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Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, Wang C, Rajaraman S, Rastas P, Zheng C, Muñoz DS, Meidanis J, Paschoal AR, Bawin Y, Krabbenhoft TJ, Wang ZQ, Fleck SJ, Aussel R, Bellanger L, Charpagne A, Fournier C, Kassam M, Lefebvre G, Métairon S, Moine D, Rigoreau M, Stolte J, Hamon P, Couturon E, Tranchant-Dubreuil C, Mukherjee M, Lan T, Engelhardt J, Stadler P, Correia De Lemos SM, Suzuki SI, Sumirat U, Wai CM, Dauchot N, Orozco-Arias S, Garavito A, Kiwuka C, Musoli P, Nalukenge A, Guichoux E, Reinout H, Smit M, Carretero-Paulet L, Filho OG, Braghini MT, Padilha L, Sera GH, Ruttink T, Henry R, Marraccini P, Van de Peer Y, Andrade A, Domingues D, Giuliano G, Mueller L, Pereira LF, Plaisance S, Poncet V, Rombauts S, Sankoff D, Albert VA, Crouzillat D, de Kochko A, Descombes P. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 2024; 56:721-731. [PMID: 38622339 PMCID: PMC11018527 DOI: 10.1038/s41588-024-01695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
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Affiliation(s)
- Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Aditi Rambani
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Zhe Yu
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Susan Strickler
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Maud Lepelley
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Cui Wang
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniella Santos Muñoz
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - João Meidanis
- Institute of Computing, University of Campinas, Campinas, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, The Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Yves Bawin
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Zhen Qin Wang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Rudy Aussel
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille, France
| | | | - Aline Charpagne
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Coralie Fournier
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Mohamed Kassam
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Gregory Lefebvre
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Sylviane Métairon
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Déborah Moine
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Michel Rigoreau
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Jens Stolte
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Perla Hamon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Emmanuel Couturon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | | | - Minakshi Mukherjee
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jan Engelhardt
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Peter Stadler
- Department of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | | | | | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia
| | - Ching Man Wai
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicolas Dauchot
- Research Unit in Plant Cellular and Molecular Biology, University of Namur, Namur, Belgium
| | - Simon Orozco-Arias
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Andrea Garavito
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Catherine Kiwuka
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Pascal Musoli
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Anne Nalukenge
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Erwan Guichoux
- Biodiversité Gènes & Communautés, INRA, Bordeaux, France
| | | | - Martin Smit
- Hortus Botanicus Amsterdam, Amsterdam, the Netherlands
| | | | - Oliveiro Guerreiro Filho
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Masako Toma Braghini
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Lilian Padilha
- Embrapa Café/Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Pierre Marraccini
- CIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501, Montpellier, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Alan Andrade
- Embrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG, Lavras, Brazil
| | - Douglas Domingues
- Group of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Rome, Italy
| | - Lukas Mueller
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Luiz Filipe Pereira
- Embrapa Café/Lab. Biotecnologia, Área de Melhoramento Genético, Londrina, Brazil
| | | | - Valerie Poncet
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | | | - Alexandre de Kochko
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
| | - Patrick Descombes
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
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Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, Parrinello H, Kiwuka C, Sumirat U, Legnate H, Kambale JL, Sonké B, Mahinga JC, Musoli P, Janssens SB, Stoffelen P, de Kochko A, Poncet V. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). Glob Chang Biol 2022; 28:4124-4142. [PMID: 35527235 DOI: 10.1111/gcb.16191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/26/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species' native range can provide valuable insights about habitat loss and the species' adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole-genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.
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Affiliation(s)
- Rémi Tournebize
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Leyli Borner
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- INRAE, Le Rheu, France
| | - Stéphanie Manel
- CEFE, CNRS, EPHE-PSL University, IRD, Univ Montpellier, Montpellier, France
| | - Christine N Meynard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Yves Vigouroux
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
| | | | - Coralie Fournier
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- School of Medicine, University of Geneva, Geneva, Switzerland
| | - Mohamed Kassam
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- Danone Nutricia Research, Singapore
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
| | | | - Hugues Parrinello
- CNRS, INSERM, Univ. Montpellier, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | | | | | - Jean-Léon Kambale
- University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | | | | | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Valérie Poncet
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
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de Aquino SO, Kiwuka C, Tournebize R, Gain C, Marraccini P, Mariac C, Bethune K, Couderc M, Cubry P, Andrade AC, Lepelley M, Darracq O, Crouzillat D, Anten N, Musoli P, Vigouroux Y, de Kochko A, Manel S, François O, Poncet V. Adaptive potential of
Coffea canephora
from Uganda in response to climate change. Mol Ecol 2022; 31:1800-1819. [DOI: 10.1111/mec.16360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
| | - Catherine Kiwuka
- NARO Kampala Uganda
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | - Clément Gain
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
| | | | - Cédric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Kévin Bethune
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Marie Couderc
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | | | | | | | | | | | - Niels Anten
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD Montpellier France
| | - Olivier François
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
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4
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Merot‐L'anthoene V, Tournebize R, Darracq O, Rattina V, Lepelley M, Bellanger L, Tranchant‐Dubreuil C, Coulée M, Pégard M, Metairon S, Fournier C, Stoffelen P, Janssens SB, Kiwuka C, Musoli P, Sumirat U, Legnaté H, Kambale J, Ferreira da Costa Neto J, Revel C, de Kochko A, Descombes P, Crouzillat D, Poncet V. Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L. Plant Biotechnol J 2019; 17:1418-1430. [PMID: 30582651 PMCID: PMC6576098 DOI: 10.1111/pbi.13066] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
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de Castro Nunes R, Orozco-Arias S, Crouzillat D, Mueller LA, Strickler SR, Descombes P, Fournier C, Moine D, de Kochko A, Yuyama PM, Vanzela ALL, Guyot R. Structure and Distribution of Centromeric Retrotransposons at Diploid and Allotetraploid Coffea Centromeric and Pericentromeric Regions. Front Plant Sci 2018; 9:175. [PMID: 29497436 PMCID: PMC5818461 DOI: 10.3389/fpls.2018.00175] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/30/2018] [Indexed: 05/18/2023]
Abstract
Centromeric regions of plants are generally composed of large array of satellites from a specific lineage of Gypsy LTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a crucial function on kinetochore formation. To study the structure and composition of centromeric regions in the genus Coffea, we annotated and classified Centromeric Retrotransposons sequences from the allotetraploid C. arabica genome and its two diploid ancestors: Coffea canephora and C. eugenioides. Ten distinct CRC (Centromeric Retrotransposons in Coffea) families were found. The sequence mapping and FISH experiments of CRC Reverse Transcriptase domains in C. canephora, C. eugenioides, and C. arabica clearly indicate a strong and specific targeting mainly onto proximal chromosome regions, which can be associated also with heterochromatin. PacBio genome sequence analyses of putative centromeric regions on C. arabica and C. canephora chromosomes showed an exceptional density of one family of CRC elements, and the complete absence of satellite arrays, contrasting with usual structure of plant centromeres. Altogether, our data suggest a specific centromere organization in Coffea, contrasting with other plant genomes.
