harand
- Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, Centro de Biociências, Universidade Federal de Pernambuco, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-901, Brazil.
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7
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Munakata R, Kitajima S, Nuttens A, Tatsumi K, Takemura T, Ichino T, Galati G, Vautrin S, Bergès H, Grosjean J, Bourgaud F, Sugiyama A, Hehn A, Yazaki K. Convergent evolution of the UbiA prenyltransferase family underlies the independent acquisition of furanocoumarins in plants. New Phytol 2020; 225:2166-2182. [PMID: 31642055 PMCID: PMC7028039 DOI: 10.1111/nph.16277] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 07/21/2019] [Accepted: 10/09/2019] [Indexed: 05/03/2023]
Abstract
Furanocoumarins (FCs) are plant-specialized metabolites with potent allelochemical properties. The distribution of FCs is scattered with a chemotaxonomical tendency towards four distant families with highly similar FC pathways. The mechanism by which this pathway emerged and spread in plants has not been elucidated. Furanocoumarin biosynthesis was investigated in Ficus carica (fig, Moraceae), focusing on the first committed reaction catalysed by an umbelliferone dimethylallyltransferase (UDT). Comparative RNA-seq analysis among latexes of different fig organs led to the identification of a UDT. The phylogenetic relationship of this UDT to previously reported Apiaceae UDTs was evaluated. The expression pattern of F. carica prenyltransferase 1 (FcPT1) was related to the FC contents in different latexes. Enzymatic characterization demonstrated that one of the main functions of FcPT1 is UDT activity. Phylogenetic analysis suggested that FcPT1 and Apiaceae UDTs are derived from distinct ancestors, although they both belong to the UbiA superfamily. These findings are supported by significant differences in the related gene structures. This report describes the identification of FcPT1 involved in FC biosynthesis in fig and provides new insights into multiple origins of the FC pathway and, more broadly, into the adaptation of plants to their environments.
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Affiliation(s)
- Ryosuke Munakata
- Laboratory of Plant Gene ExpressionResearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto611‐0011Japan
- Université de LorraineINRA, LAEF54000NancyFrance
| | - Sakihito Kitajima
- Department of Applied BiologyKyoto Institute of TechnologyMatsugasaki Sakyo‐kuKyoto606‐8585Japan
- The Center for Advanced Insect Research PromotionKyoto Institute of TechnologyMatsugasaki Sakyo‐kuKyoto606‐8585Japan
| | | | - Kanade Tatsumi
- Laboratory of Plant Gene ExpressionResearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto611‐0011Japan
| | - Tomoya Takemura
- Laboratory of Plant Gene ExpressionResearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto611‐0011Japan
| | - Takuji Ichino
- Laboratory of Plant Gene ExpressionResearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto611‐0011Japan
| | | | - Sonia Vautrin
- Centre National de Ressources Genomiques Vegetales – INRA24 Chemin de Borde RougeAuzeville CS 5262731326Castanet Tolosan CedexFrance
| | - Hélène Bergès
- Centre National de Ressources Genomiques Vegetales – INRA24 Chemin de Borde RougeAuzeville CS 5262731326Castanet Tolosan CedexFrance
| | | | - Frédéric Bourgaud
- Plant Advanced Technologies – PAT19 Avenue de la forêt de Haye54500VandoeuvreFrance
| | - Akifumi Sugiyama
- Laboratory of Plant Gene ExpressionResearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto611‐0011Japan
| | - Alain Hehn
- Université de LorraineINRA, LAEF54000NancyFrance
| | - Kazufumi Yazaki
- Laboratory of Plant Gene ExpressionResearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto611‐0011Japan
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8
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Hufnagel B, Marques A, Soriano A, Marquès L, Divol F, Doumas P, Sallet E, Mancinotti D, Carrere S, Marande W, Arribat S, Keller J, Huneau C, Blein T, Aimé D, Laguerre M, Taylor J, Schubert V, Nelson M, Geu-Flores F, Crespi M, Gallardo K, Delaux PM, Salse J, Bergès H, Guyot R, Gouzy J, Péret B. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Nat Commun 2020; 11:492. [PMID: 31980615 PMCID: PMC6981116 DOI: 10.1038/s41467-019-14197-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 09/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield. White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
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Affiliation(s)
- Bárbara Hufnagel
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - André Marques
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France.,MPIPZ, Cologne, Germany
| | | | - Laurence Marquès
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Fanchon Divol
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Patrick Doumas
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | | | | | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, Castanet Tolosan, France
| | | | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
| | | | - Malika Laguerre
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | | | | | | | | | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
| | | | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, Castanet Tolosan, France
| | | | | | - Romain Guyot
- IRD, Montpellier, France INRAE / 13 Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Benjamin Péret
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France.
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9
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Mareri L, Milc J, Laviano L, Buti M, Vautrin S, Cauet S, Mascagni F, Natali L, Cavallini A, Bergès H, Pecchioni N, Francia E. Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. 'Nure' and expression analysis. Plant Sci 2020; 290:110305. [PMID: 31779917 DOI: 10.1016/j.plantsci.2019.110305] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/18/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Resequencing in resistant cultivar 'Nure' and structural comparison with the same region of susceptible 'Morex' was performed in order to gain a better insight into barley Frost-resistance-H2 locus. Accurate annotation showed copy number variation (CNV) in the proximal part of the locus. In 'Nure', two exact copies of the HvCBF4-HvCBF2A region and one of the HvCBF4-HvCBF2B segment were observed, while in 'Morex' the corresponding region harboured a single HvCBF4-HvCBF2A (22 kb) segment. Abundance and diversity of repetitive element classes, gene function gain/losses, regulatory motifs and SNPs in gene sequences were identified. An expression study of key HvCBFs with/without CNV on selected genotypes contrasting for frost resistance and estimated HvCBF4-HvCBF2B copy number (2-10 copies) was also performed. Under light stimulus at warm temperature (23 °C), CNV of HvCBF2A and HvCBF4 correlated with their expression levels and reported frost resistance of genotypes; moreover, expression levels of HvCBF2A and HvCBF14 were strongly correlated (r = 0.908, p < 0.01). On the other hand, frost resistance correlated to HvCBF14 expression (r = 0.871, p < 0.01) only after cold induction (6°C) in the dark. A complex interplay of HvCBFs expression levels under different light/temperature stimuli is discussed in light of CNV and presence/number of regulatory elements that integrate different signal transduction pathways.
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Affiliation(s)
- Lavinia Mareri
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Justyna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Luca Laviano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Matteo Buti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Flavia Mascagni
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), S.S. 673, Km 25,200, Foggia, I-71122, Italy; Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Enrico Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy.
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10
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Milon N, Chantry-Darmon C, Satge C, Fustier MA, Cauet S, Moreau S, Callot C, Bellec A, Gabrieli T, Saïas L, Boutonnet A, Ginot F, Bergès H, Bancaud A. μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome. Nucleic Acids Res 2019; 47:8050-8060. [PMID: 31505675 PMCID: PMC6736094 DOI: 10.1093/nar/gkz632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/21/2018] [Revised: 06/25/2019] [Accepted: 07/20/2019] [Indexed: 12/27/2022] Open
Abstract
Cas9-assisted targeting of DNA fragments in complex genomes is viewed as an essential strategy to obtain high-quality and continuous sequence data. However, the purity of target loci selected by pulsed-field gel electrophoresis (PFGE) has so far been insufficient to assemble the sequence in one contig. Here, we describe the μLAS technology to capture and purify high molecular weight DNA. First, the technology is optimized to perform high sensitivity DNA profiling with a limit of detection of 20 fg/μl for 50 kb fragments and an analytical time of 50 min. Then, μLAS is operated to isolate a 31.5 kb locus cleaved by Cas9 in the genome of the plant Medicago truncatula. Target purification is validated on a Bacterial Artificial Chromosome plasmid, and subsequently carried out in whole genome with μLAS, PFGE or by combining these techniques. PacBio sequencing shows an enrichment factor of the target sequence of 84 with PFGE alone versus 892 by association of PFGE with μLAS. These performances allow us to sequence and assemble one contig of 29 441 bp with 99% sequence identity to the reference sequence.