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Affiliation(s)
- Renata de Castro Nunes
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Simon Orozco-Arias
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Colombia
| | | | - Lukas A. Mueller
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Suzy R. Strickler
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | | | | | - Deborah Moine
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Alexandre de Kochko
- Institut de Recherche pour le Développement, UMR DIADE, EvoGec, Montpellier, France
| | - Priscila M. Yuyama
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Brazil
| | - André L. L. Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Brazil
- *Correspondence: André L. L. Vanzela
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Colombia
- Institut de Recherche pour le Développement, CIRAD, Univ. Montpellier, UMR IPME, Montpellier, France
- Romain Guyot
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6
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Tournebize R, Manel S, Vigouroux Y, Munoz F, de Kochko A, Poncet V. Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda. PLoS One 2017; 12:e0183412. [PMID: 28820899 PMCID: PMC5562301 DOI: 10.1371/journal.pone.0183412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 04/29/2017] [Accepted: 08/03/2017] [Indexed: 12/04/2022] Open
Abstract
Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population has remained stable. Recent asymmetric gene flow between the groups further contributed to the phylogeographical pattern. Spatially explicit coalescent modelling allowed us to estimate the location of ancestral populations with good accuracy (< 22 km) and provided indications regarding the mid-elevation pathways that facilitated post-glacial expansion.
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Affiliation(s)
- Rémi Tournebize
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
| | - Stéphanie Manel
- UMR CEFE, Ecole Pratique des Hautes Etudes, PSL Research University, CNRS, University of Montpellier, Montpellier SupAgro, IRD, INRA, Montpellier, France
| | - Yves Vigouroux
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
| | - François Munoz
- UMR AMAP, University of Montpellier, Montpellier, France
- French Institute of Pondicherry, Pondicherry, India
| | - Alexandre de Kochko
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
| | - Valérie Poncet
- UMR DIADE, Institut de Recherche pour le développement, University of Montpellier, Montpellier, France
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7
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Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 2017; 109:351-361. [PMID: 28212875 DOI: 10.1016/j.ympev.2017.02.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 08/08/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.
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Affiliation(s)
- Perla Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom.
| | | | | | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | - Hosahalli L Sreenath
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570006, India.
| | - Piet Stoffelen
- Herbarium Plantentuin Meise, Nieuwelaan 38, 1860 Meise, Belgium.
| | - Sharon E Mitchell
- Cornell University, Institute of Biotechnology, Genomic Diversity Facility, Ithaca, NY, USA.
| | | | - Serge Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | | | | | - Michel Rigoreau
- Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France.
| | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute Jl. PB Sudirman 90, Jember 68118, Indonesia.
| | | | - Romain Guyot
- UMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
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8
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Guyot R, Darré T, Dupeyron M, de Kochko A, Hamon S, Couturon E, Crouzillat D, Rigoreau M, Rakotomalala JJ, Raharimalala NE, Akaffou SD, Hamon P. Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories. Mol Genet Genomics 2016; 291:1979-90. [PMID: 27469896 DOI: 10.1007/s00438-016-1235-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.
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Affiliation(s)
- Romain Guyot
- IRD UMR IPME, CoffeeAdapt, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Thibaud Darré
- IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France
| | | | | | - Serge Hamon
- IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France
| | | | - Dominique Crouzillat
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oe ́, BP 49716, 37097, Tours Cedex 2, France
| | - Michel Rigoreau
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oe ́, BP 49716, 37097, Tours Cedex 2, France
| | | | | | | | - Perla Hamon
- IRD UMR DIADE, EvoGeC, BP 64501, 34394, Montpellier Cedex 5, France
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9
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Gomez C, Despinoy M, Hamon S, Hamon P, Salmon D, Akaffou DS, Legnate H, de Kochko A, Mangeas M, Poncet V. Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species. Ecol Evol 2016; 6:3240-55. [PMID: 27096083 PMCID: PMC4829533 DOI: 10.1002/ece3.2055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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] [Received: 11/13/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 11/06/2022] Open
Abstract
The frequency of plant species introductions has increased in a highly connected world, modifying species distribution patterns to include areas outside their natural ranges. These introductions provide the opportunity to gain new insight into the importance of flowering phenology as a component of adaptation to a new environment. Three Coffea species, C. arabica, C. canephora (Robusta), and C. liberica, native to intertropical Africa have been introduced to New Caledonia. On this archipelago, a secondary contact zone has been characterized where these species coexist, persist, and hybridize spontaneously. We investigated the impact of environmental changes undergone by each species following its introduction in New Caledonia on flowering phenology and overcoming reproductive barriers between sister species. We developed species distribution models and compared both environmental envelopes and climatic niches between native and introduced hybrid zones. Flowering phenology was monitored in a population in the hybrid zone along with temperature and precipitation sequences recorded at a nearby weather station. The extent and nature of hybridization events were characterized using chloroplast and nuclear microsatellite markers. The three Coffea species encountered weak environmental suitability compared to their native ranges when introduced to New Caledonia, especially C. arabica and C. canephora. The niche of the New Caledonia hybrid zone was significantly different from all three species' native niches based on identity tests (I Similarity and D Schoener's Similarity Indexes). This area appeared to exhibit intermediate conditions between the native conditions of the three species for temperature-related variables and divergent conditions for precipitation-related ones. Flowering pattern in these Coffea species was shown to have a strong genetic component that determined the time between the triggering rain and anthesis (flower opening), specific to each species. However, a precipitation regime different from those in Africa was directly involved in generating partial flowering overlap between species and thus in allowing hybridization and interspecific gene flow. Interspecific hybrids accounted for 4% of the mature individuals in the sympatric population and occurred between each pair of species with various level of introgression. Adaptation to new environmental conditions following introduction of Coffea species to New Caledonia has resulted in a secondary contact between three related species, which would not have happened in their native ranges, leading to hybridization and gene flow.
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Affiliation(s)
- Céline Gomez
- IRDUMR DIADEBP 6450134394Montpellier Cedex 5France
| | - Marc Despinoy
- IRDUMR ESPACE DEV (S140)BP A598848Cedex NouméaNouvelle Calédonie
| | - Serge Hamon
- IRDUMR DIADEBP 6450134394Montpellier Cedex 5France
| | - Perla Hamon
- IRDUMR DIADEBP 6450134394Montpellier Cedex 5France
| | | | | | | | | | - Morgan Mangeas
- IRDUMR ESPACE DEV (S140)BP A598848Cedex NouméaNouvelle Calédonie
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10
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Dias ES, Hatt C, Hamon S, Hamon P, Rigoreau M, Crouzillat D, Carareto CMA, de Kochko A, Guyot R. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families. Plant Mol Biol 2015; 89:83-97. [PMID: 26245353 DOI: 10.1007/s11103-015-0352-8] [Citation(s) in RCA: 9] [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: 02/20/2015] [Accepted: 07/28/2015] [Indexed: 06/04/2023]
Abstract
Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer.
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Affiliation(s)
- Elaine Silva Dias
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
- Department of Biology, UNESP-Univ. Estadual Paulista, São José do Rio Preto, Araraquara, SP, Brazil.
| | - Clémence Hatt
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Serge Hamon
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Perla Hamon
- IRD UMR DIADE, EVODYN, BP 64501, 34394, Montpellier Cedex 5, France.
| | - Michel Rigoreau
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France.
| | - Dominique Crouzillat
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France.
| | | | | | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394, Montpellier Cedex 5, France.
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11
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Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D. The Amborella vacuolar processing enzyme family. Front Plant Sci 2015; 6:618. [PMID: 26347753 PMCID: PMC4544213 DOI: 10.3389/fpls.2015.00618] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/27/2015] [Indexed: 05/30/2023]
Abstract
Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.
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Affiliation(s)
- Valérie Poncet
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Charlie Scutt
- Laboratoire Reproduction et Développement des Plantes, UMR 5667, Ecole Normale Supérieure de LyonLyon, France
| | - Rémi Tournebize
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Matthieu Villegente
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
| | - Gwendal Cueff
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, UMR 1318 Institut National de la Recherche Agronomique/AgroParisTech, ERL Centre National de la Recherche Scientifique 3559, Laboratoire d'Excellence “Saclay Plant Sciences” (LabEx SPS), RD10Versailles, France
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
| | - Loïc Rajjou
- Institut National de la Recherche Agronomique, Institut Jean-Pierre Bourgin, UMR 1318 Institut National de la Recherche Agronomique/AgroParisTech, ERL Centre National de la Recherche Scientifique 3559, Laboratoire d'Excellence “Saclay Plant Sciences” (LabEx SPS), RD10Versailles, France
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
| | - Thierry Balliau
- Institut National de la Recherche Agronomique, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Institut National de la Recherche Agronomique/Université Paris-Sud/Centre National de la Recherche Scientifique/AgroParisTech, UMR 0320/UMR 8120 Génétique Quantitative et Evolution – Le MoulonGif-sur-Yvette, France
| | - Michel Zivy
- Institut National de la Recherche Agronomique, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Institut National de la Recherche Agronomique/Université Paris-Sud/Centre National de la Recherche Scientifique/AgroParisTech, UMR 0320/UMR 8120 Génétique Quantitative et Evolution – Le MoulonGif-sur-Yvette, France
| | - Bruno Fogliani
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
- Institut Agronomique Néo-Calédonien, Diversités Biologique et Fonctionnelle des Ecosystèmes TerrestresPaïta, New Caledonia
| | - Claudette Job
- UMR 5240 Laboratoire Mixte Centre National de la Recherche Scientifique/Institut National des Sciences Appliquées/Université Claude Bernard Lyon 1/Bayer CropScienceLyon, France
| | - Alexandre de Kochko
- Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des PlantesMontpellier, France
| | - Valérie Sarramegna-Burtet
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-CalédonieNouméa, New Caledonia
| | - Dominique Job
- AgroParisTech, Chaire de Physiologie VégétaleParis, France
- UMR 5240 Laboratoire Mixte Centre National de la Recherche Scientifique/Institut National des Sciences Appliquées/Université Claude Bernard Lyon 1/Bayer CropScienceLyon, France
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12
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Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ON, Rakotomalala JJ, Nowak MD, Davis AP, de Kochko A. Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species. Mol Genet Genomics 2015; 291:155-68. [PMID: 26231981 DOI: 10.1007/s00438-015-1098-3] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/21/2015] [Indexed: 01/10/2023]
Abstract
The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.
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Affiliation(s)
- Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, A1B 3X9, Canada. .,UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France.
| | - Romain Guyot
- UMR IPME, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France
| | - Perla Hamon
- UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France
| | - Dominique Crouzillat
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France
| | - Michel Rigoreau
- Nestlé R&D Tours, 101 AV. G. Eiffel, Notre Dame d'Oé, BP 49716, 37097, Tours, Cedex 2, France
| | | | | | - Michael D Nowak
- Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 17165, Solna, Sweden
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
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13
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Chaparro C, Gayraud T, de Souza RF, Domingues DS, Akaffou S, Laforga Vanzela AL, Kochko AD, Rigoreau M, Crouzillat D, Hamon S, Hamon P, Guyot R. Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements. Genome Biol Evol 2015; 7:493-504. [PMID: 25573958 PMCID: PMC4350172 DOI: 10.1093/gbe/evv001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes.
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Affiliation(s)
- Cristian Chaparro
- 2EI UMR5244 Université de Perpignan Via Domitia, UMR 5244 CNRS Ecologie et Evolution des Interactions (2EI), Perpignan, France
| | - Thomas Gayraud
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | | | - Douglas Silva Domingues
- Departamento de Botanica, Instituto de Biociencias, Univ Estadual Paulista, UNESP, Rio Claro, SP, Brazil
| | | | | | - Alexandre de Kochko
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | | | | | - Serge Hamon
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | - Perla Hamon
- Institut de Recherche pour le Développement (IRD), UMR DIADE (CIRAD, IRD, UM2), Montpellier, France
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR IPME, Montpellier, France
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14
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Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 2014; 345:1181-4. [PMID: 25190796 DOI: 10.1126/science.1255274] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
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Affiliation(s)
- France Denoeud
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Lorenzo Carretero-Paulet
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Gaëtan Droc
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Romain Guyot
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Marco Pietrella
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Adriana Alberti
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - François Anthony
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Stéphanie Bocs
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Claudine Campa
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Alberto Cenci
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Marie-Christine Combes
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Dominique Crouzillat
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | | | - Fabien De Bellis
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Stéphane Dussert
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Olivier Garsmeur
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Thomas Gayraud
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Katharina Jahn
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universität Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Véronique Jamilloux
- Institut National de la Recherche Agronomique (INRA), Unité de Recherches en Génomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France
| | - Thierry Joët
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Tianying Lan
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China
| | - Julie Leclercq
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Maud Lepelley
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Thierry Leroy
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Lei-Ting Li
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pablo Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | | | - Adriana Muñoz
- Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Benjamin Noel
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | | | - Valérie Poncet
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - David Pot
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Priyono
- Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia
| | - Michel Rigoreau
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - Christine Tranchant-Dubreuil
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Robert VanBuren
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qiong Zhang
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alan C Andrade
- Laboratório de Genética Molecular, Núcleo de Biotecnologia (NTBio), Embrapa Recursos Genéticos e Biotecnologia, Final Av. W/5 Norte, Parque Estação Biológia, Brasília-DF 70770-917, Brazil
| | - Xavier Argout
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Benoît Bertrand
- CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Alexandre de Kochko
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Giorgio Graziosi
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia
| | - Jayarama
- Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India
| | - Ray Ming
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chifumi Nagai
- Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA
| | - Steve Rounsley
- BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Victor A Albert
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France.
| | - Philippe Lashermes
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France.