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Affiliation(s)
- Nicolas Milon
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400, Toulouse, France.,Adelis Technologies, 478 Rue de la Découverte, 31670 Labège, France
| | - Céline Chantry-Darmon
- French Plant Genomic Resource Center, INRA-CNRGV, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Carine Satge
- French Plant Genomic Resource Center, INRA-CNRGV, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Margaux-Alison Fustier
- French Plant Genomic Resource Center, INRA-CNRGV, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Stephane Cauet
- French Plant Genomic Resource Center, INRA-CNRGV, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Sandra Moreau
- Laboratory of Plant-Microbe Interactions, INRA-LIPM, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Caroline Callot
- French Plant Genomic Resource Center, INRA-CNRGV, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Arnaud Bellec
- French Plant Genomic Resource Center, INRA-CNRGV, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Tslil Gabrieli
- School of Chemistry, Center of Nanoscience and Nanotechnology, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Laure Saïas
- Adelis Technologies, 478 Rue de la Découverte, 31670 Labège, France
| | - Audrey Boutonnet
- Adelis Technologies, 478 Rue de la Découverte, 31670 Labège, France
| | - Frédéric Ginot
- Adelis Technologies, 478 Rue de la Découverte, 31670 Labège, France
| | - Hélène Bergès
- French Plant Genomic Resource Center, INRA-CNRGV, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Aurélien Bancaud
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400, Toulouse, France
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11
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Duriez P, Vautrin S, Auriac MC, Bazerque J, Boniface MC, Callot C, Carrère S, Cauet S, Chabaud M, Gentou F, Lopez-Sendon M, Paris C, Pegot-Espagnet P, Rousseaux JC, Pérez-Vich B, Velasco L, Bergès H, Piquemal J, Muños S. A receptor-like kinase enhances sunflower resistance to Orobanche cumana. Nat Plants 2019; 5:1211-1215. [PMID: 31819219 DOI: 10.1038/s41477-019-0556-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 10/18/2019] [Indexed: 05/19/2023]
Abstract
Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that infects sunflower roots, causing yield losses. Here, by using a map-based cloning strategy, we identified HaOr7-a gene that confers resistance to O. cumana race F-which was found to encode a leucine-rich repeat receptor-like kinase. The complete HAOR7 protein is present in resistant lines of sunflower and prevents O. cumana from connecting to the vascular system of sunflower roots, whereas susceptible lines encode a truncated protein that lacks transmembrane and kinase domains.
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Affiliation(s)
- Pauline Duriez
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- Syngenta Seeds, Saint-Sauveur, France
| | | | | | - Julia Bazerque
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | | | | | | | - Mireille Chabaud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | | | | | | | | | | | | | | | | | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
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12
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Bachmann JA, Tedder A, Laenen B, Fracassetti M, Désamoré A, Lafon-Placette C, Steige KA, Callot C, Marande W, Neuffer B, Bergès H, Köhler C, Castric V, Slotte T. Genetic basis and timing of a major mating system shift in Capsella. New Phytol 2019; 224:505-517. [PMID: 31254395 DOI: 10.1111/nph.16035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 05/09/2019] [Accepted: 06/20/2019] [Indexed: 05/23/2023]
Abstract
A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.
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Affiliation(s)
- Jörg A Bachmann
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Andrew Tedder
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Benjamin Laenen
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Marco Fracassetti
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Aurélie Désamoré
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Clément Lafon-Placette
- Department of Plant Biology, Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, SE-750 07, Uppsala, Sweden
| | - Kim A Steige
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Caroline Callot
- Institut National de la Recherche Agronomique, UPR 1258, Centre National des Ressources Génomiques Végétales, 31326, Castanet-Tolosan, France
| | - William Marande
- Institut National de la Recherche Agronomique, UPR 1258, Centre National des Ressources Génomiques Végétales, 31326, Castanet-Tolosan, France
| | - Barbara Neuffer
- Department of Botany, University of Osnabruck, 49076, Osnabrück, Germany
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, UPR 1258, Centre National des Ressources Génomiques Végétales, 31326, Castanet-Tolosan, France
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, SE-750 07, Uppsala, Sweden
| | - Vincent Castric
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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13
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Sader MA, Dias Y, Costa ZP, Munhoz C, Penha H, Bergès H, Vieira MLC, Pedrosa-Harand A. Identification of passion fruit (Passiflora edulis) chromosomes using BAC-FISH. Chromosome Res 2019; 27:299-311. [PMID: 31321607 DOI: 10.1007/s10577-019-09614-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/13/2019] [Accepted: 07/05/2019] [Indexed: 12/11/2022]
Abstract
Passiflora edulis, the yellow passion fruit, is the main crop from the Passiflora genus, which comprises 525 species with its diversity center in South America. Genetic maps and a BAC (bacterial artificial chromosome) genomic library are available, but the nine chromosome pairs of similar size and morphology (2n = 18) hamper chromosome identification, leading to different proposed karyotypes. Thus, the aim of this study was to establish chromosome-specific markers for the yellow passion fruit using single-copy and repetitive sequences as probes in fluorescent in situ hybridizations (FISH) to allow chromosome identification and future integration with whole genome data. Thirty-six BAC clones harboring genes and three retrotransposons (Ty1-copy, Ty3-gypsy, and LINE) were selected. Twelve BACs exhibited a dispersed pattern similar to that revealed by retroelements, and one exhibited subtelomeric distribution. Twelve clones showed unique signals in terminal or subterminal regions of the chromosomes, allowing their genes to be anchored to six chromosome pairs that can be identified with single-copy markers. The markers developed herein will provide an important tool for genomic and evolutionary studies in the Passiflora genus.
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Affiliation(s)
- M A Sader
- Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Y Dias
- Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Z P Costa
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - C Munhoz
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - H Penha
- Department of Technology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - H Bergès
- French Plant Genomic Resources Center (CNRGV)/ INRA, Toulouse, France
| | - M L C Vieira
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Andrea Pedrosa-Harand
- Department of Botany, Federal University of Pernambuco, Recife, Brazil.
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-901, Brazil.
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14
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Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Muños S, Bendahmane A, Bergès H, Niebel A, Buitink J, Frugier F, Benhamed M, Crespi M, Gouzy J, Gamas P. Whole-genome landscape of Medicago truncatula symbiotic genes. Nat Plants 2018; 4:1017-1025. [PMID: 30397259 DOI: 10.1038/s41477-018-0286-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 09/21/2018] [Indexed: 05/07/2023]
Abstract
Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.
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Affiliation(s)
- Yann Pecrix
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Erika Sallet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Christine Lelandais-Brière
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Sandra Moreau
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Thomas Blein
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | | | - David Latrasse
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Mohamed Zouine
- GBF, Université de Toulouse, INPT, ENSAT, Castanet-Tolosan, France
| | - Margot Zahm
- GBF, Université de Toulouse, INPT, ENSAT, Castanet-Tolosan, France
| | | | | | - Carine Satgé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- CNRGV, INRA, Castanet-Tolosan, France
| | - Magali Perez
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | | | | | | | | | | | - Aurélie Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - Frédéric Debellé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Abdelhafid Bendahmane
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | | | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Julia Buitink
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, Beaucouzé, France
| | - Florian Frugier
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Moussa Benhamed
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Martin Crespi
- IPS2, CNRS, INRA, Universities of Paris Diderot and Sorbonne Paris Cité, Gif sur Yvette, France
- IPS2, CNRS, INRA, Universities of Paris Diderot, Paris Sud, Evry and Paris-Saclay, Gif sur Yvette, France
| | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
| | - Pascal Gamas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France.
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15
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Munhoz CF, Costa ZP, Cauz-Santos LA, Reátegui ACE, Rodde N, Cauet S, Dornelas MC, Leroy P, Varani ADM, Bergès H, Vieira MLC. A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species. Sci Rep 2018; 8:13024. [PMID: 30158558 PMCID: PMC6115403 DOI: 10.1038/s41598-018-31330-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 04/23/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022] Open
Abstract
Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.
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Affiliation(s)
- Carla Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Zirlane Portugal Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Luiz Augusto Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Alina Carmen Egoávil Reátegui
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Nathalie Rodde
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Stéphane Cauet
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Marcelo Carnier Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brazil
| | - Philippe Leroy
- INRA, UCA, UMR 1095, GDEC, 63000, Clermont-Ferrand, France
| | - Alessandro de Mello Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, 14884-900, Jaboticabal, Brazil
| | - Hélène Bergès
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
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16
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Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan A, Van Sluys MA, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, van der Vossen E, Henry R, Schmutz J, D'Hont A. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nat Commun 2018; 9:2638. [PMID: 29980662 PMCID: PMC6035169 DOI: 10.1038/s41467-018-05051-5] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [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: 01/08/2018] [Accepted: 06/13/2018] [Indexed: 01/31/2023] Open
Abstract
Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.
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Affiliation(s)
- Olivier Garsmeur
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Gaetan Droc
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - Bernard Potier
- SASRI (South African Sugarcane Research Institute), Mount Edgecombe, 4300, South Africa
| | - Karen Aitken
- CSIRO (Commonwealth Scientific and Industrial Research Organisation), St. Lucia, QLD, 4067, Australia
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - Guillaume Martin
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Carine Charron
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Catherine Hervouet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Laurent Costet
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
| | - Nabila Yahiaoui
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - David Sims
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | | | | | - Andrzej Kilian
- Diversity Arrays Technology, Yarralumla, ACT, 2600, Australia
| | - Agnes Chan
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | | | | | - Hélène Bergès
- INRA-CNRGV, 31326, Toulouse, Castanet-Tolosan, France
| | - Blake Simmons
- JBEI Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jean Christophe Glaszmann
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | | | - Robert Henry
- QAAFI (Queensland Alliance for Agriculture and Food Innovation), University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA.,Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Angélique D'Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France. .,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France.
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17
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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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18
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Tsuchimatsu T, Goubet PM, Gallina S, Holl AC, Fobis-Loisy I, Bergès H, Marande W, Prat E, Meng D, Long Q, Platzer A, Nordborg M, Vekemans X, Castric V. Patterns of Polymorphism at the Self-Incompatibility Locus in 1,083 Arabidopsis thaliana Genomes. Mol Biol Evol 2018; 34:1878-1889. [PMID: 28379456 PMCID: PMC5850868 DOI: 10.1093/molbev/msx122] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 01/03/2023] Open
Abstract
Although the transition to selfing in the model plant Arabidopsis thaliana involved the loss of the self-incompatibility (SI) system, it clearly did not occur due to the fixation of a single inactivating mutation at the locus determining the specificities of SI (the S-locus). At least three groups of divergent haplotypes (haplogroups), corresponding to ancient functional S-alleles, have been maintained at this locus, and extensive functional studies have shown that all three carry distinct inactivating mutations. However, the historical process of loss of SI is not well understood, in particular its relation with the last glaciation. Here, we took advantage of recently published genomic resequencing data in 1,083 Arabidopsis thaliana accessions that we combined with BAC sequencing to obtain polymorphism information for the whole S-locus region at a species-wide scale. The accessions differed by several major rearrangements including large deletions and interhaplogroup recombinations, forming a set of haplogroups that are widely distributed throughout the native range and largely overlap geographically. “Relict” A. thaliana accessions that directly derive from glacial refugia are polymorphic at the S-locus, suggesting that the three haplogroups were already present when glacial refugia from the last Ice Age became isolated. Interhaplogroup recombinant haplotypes were highly frequent, and detailed analysis of recombination breakpoints suggested multiple independent origins. These findings suggest that the complete loss of SI in A. thaliana involved independent self-compatible mutants that arose prior to the last Ice Age, and experienced further rearrangements during postglacial colonization.
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Affiliation(s)
- Takashi Tsuchimatsu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.,Department of Biology, Chiba University, Inage-ku, Chiba, Japan
| | | | - Sophie Gallina
- Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France
| | | | - Isabelle Fobis-Loisy
- Reproduction et Développement des Plantes, Univ. Lyon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Claude Bernard Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - William Marande
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Elisa Prat
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Quan Long
- Department of Biochemistry and Molecular Biology & Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Alexander Platzer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Xavier Vekemans
- Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France
| | - Vincent Castric
- Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France
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19
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Blary A, Gonzalo A, Eber F, Bérard A, Bergès H, Bessoltane N, Charif D, Charpentier C, Cromer L, Fourment J, Genevriez C, Le Paslier MC, Lodé M, Lucas MO, Nesi N, Lloyd A, Chèvre AM, Jenczewski E. FANCM Limits Meiotic Crossovers in Brassica Crops. Front Plant Sci 2018; 9:368. [PMID: 29628933 PMCID: PMC5876677 DOI: 10.3389/fpls.2018.00368] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/06/2018] [Indexed: 05/18/2023]
Abstract
Meiotic crossovers (COs) are essential for proper chromosome segregation and the reshuffling of alleles during meiosis. In WT plants, the number of COs is usually small, which limits the genetic variation that can be captured by plant breeding programs. Part of this limitation is imposed by proteins like FANCM, the inactivation of which results in a 3-fold increase in COs in Arabidopsis thaliana. Whether the same holds true in crops needed to be established. In this study, we identified EMS induced mutations in FANCM in two species of economic relevance within the genus Brassica. We showed that CO frequencies were increased in fancm mutants in both diploid and tetraploid Brassicas, Brassica rapa and Brassica napus respectively. In B. rapa, we observed a 3-fold increase in the number of COs, equal to the increase observed previously in Arabidopsis. In B. napus we observed a lesser but consistent increase (1.3-fold) in both euploid (AACC) and allohaploid (AC) plants. Complementation tests in A. thaliana suggest that the smaller increase in crossover frequency observed in B. napus reflects residual activity of the mutant C copy of FANCM. Altogether our results indicate that the anti-CO activity of FANCM is conserved across the Brassica, opening new avenues to make a wider range of genetic diversity accessible to crop improvement.
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Affiliation(s)
- Aurélien Blary
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Adrián Gonzalo
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Frédérique Eber
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Aurélie Bérard
- EPGV US 1279, Institut National de la Recherche Agronomique, CEA-IG-CNG, Université Paris-Saclay, Evry, France
| | - Hélène Bergès
- Institut National de la Recherche Agronomique UPR 1258, Centre National des Ressources Génomiques Végétales, Castanet-Tolosan, France
| | - Nadia Bessoltane
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Delphine Charif
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Catherine Charpentier
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Laurence Cromer
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Joelle Fourment
- Institut National de la Recherche Agronomique UPR 1258, Centre National des Ressources Génomiques Végétales, Castanet-Tolosan, France
| | - Camille Genevriez
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Marie-Christine Le Paslier
- EPGV US 1279, Institut National de la Recherche Agronomique, CEA-IG-CNG, Université Paris-Saclay, Evry, France
| | - Maryse Lodé
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Marie-Odile Lucas
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Nathalie Nesi
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Andrew Lloyd
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Anne-Marie Chèvre
- IGEPP, Institut National de la Recherche Agronomique, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Eric Jenczewski
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National De La Recherche Scientifique, Université Paris-Saclay, Versailles, France
- *Correspondence: Eric Jenczewski
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20
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Gilles LM, Khaled A, Laffaire JB, Chaignon S, Gendrot G, Laplaige J, Bergès H, Beydon G, Bayle V, Barret P, Comadran J, Martinant JP, Rogowsky PM, Widiez T. Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maize. EMBO J 2017; 36:707-717. [PMID: 28228439 PMCID: PMC5350562 DOI: 10.15252/embj.201796603] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 12/27/2022] Open
Abstract
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
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Affiliation(s)
- Laurine M Gilles
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
- Limagrain Europe SAS, Research Centre, Chappes, France
| | - Abdelsabour Khaled
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
- Department of Genetics, Faculty of Agriculture, Sohag University, Sohag, Egypt
| | | | - Sandrine Chaignon
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Ghislaine Gendrot
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Jérôme Laplaige
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Hélène Bergès
- INRA, US1258 Centre National des Ressources Génomiques Végétales, Auzeville, France
| | - Genséric Beydon
- INRA, US1258 Centre National des Ressources Génomiques Végétales, Auzeville, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Pierre Barret
- INRA, UMR1095 Génétique, Diversité, Ecophysiologie des Céréales, Clermont-Ferrand, France
| | | | | | - Peter M Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
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21
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Roselli S, Olry A, Vautrin S, Coriton O, Ritchie D, Galati G, Navrot N, Krieger C, Vialart G, Bergès H, Bourgaud F, Hehn A. A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip. Plant J 2017; 89:1119-1132. [PMID: 27943460 DOI: 10.1111/tpj.13450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 02/29/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 05/06/2023]
Abstract
Furanocoumarins are specialized metabolites that are involved in the defense of plants against phytophagous insects. The molecular and functional characterization of the genes involved in their biosynthetic pathway is only partially complete. Many recent reports have described gene clusters responsible for the biosynthesis of specialized metabolites in plants. To investigate possible co-localization of the genes involved in the furanocoumarin pathway, we sequenced parsnip BAC clones spanning two different gene loci. We found that two genes previously identified in this pathway, CYP71AJ3 and CYP71AJ4, were located on the same BAC, whereas a third gene, PsPT1, belonged to a different BAC clone. Chromosome mapping using fluorescence in situ hybridization (FISH) indicated that PsPT1 and the CYP71AJ3-CYP71AJ4 clusters are located on two different chromosomes. Sequencing the BAC clone harboring PsPT1 led to the identification of a gene encoding an Fe(II) α-ketoglutarate-dependent dioxygenase (PsDIOX) situated in the neighborhood of PsPT1 and confirmed the occurrence of a second gene cluster involved in the furanocoumarin pathway. This enzyme metabolizes p-coumaroyl CoA, leading exclusively to the synthesis of umbelliferone, an important intermediate compound in furanocoumarin synthesis. This work provides an insight into the genomic organization of genes from the furanocoumarin biosynthesis pathway organized in more than one gene cluster. It also confirms that the screening of a genomic library and the sequencing of BAC clones represent a valuable tool to identify genes involved in biosynthetic pathways dedicated to specialized metabolite synthesis.