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Poncet V, Munoz F, Munzinger J, Pillon Y, Gomez C, Couderc M, Tranchant-Dubreuil C, Hamon S, de Kochko A. Phylogeography and niche modelling of the relict plantAmborella trichopoda(Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia. Mol Ecol 2013; 22:6163-78. [DOI: 10.1111/mec.12554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Valérie Poncet
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
| | - François Munoz
- UM2 and IRD; UMR AMAP; Boulevard de la Lironde, PS 2 34398 Montpellier France
| | - Jérôme Munzinger
- UM2 and IRD; UMR AMAP; Boulevard de la Lironde, PS 2 34398 Montpellier France
- IRD; UMR AMAP; Herbarium NOU 98848 Nouméa New Caledonia
| | - Yohan Pillon
- IRD; UMR DIADE; 98848 Nouméa New Caledonia
- Tropical Conservation Biology and Environmental Science; University of Hawai'i at Hilo; 200 West Kawili St. Hilo HI 96720 USA
| | - Céline Gomez
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
- IRD; UMR DIADE; 98848 Nouméa New Caledonia
| | - Marie Couderc
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
| | | | - Serge Hamon
- IRD; UMR DIADE; BP 64501 34394 Montpellier Cedex 5 France
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16
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Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, Combes MC, Gavory F, de Kochko A, Kudrna D, Leroy T, Poulain J, Rondeau M, Song X, Wing R, Lashermes P. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution. Plant Mol Biol 2013; 83:177-189. [PMID: 23708951 DOI: 10.1007/s11103-013-0077-5] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/14/2013] [Indexed: 06/02/2023]
Abstract
Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.
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Affiliation(s)
- Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394, Montpellier Cedex 5, France
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17
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Poncet V, Couderc M, Tranchant-Dubreuil C, Gomez C, Hamon P, Hamon S, Pillon Y, Munzinger J, de Kochko A. Microsatellite markers for Amborella (Amborellaceae), a monotypic genus endemic to New Caledonia. Am J Bot 2012; 99:e411-e414. [PMID: 23028001 DOI: 10.3732/ajb.1200131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Informative markers are required for assessing the diversity of Amborella trichopoda, the only species of its order, endemic to New Caledonia and considered to be the sister species to all flowering plants. Therefore, expressed sequence tag (EST)-based microsatellite markers were developed. • METHODS AND RESULTS Fifty-five microsatellite loci were characterized in 14896 putative unigenes, which were generated by assembling A. trichopoda ESTs from the public sequence database. Seventeen markers revealed polymorphism in 80 adult shrubs from three populations. The number of alleles per locus ranged from two to 12, with a total of 132 alleles scored. The mean expected heterozygosity per population ranged from 0.336 to 0.567. • CONCLUSIONS These markers offer an appropriate amount of variation to investigate genetic diversity structure, gene flow, and other conservation issues.
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Affiliation(s)
- Valérie Poncet
- Institut de Recherche pour le Développement (IRD), Unité Mixte de Recherche-Diversité Adaptation et Développement des plantes (UMR DIADE), BP 64501, 34394 Montpellier Cedex 5, France.
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18
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Lepelley M, Mahesh V, McCarthy J, Rigoreau M, Crouzillat D, Chabrillange N, de Kochko A, Campa C. Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae). Planta 2012; 236:313-26. [PMID: 22349733 PMCID: PMC3382651 DOI: 10.1007/s00425-012-1613-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 02/08/2012] [Indexed: 05/20/2023]
Abstract
Phenylalanine ammonia lyase (PAL) is the first entry enzyme of the phenylpropanoid pathway producing phenolics, widespread constituents of plant foods and beverages, including chlorogenic acids, polyphenols found at remarkably high levels in the coffee bean and long recognized as powerful antioxidants. To date, whereas PAL is generally encoded by a small gene family, only one gene has been characterized in Coffea canephora (CcPAL1), an economically important species of cultivated coffee. In this study, a molecular- and bioinformatic-based search for CcPAL1 paralogues resulted successfully in identifying two additional genes, CcPAL2 and CcPAL3, presenting similar genomic structures and encoding proteins with close sequences. Genetic mapping helped position each gene in three different coffee linkage groups, CcPAL2 in particular, located in a coffee genome linkage group (F) which is syntenic to a region of Tomato Chromosome 9 containing a PAL gene. These results, combined with a phylogenetic study, strongly suggest that CcPAL2 may be the ancestral gene of C. canephora. A quantitative gene expression analysis was also conducted in coffee tissues, showing that all genes are transcriptionally active, but they present distinct expression levels and patterns. We discovered that CcPAL2 transcripts appeared predominantly in flower, fruit pericarp and vegetative/lignifying tissues like roots and branches, whereas CcPAL1 and CcPAL3 were highly expressed in immature fruit. This is the first comprehensive study dedicated to PAL gene family characterization in coffee, allowing us to advance functional studies which are indispensable to learning to decipher what role this family plays in channeling the metabolism of coffee phenylpropanoids.
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Affiliation(s)
- Maud Lepelley
- Nestlé R&D Center, 101 Av. Gustave Eiffel, Notre Dame D'Oé, BP 49716, 37097, Tours, France.
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Guyot R, Lefebvre-Pautigny F, Tranchant-Dubreuil C, Rigoreau M, Hamon P, Leroy T, Hamon S, Poncet V, Crouzillat D, de Kochko A. Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades. BMC Genomics 2012; 13:103. [PMID: 22433423 PMCID: PMC3372433 DOI: 10.1186/1471-2164-13-103] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [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: 10/27/2011] [Accepted: 03/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coffee trees (Rubiaceae) and tomato (Solanaceae) belong to the Asterid clade, while grapevine (Vitaceae) belongs to the Rosid clade. Coffee and tomato separated from grapevine 125 million years ago, while coffee and tomato diverged 83-89 million years ago. These long periods of divergent evolution should have permitted the genomes to reorganize significantly. So far, very few comparative mappings have been performed between very distantly related species belonging to different clades. We report the first multiple comparison between species from Asterid and Rosid clades, to examine both macro-and microsynteny relationships. RESULTS Thanks to a set of 867 COSII markers, macrosynteny was detected between coffee, tomato and grapevine. While coffee and tomato genomes share 318 orthologous markers and 27 conserved syntenic segments (CSSs), coffee and grapevine also share a similar number of syntenic markers and CSSs: 299 and 29 respectively. Despite large genome macrostructure reorganization, several large chromosome segments showed outstanding macrosynteny shedding new insights into chromosome evolution between Asterids and Rosids. We also analyzed a sequence of 174 kb containing the ovate gene, conserved in a syntenic block between coffee, tomato and grapevine that showed a high-level of microstructure conservation. A higher level of conservation was observed between coffee and grapevine, both woody and long life-cycle plants, than between coffee and tomato. Out of 16 coffee genes of this syntenic segment, 7 and 14 showed complete synteny between coffee and tomato or grapevine, respectively. CONCLUSIONS These results show that significant conservation is found between distantly related species from the Asterid (Coffea canephora and Solanum sp.) and Rosid (Vitis vinifera) clades, at the genome macrostructure and microstructure levels. At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time factor alone does not explain divergences. Our results are considerably useful for syntenic studies between supposedly remote species for the isolation of important genes for agronomy.
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Affiliation(s)
- Romain Guyot
- UMR DIADE, Evolution et Dynamique des Génomes, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
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20
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Dubreuil-Tranchant C, Guyot R, Guellim A, Duret C, de la Mare M, Razafinarivo N, Poncet V, Hamon S, Hamon P, de Kochko A. Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow. Int J Evol Biol 2011; 2011:358412. [PMID: 21961075 PMCID: PMC3180848 DOI: 10.4061/2011/358412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/16/2011] [Indexed: 11/25/2022]
Abstract
Miniature Inverted-repeat Transposable Elements (MITEs) are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex) in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.
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Yu Q, Guyot R, de Kochko A, Byers A, Navajas-Pérez R, Langston BJ, Dubreuil-Tranchant C, Paterson AH, Poncet V, Nagai C, Ming R. Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea). Plant J 2011; 67:305-17. [PMID: 21457367 DOI: 10.1111/j.1365-313x.2011.04590.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.
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Affiliation(s)
- Qingyi Yu
- Hawaii Agriculture Research Center, Waipahu, HI 96797, USA
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22
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Privat I, Bardil A, Gomez AB, Severac D, Dantec C, Fuentes I, Mueller L, Joët T, Pot D, Foucrier S, Dussert S, Leroy T, Journot L, de Kochko A, Campa C, Combes MC, Lashermes P, Bertrand B. The 'PUCE CAFE' Project: the first 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits. BMC Genomics 2011; 12:5. [PMID: 21208403 PMCID: PMC3025959 DOI: 10.1186/1471-2164-12-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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: 06/24/2010] [Accepted: 01/05/2011] [Indexed: 11/30/2022] Open
Abstract
Background Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. Conclusion We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Génoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research.
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Affiliation(s)
- Isabelle Privat
- Nestlé R&D Tours, 101 Avenue Gustave Eiffel, Notre Dame d'Oé, BP 49716, 37097 Tours Cedex 2, France.
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23
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Carrier G, Santoni S, Rodier-Goud M, Canaguier A, Kochko AD, Dubreuil-Tranchant C, This P, Boursiquot JM, Le Cunff L. An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods. Am J Bot 2011; 98:e13-5. [PMID: 21613076 DOI: 10.3732/ajb.1000371] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
PREMISE OF THE STUDY In this study, we developed a nuclear DNA extraction protocol for Next Generation Sequencers (NGS). METHODS AND RESULTS We applied this extraction method to grapevines and coffee trees, which are known to contain many secondary metabolites. The nuclear DNA obtained was sequenced by the 454/GS-FLX method. We obtained excellent results, with less than 4% cytoplasmic DNA, in a similar way to a BAC (Bacterial Artificial Chromosome)-building protocol. We also compared our protocol with a classic DNA extraction using specific cytoplasmic DNA amplification. Results showed a lower cytoplasmic DNA contamination with the new protocol. CONCLUSIONS The method presented here is fast and economical. The DNA obtained is of high quality, with a low level of cytoplasmic DNA contamination, and very efficient for the construction of sequencing libraries.
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Affiliation(s)
- Gregory Carrier
- UMT Geno-Vigne, IFV-INRA-Montpellier Supagro, 2 place Viala, Montpellier, France.
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Gomez C, Batti A, Le Pierrès D, Campa C, Hamon S, de Kochko A, Hamon P, Huynh F, Despinoy M, Poncet V. Favourable habitats forCoffeainter-specific hybridization in central New Caledonia: combined genetic and spatial analyses. J Appl Ecol 2010. [DOI: 10.1111/j.1365-2664.2009.01762.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Plechakova O, Tranchant-Dubreuil C, Benedet F, Couderc M, Tinaut A, Viader V, De Block P, Hamon P, Campa C, de Kochko A, Hamon S, Poncet V. MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family. BMC Plant Biol 2009; 9:123. [PMID: 19788737 PMCID: PMC2760556 DOI: 10.1186/1471-2229-9-123] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 09/29/2009] [Indexed: 05/08/2023]
Abstract
BACKGROUND In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus (coffee trees). An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. Similar genomic information is available for e.g. tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in Rubiaceae. DESCRIPTION MoccaDB is an online MySQL-PHP driven relational database that houses annotated and/or mapped microsatellite markers in Rubiaceae. In its current release, the database stores 638 markers that have been defined on 259 ESTs and 379 genomic sequences. Marker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. DNA sequences were derived from three Coffea species/hybrids. Microsatellite markers were checked for similarity, in vitro tested for cross-amplification and diversity/polymorphism status in up to 38 Rubiaceae species belonging to the Cinchonoideae and Rubioideae subfamilies. Functional annotation was provided and some markers associated with described metabolic pathways were also integrated. Users can search the database for marker, sequence, map or diversity information through multi-option query forms. The retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. MoccaDB also integrates bioinformatics tools (CMap viewer and local BLAST) and hyperlinks to related external data sources (NCBI GenBank and PubMed, SOL Genomic Network database). CONCLUSION We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular.