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Affiliation(s)
- Sandro Roselli
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alexandre Olry
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales - INRA - 24 Chemin de Borde Rouge - Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
| | - Olivier Coriton
- Plate-Forme de Cytogénétique Moléculaire - UMR1349 IGEPP INRA - Agrocampus Ouest-Université de Rennes 1, 35653, Le Rheu, France
| | - Dave Ritchie
- INRIA Nancy Grand Est, 615 rue du Jardin Botanique, 54600, Villers-lès-Nancy, France
| | - Gianni Galati
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Nicolas Navrot
- Institut de biologie moléculaire des plantes - UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer - 67084, Strasbourg Cedex, France
| | - Célia Krieger
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Guilhem Vialart
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales - INRA - 24 Chemin de Borde Rouge - Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
| | - Frédéric Bourgaud
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alain Hehn
- Laboratoire Agronomie et Environnement, INRA UMR1121, 2 avenue de la forêt de Haye TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- Laboratoire Agronomie et Environnement, Université de Lorraine UMR1121, 2 avenue de la forêt de Haye - TSA 40602, 54518, Vandœuvre-lès-Nancy, France
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22
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Cauz-Santos LA, Munhoz CF, Rodde N, Cauet S, Santos AA, Penha HA, Dornelas MC, Varani AM, Oliveira GCX, Bergès H, Vieira MLC. The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales. Front Plant Sci 2017; 8:334. [PMID: 28344587 PMCID: PMC5345083 DOI: 10.3389/fpls.2017.00334] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/27/2017] [Indexed: 05/20/2023]
Abstract
The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P. edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs, and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151, 3,765 and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.
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Affiliation(s)
- Luiz A. Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
| | - Carla F. Munhoz
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
| | - Nathalie Rodde
- Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-TolosanFrance
| | - Stephane Cauet
- Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-TolosanFrance
| | - Anselmo A. Santos
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
- FuturaGene Brasil Tecnologia Ltda., São PauloBrazil
| | - Helen A. Penha
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, JaboticabalBrazil
| | - Marcelo C. Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CampinasBrazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, JaboticabalBrazil
| | - Giancarlo C. X. Oliveira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-TolosanFrance
| | - Maria Lucia C. Vieira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, PiracicabaBrazil
- *Correspondence: Maria Lucia C. Vieira,
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23
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Hen-Avivi S, Savin O, Racovita RC, Lee WS, Adamski NM, Malitsky S, Almekias-Siegl E, Levy M, Vautrin S, Bergès H, Friedlander G, Kartvelishvily E, Ben-Zvi G, Alkan N, Uauy C, Kanyuka K, Jetter R, Distelfeld A, Aharoni A. A Metabolic Gene Cluster in the Wheat W1 and the Barley Cer-cqu Loci Determines β-Diketone Biosynthesis and Glaucousness. Plant Cell 2016; 28:1440-60. [PMID: 27225753 PMCID: PMC4944414 DOI: 10.1105/tpc.16.00197] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The glaucous appearance of wheat (Triticum aestivum) and barley (Hordeum vulgare) plants, that is the light bluish-gray look of flag leaf, stem, and spike surfaces, results from deposition of cuticular β-diketone wax on their surfaces; this phenotype is associated with high yield, especially under drought conditions. Despite extensive genetic and biochemical characterization, the molecular genetic basis underlying the biosynthesis of β-diketones remains unclear. Here, we discovered that the wheat W1 locus contains a metabolic gene cluster mediating β-diketone biosynthesis. The cluster comprises genes encoding proteins of several families including type-III polyketide synthases, hydrolases, and cytochrome P450s related to known fatty acid hydroxylases. The cluster region was identified in both genetic and physical maps of glaucous and glossy tetraploid wheat, demonstrating entirely different haplotypes in these accessions. Complementary evidence obtained through gene silencing in planta and heterologous expression in bacteria supports a model for a β-diketone biosynthesis pathway involving members of these three protein families. Mutations in homologous genes were identified in the barley eceriferum mutants defective in β-diketone biosynthesis, demonstrating a gene cluster also in the β-diketone biosynthesis Cer-cqu locus in barley. Hence, our findings open new opportunities to breed major cereal crops for surface features that impact yield and stress response.
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Affiliation(s)
- Shelly Hen-Avivi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Orna Savin
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Radu C Racovita
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Wing-Sham Lee
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Nikolai M Adamski
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Almekias-Siegl
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Matan Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sonia Vautrin
- INRA-Centre National de Ressources Génomiques Végétales, F-31326 Castanet Tolosan, France
| | - Hélène Bergès
- INRA-Centre National de Ressources Génomiques Végétales, F-31326 Castanet Tolosan, France
| | - Gilgi Friedlander
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elena Kartvelishvily
- Electron Microscopy Unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Kostya Kanyuka
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Reinhard Jetter
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada Department of Botany, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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24
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Ribeiro T, Barrela RM, Bergès H, Marques C, Loureiro J, Morais-Cecílio L, Paiva JAP. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes. Front Plant Sci 2016; 7:510. [PMID: 27148332 PMCID: PMC4840385 DOI: 10.3389/fpls.2016.00510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus.
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Affiliation(s)
- Teresa Ribeiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Ricardo M. Barrela
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques VégétalesCastanet-Tolosan, France
| | - Cristina Marques
- RAIZ, Instituto de Investigação da Floresta e PapelAveiro, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of CoimbraCoimbra, Portugal
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Jorge A. P. Paiva
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
- Department of Integrative Plant Biology, Instytut Genetyki Roślin, Polskiej Akademii NaukPoznań, Poland
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25
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Yousfi FE, Makhloufi E, Marande W, Ghorbel AW, Bouzayen M, Bergès H. Comparative Analysis of WRKY Genes Potentially Involved in Salt Stress Responses in Triticum turgidum L. ssp. durum. Front Plant Sci 2016; 7:2034. [PMID: 28197152 PMCID: PMC5281569 DOI: 10.3389/fpls.2016.02034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/20/2016] [Indexed: 05/06/2023]
Abstract
WRKY transcription factors are involved in multiple aspects of plant growth, development and responses to biotic stresses. Although they have been found to play roles in regulating plant responses to environmental stresses, these roles still need to be explored, especially those pertaining to crops. Durum wheat is the second most widely produced cereal in the world. Complex, large and unsequenced genomes, in addition to a lack of genomic resources, hinder the molecular characterization of tolerance mechanisms. This paper describes the isolation and characterization of five TdWRKY genes from durum wheat (Triticum turgidum L. ssp. durum). A PCR-based screening of a T. turgidum BAC genomic library using primers within the conserved region of WRKY genes resulted in the isolation of five BAC clones. Following sequencing fully the five BACs, fine annotation through Triannot pipeline revealed 74.6% of the entire sequences as transposable elements and a 3.2% gene content with genes organized as islands within oceans of TEs. Each BAC clone harbored a TdWRKY gene. The study showed a very extensive conservation of genomic structure between TdWRKYs and their orthologs from Brachypodium, barley, and T. aestivum. The structural features of TdWRKY proteins suggested that they are novel members of the WRKY family in durum wheat. TdWRKY1/2/4, TdWRKY3, and TdWRKY5 belong to the group Ia, IIa, and IIc, respectively. Enrichment of cis-regulatory elements related to stress responses in the promoters of some TdWRKY genes indicated their potential roles in mediating plant responses to a wide variety of environmental stresses. TdWRKY genes displayed different expression patterns in response to salt stress that distinguishes two durum wheat genotypes with contrasting salt stress tolerance phenotypes. TdWRKY genes tended to react earlier with a down-regulation in sensitive genotype leaves and with an up-regulation in tolerant genotype leaves. The TdWRKY transcripts levels in roots increased in tolerant genotype compared to sensitive genotype. The present results indicate that these genes might play some functional role in the salt tolerance in durum wheat.