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Affiliation(s)
- Olga Plechakova
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | | | - Fabrice Benedet
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
- CIRAD TA C 37/D, Campus International de Baillarguet 34398 Montpellier Cedex 5, France
| | - Marie Couderc
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Alexandra Tinaut
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Véronique Viader
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
- UMR DIAPC, INRA, Domaine de MelgueiI, Chemin de Mézouls, 34130 Mauguio, France
| | - Petra De Block
- National Botanic Garden of Belgium, Domein van Bouchout, 1860 Meise, Belgium
| | - Perla Hamon
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Claudine Campa
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Alexandre de Kochko
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Serge Hamon
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Valérie Poncet
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
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Gomez C, Dussert S, Hamon P, Hamon S, Kochko AD, Poncet V. Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evol Biol 2009; 9:167. [PMID: 19607674 PMCID: PMC2717059 DOI: 10.1186/1471-2148-9-167] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [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: 12/19/2008] [Accepted: 07/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone. RESULTS Both markers were first compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among wild C. canephora genotypes. As expected, SSR markers were found to have a higher genetic distance detection capacity than RFLP. Nevertheless, similarity matrices showed significant correlations when Mantel's test was carried out (r = 0.66, p < 0.0001). Finally, both markers were equally effective for group discrimination and phylogenetic studies, but SSR markers tended to outperform RFLP markers in discriminating the source of an individual among diversity groups and in putative hybrid detection. Five well defined genetic groups, one in the Upper Guinean forests, the four others in the Lower Guinean forests, were identified, corresponding to geographical patterning in the individuals. CONCLUSION Our data suggested that the Dahomey Gap, a biogeographical barrier, played a role in wild C. canephora differentiation. Climatic variations during the Pleistocene and/or Holocene probably caused the subgroup differentiation in the Congolese zone through the presence of a mosaic of putative refugia. Recent hybridization between C. canephora diversity groups, both for spontaneous individuals and cultivars, was further characterised according to their geographic dissemination or breeding history as a consequence of human activities.
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Affiliation(s)
- Céline Gomez
- UMR DIAPC, IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier CEDEX 5, France.
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Guyot R, de la Mare M, Viader V, Hamon P, Coriton O, Bustamante-Porras J, Poncet V, Campa C, Hamon S, de Kochko A. Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes. BMC Plant Biol 2009; 9:22. [PMID: 19243618 PMCID: PMC2656508 DOI: 10.1186/1471-2229-9-22] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 02/25/2009] [Indexed: 05/11/2023]
Abstract
BACKGROUND Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis. RESULTS This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago. CONCLUSION This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high conservation with other distant dicotyledonous reference genomes. Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing. Future large-scale sequence comparison between C. canephora and reference sequenced genomes will help in understanding the evolutionary history of dicotyledonous plants.
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Affiliation(s)
- Romain Guyot
- UMR GDP, IRD BP 64501, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Marion de la Mare
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Véronique Viader
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Perla Hamon
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Olivier Coriton
- UMR 118, INRA Agrocampus Rennes Amélioration des Plantes, Domaine de la Motte – BP 35327, 35650 Le Rheu cedex, France
| | - José Bustamante-Porras
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Valérie Poncet
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Claudine Campa
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Serge Hamon
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
| | - Alexandre de Kochko
- UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France
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Joët T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, de Kochko A, Dussert S. Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study. New Phytol 2009; 182:146-162. [PMID: 19207685 PMCID: PMC2713855 DOI: 10.1111/j.1469-8137.2008.02742.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [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: 09/27/2008] [Accepted: 11/28/2008] [Indexed: 05/18/2023]
Abstract
* The genomic era facilitates the understanding of how transcriptional networks are interconnected to program seed development and filling. However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm. Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin. * The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids. For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling. * Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides. * Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue.
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Affiliation(s)
- Thierry Joët
- IRD, UMR DIA-PC, Pôle de Protection des Plantes97410, Saint Pierre, La Réunion, France
| | | | - Jordi Salmona
- IRD, UMR DIA-PC, Pôle de Protection des Plantes97410, Saint Pierre, La Réunion, France
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Dussert S, Laffargue A, de Kochko A, Joët T. Effectiveness of the fatty acid and sterol composition of seeds for the chemotaxonomy of Coffea subgenus Coffea. Phytochemistry 2008; 69:2950-2960. [PMID: 18995872 DOI: 10.1016/j.phytochem.2008.09.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 09/25/2008] [Accepted: 09/25/2008] [Indexed: 05/27/2023]
Abstract
The chemotaxonomic relationships between Coffea (subgenus Coffea) species have been poorly studied to date and the compounds tested so far - chlorogenic acids, diterpenoids and purine alkaloids - did not enable the establishment of phylogenetic relationships analogous to those revealed by chloroplast and nuclear DNA studies. In the present study, the relationships between African Coffea species were assessed on the basis of their seed lipid composition. Fatty acids and sterols were determined in 59 genotypes belonging to 17 distinct Coffea species/origins. Principal Component Analysis of fatty acid and sterol data enabled easy identification of the few species for which one or several compounds could serve as a quantitative signature. Hierarchical Clustering classified the Coffea species in seven groups with both fatty acids and sterols. However, while groupings based on seed fatty acid composition showed remarkable ecological and geographical coherence, no phylogeographic explanation was found for the clusters retrieved from sterol data. When compared with previous phylogenetic studies, the groups deduced from seed fatty acid composition were remarkably congruent with the clades inferred from nuclear and plastid DNA sequences.
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Poncet V, Dufour M, Hamon P, Hamon S, de Kochko A, Leroy T. Development of genomic microsatellite markers in Coffea canephora and their transferability to other coffee species. Genome 2008; 50:1156-61. [PMID: 18059542 DOI: 10.1139/g07-073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Of the 103 accepted Coffea species, 70% are threatened with extinction but only a few of them have been studied. A set of 40 polymorphic microsatellite markers was developed using a GA/GT-enriched Coffea canephora genomic library. Amplification of these markers was tested in accessions of C. heterocalyx (a Critically Endangered species) and C. pseudozanguebariae (a Vulnerable species) belonging to different African geographical clades. All microsatellites were polymorphic in C. canephora, with a mean allele number per polymorphic locus of more than 3 (at least 9 genotypes were tested). Observed and expected heterozygosities calculated for C. canephora and C. pseudozanguebariae varied from 0.10 to 0.91 and from 0.20 to 0.77, respectively. In total, 38 primer pairs (95%) were amplified in C. heterocalyx and C. pseudozanguebariae, indicating their high level of transferability across the genus Coffea. This large marker set will be useful for more extensive genetic studies of threatened Coffea species.
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Affiliation(s)
- Valérie Poncet
- IRD, UMR DIA-PC, 911 avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France.