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Affiliation(s)
- Fatma-Ezzahra Yousfi
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Borj Cedria Science and Technology ParkHammam-lif, Tunisia
- Centre National de Ressources Genomiques Vegetales, French Plant Genomic Center, INRA–CNRGVCastanet-Tolosan, France
- INRA, UMR990 Genomique et Biotechnologie des FruitsCastanet-Tolosan, France
| | - Emna Makhloufi
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Borj Cedria Science and Technology ParkHammam-lif, Tunisia
- Centre National de Ressources Genomiques Vegetales, French Plant Genomic Center, INRA–CNRGVCastanet-Tolosan, France
- INRA, UMR990 Genomique et Biotechnologie des FruitsCastanet-Tolosan, France
- INPT, Laboratoire de Genomique et Biotechnologie des Fruits, University of ToulouseCastanet-Tolosan, France
| | - William Marande
- Centre National de Ressources Genomiques Vegetales, French Plant Genomic Center, INRA–CNRGVCastanet-Tolosan, France
| | - Abdel W. Ghorbel
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Borj Cedria Science and Technology ParkHammam-lif, Tunisia
| | - Mondher Bouzayen
- INRA, UMR990 Genomique et Biotechnologie des FruitsCastanet-Tolosan, France
- INPT, Laboratoire de Genomique et Biotechnologie des Fruits, University of ToulouseCastanet-Tolosan, France
| | - Hélène Bergès
- Centre National de Ressources Genomiques Vegetales, French Plant Genomic Center, INRA–CNRGVCastanet-Tolosan, France
- *Correspondence: Hélène Bergès
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26
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Mago R, Zhang P, Vautrin S, Šimková H, Bansal U, Luo MC, Rouse M, Karaoglu H, Periyannan S, Kolmer J, Jin Y, Ayliffe MA, Bariana H, Park RF, McIntosh R, Doležel J, Bergès H, Spielmeyer W, Lagudah ES, Ellis JG, Dodds PN. The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus. Nat Plants 2015; 1:15186. [PMID: 27251721 DOI: 10.1038/nplants.2015.186] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 05/18/2023]
Abstract
We identify the wheat stem rust resistance gene Sr50 (using physical mapping, mutation and complementation) as homologous to barley Mla, encoding a coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) protein. We show that Sr50 confers a unique resistance specificity different from Sr31 and other genes on rye chromosome 1RS, and is effective against the broadly virulent Ug99 race lineage. Extensive haplotype diversity at the rye Sr50 locus holds promise for mining effective resistance genes.
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Affiliation(s)
- Rohit Mago
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Sonia Vautrin
- INRA - CNRGV, 24 Chemin de Borde Rouge - Auzeville, CS 52627, Castanet Tolosan Cedex 31326, France
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Urmil Bansal
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Matthew Rouse
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Haydar Karaoglu
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | | | - James Kolmer
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | - Yue Jin
- USDA, ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108, USA
| | | | - Harbans Bariana
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Robert F Park
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Robert McIntosh
- Plant Breeding Institute, The University of Sydney, Private Bag 4011, Narellan, New South Wales 2567, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc CZ-78371, Czech Republic
| | - Hélène Bergès
- INRA - CNRGV, 24 Chemin de Borde Rouge - Auzeville, CS 52627, Castanet Tolosan Cedex 31326, France
| | | | - Evans S Lagudah
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Jeff G Ellis
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Peter N Dodds
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
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27
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Akpinar BA, Magni F, Yuce M, Lucas SJ, Šimková H, Šafář J, Vautrin S, Bergès H, Cattonaro F, Doležel J, Budak H. The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements. BMC Genomics 2015; 16:453. [PMID: 26070810 PMCID: PMC4465308 DOI: 10.1186/s12864-015-1641-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 10/20/2014] [Accepted: 05/19/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The substantially large bread wheat genome, organized into highly similar three sub-genomes, renders genomic research challenging. The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. RESULTS The physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. Fifty-eight of the contigs were larger than 1 Mb, with the largest contig spanning 6,649 kb. A total of 1,864 molecular markers were assigned to the map at a density of 10.5 markers/Mb, anchoring 100 of the 120 contigs (>5 clones) that constitute ~95 % of the cumulative length of the map. Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. Analysis of the gene space of 5DS suggested an increasing gradient of genes organized in islands towards the telomere, with the highest gene density of 5.17 genes/Mb in the 0.67-0.78 deletion bin, 1.4 to 1.6 times that of all other bins. CONCLUSIONS Here, we provide a chromosome-specific view into the organization and evolution of the D genome of bread wheat, in comparison to one of its ancestors, revealing recent genome rearrangements. The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit.
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Affiliation(s)
- Bala Ani Akpinar
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Federica Magni
- Instituto di Genomica Applicata, Via J.Linussio 51, Udine, 33100, Italy.
| | - Meral Yuce
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Stuart J Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Sonia Vautrin
- Centre Nationales Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326, Castanet-Tolosan, France.
| | - Hélène Bergès
- Centre Nationales Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326, Castanet-Tolosan, France.
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J.Linussio 51, Udine, 33100, Italy.
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Hikmet Budak
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey.
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28
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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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29
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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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Durand E, Méheust R, Soucaze M, Goubet PM, Gallina S, Poux C, Fobis-Loisy I, Guillon E, Gaude T, Sarazin A, Figeac M, Prat E, Marande W, Bergès H, Vekemans X, Billiard S, Castric V. Dominance hierarchy arising from the evolution of a complex small RNA regulatory network. Science 2014; 346:1200-5. [PMID: 25477454 DOI: 10.1126/science.1259442] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The prevention of fertilization through self-pollination (or pollination by a close relative) in the Brassicaceae plant family is determined by the genotype of the plant at the self-incompatibility locus (S locus). The many alleles at this locus exhibit a dominance hierarchy that determines which of the two allelic specificities of a heterozygous genotype is expressed at the phenotypic level. Here, we uncover the evolution of how at least 17 small RNA (sRNA)-producing loci and their multiple target sites collectively control the dominance hierarchy among alleles within the gene controlling the pollen S-locus phenotype in a self-incompatible Arabidopsis species. Selection has created a dynamic repertoire of sRNA-target interactions by jointly acting on sRNA genes and their target sites, which has resulted in a complex system of regulation among alleles.
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Affiliation(s)
- Eléonore Durand
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Raphaël Méheust
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Marion Soucaze
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Pauline M Goubet
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Sophie Gallina
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Céline Poux
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Isabelle Fobis-Loisy
- Reproduction et Développement des Plantes, Institut Fédératif de Recherche 128, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Claude Bernard Lyon I, Ecole Normale Supérieure de Lyon, F-69364 Lyon, Cedex 07, France
| | - Eline Guillon
- Reproduction et Développement des Plantes, Institut Fédératif de Recherche 128, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Claude Bernard Lyon I, Ecole Normale Supérieure de Lyon, F-69364 Lyon, Cedex 07, France
| | - Thierry Gaude
- Reproduction et Développement des Plantes, Institut Fédératif de Recherche 128, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Claude Bernard Lyon I, Ecole Normale Supérieure de Lyon, F-69364 Lyon, Cedex 07, France
| | - Alexis Sarazin
- Department of Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Martin Figeac
- UDSL Université Lille 2 Droit et Santé, and Plate-forme de génomique fonctionnelle et structurale IFR-114, F-59000 Lille, France
| | - Elisa Prat
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - William Marande
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Xavier Vekemans
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Sylvain Billiard
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France
| | - Vincent Castric
- Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, F-59655 Villeneuve d'Ascq cedex, France.