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Salmona J, Dussert S, Descroix F, de Kochko A, Bertrand B, Joët T. Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches. Plant Mol Biol 2008; 66:105-24. [PMID: 18026845 DOI: 10.1007/s11103-007-9256-6] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 10/27/2007] [Indexed: 05/04/2023]
Abstract
Due to its economic importance, Coffea arabica is becoming the subject of increasing genomic research and, in particular, the genes involved in the final chemical composition of the bean and the sensorial quality of the coffee beverage. The aim of the present study was to decipher the transcriptional networks that govern the development of the C. arabica seed, a model for non-orthodox albuminous seeds of tropical origin. For this purpose, we developed a transcriptomic approach combining two techniques: targeted cDNA arrays, containing 266 selected candidate gene sequences, and real-time RT-PCR on a large subset of 111 genes. The combination of the two techniques allowed us to limit detection of false positives and to reveal the advantages of using large real-time RT-PCR screening. Multivariate analysis was conducted on both datasets and results were broadly convergent. First, principle component analysis (PCA) revealed a dramatic re-programming of the transcriptional machinery between early cell division and elongation, storage and maturation phases. Second, hierarchical clustering analysis (HCA) led to the identification of 11 distinct patterns of gene expression during seed development as well as to the detection of genes expressed at specific developmental stages that can be used as functional markers of phenological changes. In addition, this study led to the description of gene expression profiles for quality-related genes, most of them formerly uncharacterised in Coffea. Their involvement in storage compound synthesis and accumulation during endosperm development and final metabolic re-adjustments during maturation is discussed.
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Affiliation(s)
- Jordi Salmona
- IRD, UMR DIAPC, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, ligne Paradis, 97410 Saint Pierre, France
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Mahesh V, Million-Rousseau R, Ullmann P, Chabrillange N, Bustamante J, Mondolot L, Morant M, Noirot M, Hamon S, de Kochko A, Werck-Reichhart D, Campa C. Functional characterization of two p-coumaroyl ester 3'-hydroxylase genes from coffee tree: evidence of a candidate for chlorogenic acid biosynthesis. Plant Mol Biol 2007; 64:145-59. [PMID: 17333503 DOI: 10.1007/s11103-007-9141-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 01/24/2007] [Indexed: 05/02/2023]
Abstract
Chlorogenic acid (5-CQA) is one of the major soluble phenolic compounds that is accumulated in coffee green beans. With other hydroxycinnamoyl quinic acids (HQAs), this compound is accumulated in particular in green beans of the cultivated species Coffea canephora. Recent work has indicated that the biosynthesis of 5-CQA can be catalyzed by a cytochrome P450 enzyme, CYP98A3 from Arabidopsis. Two full-length cDNA clones (CYP98A35 and CYP98A36) that encode putative p-coumaroylester 3'-hydroxylases (C3'H) were isolated from C. canephora cDNA libraries. Recombinant protein expression in yeast showed that both metabolized p-coumaroyl shikimate at similar rates, but that only one hydroxylates the chlorogenic acid precursor p-coumaroyl quinate. CYP98A35 appears to be the first C3'H capable of metabolising p-coumaroyl quinate and p-coumaroyl shikimate with the same efficiency. We studied the expression patterns of both genes on 4-month old C. canephora plants and found higher transcript levels in young and in highly vascularized organs for both genes. Gene expression and HQA content seemed to be correlated in these organs. Histolocalization and immunolocalization studies revealed similar tissue localization for caffeoyl quinic acids and p-coumaroylester 3'-hydroxylases. The results indicated that HQA biosynthesis and accumulation occurred mainly in the shoot tip and in the phloem of the vascular bundles. The lack of correlation between gene expression and HQA content observed in some organs is discussed in terms of transport and accumulation mechanisms.
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Affiliation(s)
- Venkataramaiah Mahesh
- Laboratoire de Génomique et Qualité du café, IRD, UMR 1097 DGPC, 911 Avenue Agropolis, BP 64501, 34394, Montpellier cedex 5, France
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Laffargue A, de Kochko A, Dussert S. Development of solid-phase extraction and methylation procedures to analyse free fatty acids in lipid-rich seeds. Plant Physiol Biochem 2007; 45:250-7. [PMID: 17360190 DOI: 10.1016/j.plaphy.2007.01.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 01/22/2007] [Indexed: 05/14/2023]
Abstract
In order to develop a sensitive and reliable method for FFA quantification in lipid matrices of seeds, two SPE procedures employed in meat and dairy chemistry were compared using a 100/1 mixture of triolein/heptadecanoic acid. The overall efficiency of the SPE procedure retained was satisfactory since it allowed removal of 99.8% of triacylglycerols (TAG) and recovery of 99.2% of FFA as quantified by gas chromatography of fatty acid methyl esters (FAME). However, the low amount of TAG eluted in the FFA fraction represented a non-negligible percentage (17%) of FAME and the procedure thus required further improvement. TAG pollution was successively decreased to 12%, 8% and finally 1.5% by: i) modifying the volume of elution of TAG; ii) removing the saponification step initially performed according to the standard FAME procedure; and iii) reducing the duration of the BF(3)-catalyzed methylation reaction to 1 min. The new SPE/methylation procedure described here was then compared to the most widely used method for FFA measurement in plants which is based on thin-layer chromatography (TLC). Both procedures were applied to coffee seeds stored for 0-18 months at 15 degrees C under 62% relative humidity and provided consistent results. A very clear negative correlation was observed between the loss of seed viability and the accumulation of FFA in seeds during the course of storage independent of the method employed for FFA quantification. However, we demonstrated that the TLC/on-silica methylation procedure underestimates FFA contents in comparison with the new SPE/methylation procedure because of a selective loss of unsaturated FA.
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Affiliation(s)
- Andréina Laffargue
- IRD, UR 188, UMR DIA-PC, 911 Avenue d'Agropolis, BP 64501, F-34394 Montpellier Cedex, France
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Bustamante-Porras J, Campa C, Poncet V, Noirot M, Leroy T, Hamon S, de Kochko A. Molecular characterization of an ethylene receptor gene (CcETR1) in coffee trees, its relationship with fruit development and caffeine content. Mol Genet Genomics 2007; 277:701-12. [PMID: 17318584 DOI: 10.1007/s00438-007-0219-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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: 12/06/2006] [Accepted: 02/01/2007] [Indexed: 11/30/2022]
Abstract
To understand the importance of ethylene receptor genes in the quality of coffee berries three full-length cDNAs corresponding to a putative ethylene receptor gene (ETR1) were isolated from Coffea canephora cDNA libraries. They differed by their 3'UTR and contained a main ORF and a 5'UTR short ORF putatively encoding a small polypeptide. The CcETR1 gene, present as a single copy in the C. canephora genome, contained five introns in the coding region and one in its 5'UTR. Alternative splicing can occur in C. canephora and C. pseudozanguebariae, leading to a truncated polypeptide. C. pseudozanguebariae ETR1 transcripts showed various forms of splicing alterations. This gene was equally expressed at all stages of fruit development. A segregation study on an inter-specific progeny showed that ETR1 is related to the fructification time, the caffeine content of the green beans, and seed weight. Arabidopsis transformed etiolated seedlings, which over-expressed CcETR1, displayed highly reduced gravitropism, but the triple response was observed in an ethylene enriched environment. These plants behaved like a low-concentration ethylene-insensitive mutant thus confirming the receptor function of the encoded protein. This gene showed no induction during the climacteric crisis but some linkage with traits related to quality.