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Makhloufi E, Yousfi FE, Marande W, Mila I, Hanana M, Bergès H, Mzid R, Bouzayen M. Isolation and molecular characterization of ERF1, an ethylene response factor gene from durum wheat (Triticum turgidum L. subsp. durum), potentially involved in salt-stress responses. J Exp Bot 2014; 65:6359-71. [PMID: 25205575 DOI: 10.1093/jxb/eru352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As food crop, wheat is of prime importance for human society. Nevertheless, our understanding of the genetic and molecular mechanisms controlling wheat productivity conditions has been, so far, hampered by the lack of sufficient genomic resources. The present work describes the isolation and characterization of TdERF1, an ERF gene from durum wheat (Triticum turgidum L. subsp. durum). The structural features of TdERF1 supported the hypothesis that it is a novel member of the ERF family in durum wheat and, considering its close similarity to TaERF1 of Triticum aestivum, it probably plays a similar role in mediating responses to environmental stresses. TdERF1 displayed an expression pattern that discriminated between two durum wheat genotypes contrasted with regard to salt-stress tolerance. The high number of cis-regulatory elements related to stress responses present in the TdERF1 promoter and the ability of TdERF1 to regulate the transcription of ethylene and drought-responsive promoters clearly indicated its potential role in mediating plant responses to a wide variety of environmental constrains. TdERF1 was also regulated by abscisic acid, ethylene, auxin, and salicylic acid, suggesting that it may be at the crossroads of multiple hormone signalling pathways. Four TdERF1 allelic variants have been identified in durum wheat genome, all shown to be transcriptionally active. Interestingly, the expression of one allelic form is specific to the tolerant genotype, further supporting the hypothesis that this gene is probably associated with the susceptibility/tolerance mechanism to salt stress. In this regard, the TdERF1 gene may provide a discriminating marker between tolerant and sensitive wheat varieties.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Chromosomes, Artificial, Bacterial/metabolism
- DNA, Complementary/genetics
- Droughts
- Ethylenes/metabolism
- Ethylenes/pharmacology
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant
- Genotype
- Molecular Sequence Annotation
- Molecular Sequence Data
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- Protein Transport/drug effects
- Salt Tolerance
- Sequence Alignment
- Sequence Analysis, DNA
- Sodium Chloride/pharmacology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Transcription, Genetic/drug effects
- Triticum/drug effects
- Triticum/genetics
- Triticum/physiology
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Affiliation(s)
- Emna Makhloufi
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Fatma-Ezzahra Yousfi
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - William Marande
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, 24 Chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan, France
| | - Isabelle Mila
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Mohsen Hanana
- Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, 24 Chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan, France
| | - Rim Mzid
- Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
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32
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Santos AA, Penha HA, Bellec A, Munhoz CDF, Pedrosa-Harand A, Bergès H, Vieira MLC. Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome. BMC Genomics 2014; 15:816. [PMID: 25260959 PMCID: PMC4189760 DOI: 10.1186/1471-2164-15-816] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 05/13/2014] [Accepted: 09/22/2014] [Indexed: 12/16/2022] Open
Abstract
Background The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. Results The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). Conclusions We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-816) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", P,O, Box 83, 13400-970 Piracicaba, Brazil.
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de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GMQ, Del Bem LE, Vicentini R, Nogueira FTS, Campos RA, Nunes SL, Turrini PCG, Vieira AP, Ochoa Cruz EA, Corrêa TCS, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY, Cardoso-Silva CB, Scortecci KC, Garcia AAF, Carneiro MS, Kim C, Paterson AH, Bergès H, D'Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics 2014; 15:540. [PMID: 24984568 PMCID: PMC4122759 DOI: 10.1186/1471-2164-15-540] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [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: 12/17/2013] [Accepted: 06/19/2014] [Indexed: 01/24/2023] Open
Abstract
Background Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marie-Anne Van Sluys
- Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil.
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Lloyd AH, Ranoux M, Vautrin S, Glover N, Fourment J, Charif D, Choulet F, Lassalle G, Marande W, Tran J, Granier F, Pingault L, Remay A, Marquis C, Belcram H, Chalhoub B, Feuillet C, Bergès H, Sourdille P, Jenczewski E. Meiotic Gene Evolution: Can You Teach a New Dog New Tricks? Mol Biol Evol 2014; 31:1724-7. [DOI: 10.1093/molbev/msu119] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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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Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simková H, Magni F, Cattonaro F, Vautrin S, Bergès H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Doležel J, Feuillet C, Korol A, Fahima T. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biol 2013; 14:R138. [PMID: 24359668 PMCID: PMC4053865 DOI: 10.1186/gb-2013-14-12-r138] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/20/2013] [Indexed: 11/16/2022] Open
Abstract
Background The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. Results Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere. Conclusions This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.
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Ferreira de Carvalho J, Chelaifa H, Boutte J, Poulain J, Couloux A, Wincker P, Bellec A, Fourment J, Bergès H, Salmon A, Ainouche M. Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis. Plant Mol Biol 2013; 83:591-606. [PMID: 23877482 DOI: 10.1007/s11103-013-0111-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/13/2013] [Indexed: 06/02/2023]
Abstract
Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91% of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67%). Non-LTR retrotransposons represent 0.75%, DNA transposons 0.99%, whereas small RNA, simple repeats and low-complexity sequences account for 1.38% of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1% of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6% of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family.
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Affiliation(s)
- J Ferreira de Carvalho
- UMR CNRS 6553 ECOBIO, OSUR, University of Rennes 1, Bât 14A Campus Scientifique de Beaulieu, 35042, Rennes Cedex, France
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Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Philippe R, Spielmeyer W, Šimková H, Šafář J, Cattonaro F, Scalabrin S, Magni F, Vautrin S, Bergès H, Paux E, Fahima T, Doležel J, Korol A, Feuillet C, Keller B. A physical map of the short arm of wheat chromosome 1A. PLoS One 2013; 8:e80272. [PMID: 24278269 PMCID: PMC3836966 DOI: 10.1371/journal.pone.0080272] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 05/08/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022] Open
Abstract
Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.
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Affiliation(s)
- James Breen
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | | | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Isabelle Bertin
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Romain Philippe
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | | | - Hana Šimková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | | | | | | | | | | | | | - Etienne Paux
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Catherine Feuillet
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail:
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Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Šimková H, Šafář J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KFX, Korol A, Bergès H, Doležel J, Feuillet C. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol 2013; 14:R64. [PMID: 23800011 PMCID: PMC4054855 DOI: 10.1186/gb-2013-14-6-r64] [Citation(s) in RCA: 41] [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: 03/05/2013] [Revised: 05/24/2013] [Accepted: 06/25/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. RESULTS Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. CONCLUSIONS Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
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Affiliation(s)
- Romain Philippe
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Etienne Paux
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Isabelle Bertin
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Fréderic Choulet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Christel Laugier
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Sonia Vautrin
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Federica Magni
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Simone Scalabrin
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | | | - Klaus FX Mayer
- MIPS/IBIS; Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Abraham Korol
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Catherine Feuillet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
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Bartoš J, Vlček Č, Choulet F, Džunková M, Cviková K, Šafář J, Šimková H, Pačes J, Strnad H, Sourdille P, Bergès H, Cattonaro F, Feuillet C, Doležel J. Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat. BMC Plant Biol 2012; 12:155. [PMID: 22935214 PMCID: PMC3445842 DOI: 10.1186/1471-2229-12-155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [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: 03/17/2012] [Accepted: 08/15/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functionalization leading to plant diversification, adaptation and speciation. In bread wheat, polyploidization and the prevalence of transposable elements resulted in massive gene duplication and movement. As a result, the number of genes which are non-collinear to genomes of related species seems markedly increased in wheat. RESULTS We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus. CONCLUSION Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.
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Affiliation(s)
- Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Vídeňská 1083, Praha, CZ-14220, Czech Republic
| | - Frédéric Choulet
- INRA University Blaise Pascal UMR 1095 Genetics Diversity Ecophysiology of Cereals, Clermont-Ferrand, F-63100, France
| | - Mária Džunková
- Institute of Molecular Genetics, Vídeňská 1083, Praha, CZ-14220, Czech Republic
| | - Kateřina Cviková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
| | - Jan Pačes
- Institute of Molecular Genetics, Vídeňská 1083, Praha, CZ-14220, Czech Republic
| | - Hynek Strnad
- Institute of Molecular Genetics, Vídeňská 1083, Praha, CZ-14220, Czech Republic
| | - Pierre Sourdille
- INRA University Blaise Pascal UMR 1095 Genetics Diversity Ecophysiology of Cereals, Clermont-Ferrand, F-63100, France
| | - Hélène Bergès
- INRA, National Resources Centre for Plant Genomics, Castanet Tolosan Cedex, F-31326, France
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Catherine Feuillet
- INRA University Blaise Pascal UMR 1095 Genetics Diversity Ecophysiology of Cereals, Clermont-Ferrand, F-63100, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
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Mounet F, Moing A, Kowalczyk M, Rohrmann J, Petit J, Garcia V, Maucourt M, Yano K, Deborde C, Aoki K, Bergès H, Granell A, Fernie AR, Bellini C, Rothan C, Lemaire-Chamley M. Down-regulation of a single auxin efflux transport protein in tomato induces precocious fruit development. J Exp Bot 2012; 63:4901-17. [PMID: 22844095 PMCID: PMC3427993 DOI: 10.1093/jxb/ers167] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The PIN-FORMED (PIN) auxin efflux transport protein family has been well characterized in the model plant Arabidopsis thaliana, where these proteins are crucial for auxin regulation of various aspects of plant development. Recent evidence indicates that PIN proteins may play a role in fruit set and early fruit development in tomato (Solanum lycopersicum), but functional analyses of PIN-silenced plants failed to corroborate this hypothesis. Here it is demonstrated that silencing specifically the tomato SlPIN4 gene, which is predominantly expressed in tomato flower bud and young developing fruit, leads to parthenocarpic fruits due to precocious fruit development before fertilization. This phenotype was associated with only slight modifications of auxin homeostasis at early stages of flower bud development and with minor alterations of ARF and Aux/IAA gene expression. However, microarray transcriptome analysis and large-scale quantitative RT-PCR profiling of transcription factors in developing flower bud and fruit highlighted differentially expressed regulatory genes, which are potential targets for auxin control of fruit set and development in tomato. In conclusion, this work provides clear evidence that the tomato PIN protein SlPIN4 plays a major role in auxin regulation of tomato fruit set, possibly by preventing precocious fruit development in the absence of pollination, and further gives new insights into the target genes involved in fruit set.