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Mahesh V, Rakotomalala JJ, Le Gal L, Vigne H, de Kochko A, Hamon S, Noirot M, Campa C. Isolation and genetic mapping of a Coffea canephora phenylalanine ammonia-lyase gene (CcPAL1) and its involvement in the accumulation of caffeoyl quinic acids. Plant Cell Rep 2006; 25:986-92. [PMID: 16586075 DOI: 10.1007/s00299-006-0152-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Revised: 02/22/2006] [Accepted: 03/02/2006] [Indexed: 05/08/2023]
Abstract
Biosynthesis of caffeoylquinic acids occurs via the phenylpropanoid pathway in which the phenylalanine ammonia-lyase (PAL) acts as a key-control enzyme. A full-length cDNA (pF6), corresponding to a PAL gene (CcPAL1), was isolated by screening a Coffea canephora fruit cDNA library and its corresponding genomic sequence was characterized. Amplification of total DNA from seven Coffea species revealed differences in intronic length. This interspecific polymorphism was used to locate the gene on a genetic map established for a backcross progeny between Coffea pseudozanguebariae and C. dewevrei. The CcPAL1 gene was found on the same linkage group, but genetically independent, as a caffeoyl-coenzyme A-O-methyltransferase gene, another gene intervening in the phenylpropanoid pathway. In the same backcross, a lower caffeoylquinic acid content was observed in seeds harvested from plants harbouring the C. pseudozanguebariae CcPAL1 allele. Involvement of the CcPAL1 allelic form in the differential accumulation of caffeoylquinic acids in coffee green beans is then discussed.
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Affiliation(s)
- Venkataramaiah Mahesh
- IRD, Génomique et qualité du Café, UMR DGPC, BP 64501, 34304, Montpellier Cedex 5, France
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Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, de Kochko A, Hamon P. SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus. Mol Genet Genomics 2006; 276:436-49. [PMID: 16924545 DOI: 10.1007/s00438-006-0153-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [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: 02/22/2006] [Accepted: 07/15/2006] [Indexed: 10/24/2022]
Abstract
Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST-SSRs) with a motif length of 1-6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST-SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST-SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies.
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Affiliation(s)
- Valérie Poncet
- UMR 1097 Diversité et Génomes des Plantes Cultivées (DGPC), IRD, Institut de Recherche pour le Développement, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.
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Talamond P, Noirot M, de Kochko A. The mechanism of action of alpha-amylase from Lactobacillus fermentum on maltooligosaccharides. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 834:42-7. [PMID: 16531129 DOI: 10.1016/j.jchromb.2006.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 09/30/2005] [Revised: 01/12/2006] [Accepted: 02/05/2006] [Indexed: 11/23/2022]
Abstract
The action pattern of Lactobacillus fermentum alpha-amylase (FERMENTA) was examined using a series of maltooligosaccharides (G2-G7) as substrates. Structurally, this enzyme has a molecular mass (106 kDa) almost twofold higher than alpha-amylases from mammalians and cereals. The product pattern was investigated through an analysis of products and substrates using HPAEC with pulsed amperometric detection. FERMENTA was consistent with an endo-type of amylase. The bond cleavage frequencies were studied using maltooligosaccharides of various chain lengths as substrate, i.e. maltose up to maltoheptaose and DP 4900-amylose catalyzed by FERMENTA. The catalytic efficiency (k(cat)/K(m)) increased with chain length from maltose (8.7 x 10(4) M(-1) s(-1)) up to amylose (1 x10(9) M(-1) s(-1)). These action pattern results revealed that FERMENTA can readily cleave the third linkage from the reducing end of the maltooligosaccharides (G5-G7).
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Affiliation(s)
- Pascale Talamond
- Institut de Recherche pour le Développement, UMR 141, 911 av. d'Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France.
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Marmey P, Rojas-Mendoza A, de Kochko A, Beachy RN, Fauquet CM. Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein. Virol J 2005; 2:33. [PMID: 15831103 PMCID: PMC1087892 DOI: 10.1186/1743-422x-2-33] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Accepted: 04/14/2005] [Indexed: 11/21/2022] Open
Abstract
Background Rice tungro bacilliform virus (RTBV) is a pararetrovirus, and a member of the family Caulimoviridae in the genus Badnavirus. RTBV has a long open reading frame that encodes a large polyprotein (P3). Pararetroviruses show similarities with retroviruses in molecular organization and replication. P3 contains a putative movement protein (MP), the capsid protein (CP), the aspartate protease (PR) and the reverse transcriptase (RT) with a ribonuclease H activity. PR is a member of the cluster of retroviral proteases and serves to proteolytically process P3. Previous work established the N- and C-terminal amino acid sequences of CP and RT, processing of RT by PR, and estimated the molecular mass of PR by western blot assays. Results A molecular mass of a protein that was associated with virions was determined by in-line HPLC electrospray ionization mass spectral analysis. Comparison with retroviral proteases amino acid sequences allowed the characterization of a putative protease domain in this protein. Structural modelling revealed strong resemblance with retroviral proteases, with overall folds surrounding the active site being well conserved. Expression in E. coli of putative domain was affected by the presence or absence of the active site in the construct. Analysis of processing of CP by PR, using pulse chase labelling experiments, demonstrated that the 37 kDa capsid protein was dependent on the presence of the protease in the constructs. Conclusion The findings suggest the characterization of the RTBV protease domain. Sequence analysis, structural modelling, in vitro expression studies are evidence to consider the putative domain as being the protease domain. Analysis of expression of different peptides corresponding to various domains of P3 suggests a processing of CP by PR. This work clarifies the organization of the RTBV polyprotein, and its processing by the RTBV protease.
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Affiliation(s)
- Philippe Marmey
- IRD, UMR «DGPC», B.P. 64501, 34394 Montpellier cedex 5, France
| | - Ana Rojas-Mendoza
- Protein Design Group, Centro Nacional de Biotecnologia, Campus Universidad Autonoma Cantoblanco, 28049 Madrid, Spain
| | | | - Roger N Beachy
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
| | - Claude M Fauquet
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
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