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Affiliation(s)
- Fabien Mounet
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Present address: UMR 5546, Laboratoire de Recherche en Sciences VégétalesF-31326 Castanet TolosanFrance
| | - Annick Moing
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA de BordeauxF-33140Villenave d’OrnonFrance
| | - Mariusz Kowalczyk
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå UniversitySE-90187 UmeåSweden
- Present address: Institute of Soil Science and Plant Cultivation, Department of Biochemistry and Crop Quality24100 PulawyPoland
| | - Johannes Rohrmann
- Max-Planck Institute for Molecular Plant PhysiologyAm Mühlenberg 1, D-14476 Potsdam-GolmGermany
| | - Johann Petit
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
| | - Virginie Garcia
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
| | - Mickaël Maucourt
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA de BordeauxF-33140Villenave d’OrnonFrance
| | - Kentaro Yano
- Meiji University1-1-1 Higashi-Mita, Tama-Ku, Kawasaki, 214-8571Japan
| | - Catherine Deborde
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Plateforme Métabolome du Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA de BordeauxF-33140Villenave d’OrnonFrance
| | - Koh Aoki
- Kazusa DNA Research Institute2-6-7 Kazusa-Kamatari, KisarazuJapan
- Present address: Osaka Prefecture University, Environmental and Life Sciences, 1-1 Gakuen-cho, Naka-ku, SakaiOsaka 599-8531Japan
| | - Hélène Bergès
- INRA-Centre National de Ressources Génomiques VégétalesF-31326 Castanet TolosanFrance
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC46022 ValenciaSpain
| | - Alisdair R. Fernie
- Max-Planck Institute for Molecular Plant PhysiologyAm Mühlenberg 1, D-14476 Potsdam-GolmGermany
| | - Catherine Bellini
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå UniversitySE-90187 UmeåSweden
- Institut Jean-Pierre Bourgin, UMR1318-INRA-AgroParisTech, INRA Centre of Versailles-GrignonF-78026 Versailles cedexFrance
| | - Christophe Rothan
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
| | - Martine Lemaire-Chamley
- INRA, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- Université de Bordeaux, UMR 1332 de Biologie du fruit et PathologieF-33140 Villenave d’OrnonFrance
- To whom correspondence should be addressed. 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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42
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Goubet PM, Bergès H, Bellec A, Prat E, Helmstetter N, Mangenot S, Gallina S, Holl AC, Fobis-Loisy I, Vekemans X, Castric V. Contrasted patterns of molecular evolution in dominant and recessive self-incompatibility haplotypes in Arabidopsis. PLoS Genet 2012; 8:e1002495. [PMID: 22457631 PMCID: PMC3310759 DOI: 10.1371/journal.pgen.1002495] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [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: 09/27/2011] [Accepted: 12/08/2011] [Indexed: 11/22/2022] Open
Abstract
Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae. Self-incompatibility is a common genetic system preventing selfing through recognition and rejection of self-pollen in hermaphroditic flowering plants. In the Brassicaceae family, this system is controlled by a single genomic region, called the S-locus, where many distinct specificities segregate in natural populations. In this study, we obtained genomic sequences comprising the S-locus in two closely related Brassicaceae species, Arabidopsis lyrata and A. halleri, and analyzed their diversity and patterns of molecular evolution. We report compelling evidence that the S-locus presents many similar properties with other genomic regions involved in the determination of mating-types in mammals, insects, plants, or fungi. In particular, in spite of their diversity, these genomic regions all show absence of similarity in intergenic sequences, large depth of genealogies, highly divergent organization, and accumulation of transposable elements. Moreover, some of these features were found to vary according to dominance of the S-locus specificities, suggesting that dominance/recessivity interactions are key drivers of the evolution of this genomic region.
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Affiliation(s)
- Pauline M. Goubet
- Laboratoire GEPV, CNRS FRE 3268, Univ Lille 1 – Univ Lille Nord de France, Cité Scientifique, Villeneuve d'Ascq, France
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Elisa Prat
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Nicolas Helmstetter
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, Castanet-Tolosan, France
| | - Sophie Mangenot
- Genoscope, Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant, Institut de Génomique, Genoscope, Evry, France
| | - Sophie Gallina
- Laboratoire GEPV, CNRS FRE 3268, Univ Lille 1 – Univ Lille Nord de France, Cité Scientifique, Villeneuve d'Ascq, France
| | - Anne-Catherine Holl
- Laboratoire GEPV, CNRS FRE 3268, Univ Lille 1 – Univ Lille Nord de France, Cité Scientifique, Villeneuve d'Ascq, France
| | - Isabelle Fobis-Loisy
- Reproduction et Développement des Plantes, Institut Fédératif de Recherche 128, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Claude Bernard Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Xavier Vekemans
- Laboratoire GEPV, CNRS FRE 3268, Univ Lille 1 – Univ Lille Nord de France, Cité Scientifique, Villeneuve d'Ascq, France
| | - Vincent Castric
- Laboratoire GEPV, CNRS FRE 3268, Univ Lille 1 – Univ Lille Nord de France, Cité Scientifique, Villeneuve d'Ascq, France
- * E-mail:
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Rustenholz C, Choulet F, Laugier C, Šafář J, Šimková H, Doležel J, Magni F, Scalabrin S, Cattonaro F, Vautrin S, Bellec A, Bergès H, Feuillet C, Paux E. A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant Physiol 2011; 157:1596-608. [PMID: 22034626 PMCID: PMC3327205 DOI: 10.1104/pp.111.183921] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
To improve our understanding of the organization and regulation of the wheat (Triticum aestivum) gene space, we established a transcription map of a wheat chromosome (3B) by hybridizing a newly developed wheat expression microarray with bacterial artificial chromosome pools from a new version of the 3B physical map as well as with cDNA probes derived from 15 RNA samples. Mapping data for almost 3,000 genes showed that the gene space spans the whole chromosome 3B with a 2-fold increase of gene density toward the telomeres due to an increase in the number of genes in islands. Comparative analyses with rice (Oryza sativa) and Brachypodium distachyon revealed that these gene islands are composed mainly of genes likely originating from interchromosomal gene duplications. Gene Ontology and expression profile analyses for the 3,000 genes located along the chromosome revealed that the gene islands are enriched significantly in genes sharing the same function or expression profile, thereby suggesting that genes in islands acquired shared regulation during evolution. Only a small fraction of these clusters of cofunctional and coexpressed genes was conserved with rice and B. distachyon, indicating a recent origin. Finally, genes with the same expression profiles in remote islands (coregulation islands) were identified suggesting long-distance regulation of gene expression along the chromosomes in wheat.
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MESH Headings
- Base Sequence
- Brachypodium/genetics
- Centromere/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Plant/genetics
- DNA, Intergenic/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Evolution, Molecular
- Gene Duplication
- Gene Expression Profiling
- Gene Expression Regulation, Plant/genetics
- Genes, Plant/genetics
- Genome, Plant/genetics
- Genomic Islands/genetics
- Genomic Islands/physiology
- Molecular Sequence Data
- Multigene Family
- Oligonucleotide Array Sequence Analysis
- Oryza/genetics
- Physical Chromosome Mapping/methods
- Polyploidy
- Sequence Analysis, DNA
- Telomere/genetics
- Transcriptome
- Triticum/genetics
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44
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Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KAT, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011; 480:520-4. [PMID: 22089132 PMCID: PMC3272368 DOI: 10.1038/nature10625] [Citation(s) in RCA: 762] [Impact Index Per Article: 58.6] [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: 06/13/2011] [Accepted: 10/13/2011] [Indexed: 11/09/2022]
Abstract
Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.
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Affiliation(s)
- Nevin D Young
- Department of Plant Pathology, University of Minnesota, St Paul, Minnesota 55108, USA.
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Faivre Rampant P, Lesur I, Boussardon C, Bitton F, Martin-Magniette ML, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C. Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome. BMC Genomics 2011; 12:292. [PMID: 21645357 PMCID: PMC3132169 DOI: 10.1186/1471-2164-12-292] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [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: 12/10/2010] [Accepted: 06/06/2011] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. RESULTS The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. CONCLUSIONS This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.
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46
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Paiva JAP, Prat E, Vautrin S, Santos MD, San-Clemente H, Brommonschenkel S, Fonseca PGS, Grattapaglia D, Song X, Ammiraju JSS, Kudrna D, Wing RA, Freitas AT, Bergès H, Grima-Pettenati J. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. BMC Genomics 2011; 12:137. [PMID: 21375742 PMCID: PMC3060884 DOI: 10.1186/1471-2164-12-137] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [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: 06/01/2010] [Accepted: 03/04/2011] [Indexed: 11/10/2022] Open
Abstract
Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1) digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (E. grandis BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming Eucalyptus reference genome sequence.
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Affiliation(s)
- Jorge A P Paiva
- Instituto de Investigação Científica Tropical, Centro de Florestas e dos Produtos Florestais, Tapada da Ajuda, 1349-018 Lisboa, Portugal.
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Gonthier L, Bellec A, Blassiau C, Prat E, Helmstetter N, Rambaud C, Huss B, Hendriks T, Bergès H, Quillet MC. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae). BMC Res Notes 2010; 3:225. [PMID: 20701751 PMCID: PMC2933585 DOI: 10.1186/1756-0500-3-225] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [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: 06/08/2010] [Accepted: 08/11/2010] [Indexed: 11/19/2022] Open
Abstract
Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species.
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Affiliation(s)
- Lucy Gonthier
- Univ Lille Nord de France, F-59000 Lille, France, Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), UMR INRA-USTL 1281, Bât, SN2, F-59655 Villeneuve d'Ascq, France.
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Auger B, Baron C, Lucas MO, Vautrin S, Bergès H, Chalhoub B, Fautrel A, Renard M, Nesi N. Brassica orthologs from BANYULS belong to a small multigene family, which is involved in procyanidin accumulation in the seed. Planta 2009; 230:1167-83. [PMID: 19760260 PMCID: PMC2764081 DOI: 10.1007/s00425-009-1017-0] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 09/03/2009] [Indexed: 05/03/2023]
Abstract
As part of a research programme focused on flavonoid biosynthesis in the seed coat of Brassica napus L. (oilseed rape), orthologs of the BANYULS gene that encoded anthocyanidin reductase were cloned in B. napus as well as in the related species Brassica rapa and Brassica oleracea. B. napus genome contained four functional copies of BAN, two originating from each diploid progenitor. Amino acid sequences were highly conserved between the Brassicaceae including B. napus, B. rapa, B. oleracea as well as the model plant Arabidopsis thaliana. Along the 200 bp in 5' of the ATG codon, Bna.BAN promoters (ProBna.BAN) were conserved with AtANR promoter and contained putative cis-acting elements. In addition, transgenic Arabidopsis and oilseed rape plants carrying the first 230 bp of ProBna.BAN fused to the UidA reporter gene were generated. In the two Brassicaceae backgrounds, ProBna.BAN activity was restricted to the seed coat. In B. napus seed, ProBna.BAN was activated in procyanidin-accumulating cells, namely the innermost layer of the inner integument and the micropyle-chalaza area. At the transcriptional level, the four Bna.BAN genes were expressed in the seed. Laser microdissection assays of the seed integuments showed that Bna.BAN expression was restricted to the inner integument, which was consistent with the activation profile of ProBna.BAN. Finally, Bna.BAN genes were mapped onto oilseed rape genetic maps and potential co-localisations with seed colour quantitative trait loci are discussed.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Base Sequence
- Biflavonoids/metabolism
- Brassica/enzymology
- Brassica/genetics
- Brassica/metabolism
- Brassica napus/enzymology
- Brassica napus/genetics
- Brassica napus/metabolism
- Brassica rapa/enzymology
- Brassica rapa/genetics
- Brassica rapa/metabolism
- Catechin/metabolism
- Chromosome Mapping
- Chromosomes, Plant/genetics
- Gene Expression Profiling
- Genome, Plant
- Glucuronidase/genetics
- Glucuronidase/metabolism
- Molecular Sequence Data
- Multigene Family
- NADH, NADPH Oxidoreductases/classification
- NADH, NADPH Oxidoreductases/genetics
- NADH, NADPH Oxidoreductases/metabolism
- Phylogeny
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified
- Proanthocyanidins/metabolism
- Promoter Regions, Genetic/genetics
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Seeds/genetics
- Seeds/metabolism
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Bathilde Auger
- UMR118 Amélioration des Plantes et Biotechnologies Végétales, INRA, Agrocampus Ouest, Université Rennes1, BP 35327, 35653 Le Rheu Cedex, France
| | - Cécile Baron
- UMR118 Amélioration des Plantes et Biotechnologies Végétales, INRA, Agrocampus Ouest, Université Rennes1, BP 35327, 35653 Le Rheu Cedex, France
| | - Marie-Odile Lucas
- UMR118 Amélioration des Plantes et Biotechnologies Végétales, INRA, Agrocampus Ouest, Université Rennes1, BP 35327, 35653 Le Rheu Cedex, France
| | - Sonia Vautrin
- Centre National de Ressources en Génomique Végétale (CNRGV), INRA, Chemin de Borde Rouge, BP 52627, 31326 Castanet Tolosan, France
| | - Hélène Bergès
- Centre National de Ressources en Génomique Végétale (CNRGV), INRA, Chemin de Borde Rouge, BP 52627, 31326 Castanet Tolosan, France
| | - Boulos Chalhoub
- UMR1165 Unité de Recherche en Génomique Végétale, INRA, CNRS, Université d’Evry, 2 rue Gaston Crémieux, CP 5708, 91057 Evry Cedex, France
| | - Alain Fautrel
- IFR140 Biogenouest Plate-forme d’Histopathologie, U620 INSERM, Université Rennes1, 35043 Rennes Cedex, France
| | - Michel Renard
- UMR118 Amélioration des Plantes et Biotechnologies Végétales, INRA, Agrocampus Ouest, Université Rennes1, BP 35327, 35653 Le Rheu Cedex, France
| | - Nathalie Nesi
- UMR118 Amélioration des Plantes et Biotechnologies Végétales, INRA, Agrocampus Ouest, Université Rennes1, BP 35327, 35653 Le Rheu Cedex, France
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49
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Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Bergès H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C. A physical map of the 1-gigabase bread wheat chromosome 3B. Science 2008; 322:101-4. [PMID: 18832645 DOI: 10.1126/science.1161847] [Citation(s) in RCA: 322] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As the staple food for 35% of the world's population, wheat is one of the most important crop species. To date, sequence-based tools to accelerate wheat improvement are lacking. As part of the international effort to sequence the 17-billion-base-pair hexaploid bread wheat genome (2n = 6x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)-based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs that were anchored with 1443 molecular markers, providing a major resource for genetic and genomic studies. This physical map establishes a template for the remaining wheat chromosomes and demonstrates the feasibility of constructing physical maps in large, complex, polyploid genomes with a chromosome-based approach.
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Affiliation(s)
- Etienne Paux
- Institut National de la Recherche Agronomique, Université Blaise Pascal (INRA-UBP), UMR 1095, Genetics Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
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50
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Davalos M, Fourment J, Lucas A, Bergès H, Kahn D. Nitrogen regulation inSinorhizobium melilotiprobed with whole genome arrays. FEMS Microbiol Lett 2004; 241:33-40. [PMID: 15556707 DOI: 10.1016/j.femsle.2004.09.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 07/21/2004] [Revised: 09/09/2004] [Accepted: 09/29/2004] [Indexed: 11/19/2022] Open
Abstract
Using whole genome arrays, we systematically investigated nitrogen regulation in the plant symbiotic bacterium Sinorhizobium meliloti. The use of glutamate instead of ammonium as a nitrogen source induced nitrogen catabolic genes independently of the carbon source, including two glutamine synthetase genes, various aminoacid transporters and the glnKamtB operon. These responses depended on both the ntrC and glnB nitrogen regulators. Glutamate repressible genes included glutamate synthase and a H+-translocating pyrophosphate synthase. The smc01041-ntrBC operon was negatively autoregulated in a glnB-dependent fashion, indicating an involvement of phosphorylated NtrC. In addition to the nitrogen response, glutamate remodelled expression of carbon metabolism by inhibiting expression of the Entner-Doudoroff and pentose phosphate pathways, and by stimulating gluconeogenetic genes independently of ntrC.
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Affiliation(s)
- Marcela Davalos
- Laboratoire des Interactions Plantes-Microorganismes, UMR 2594 INRA-CNRS, Chemin de Borde-Rouge, BP 27, 31326 Castanet-Tolosan Cedex, France
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