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
| Autor: | Valérie Poncet, Romain Guyot, Marion de la Mare, José Bustamante-Porras, Alexandre de Kochko, Véronique Viader, Perla Hamon, Olivier Coriton, Serge Hamon, Claudine Campa |
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| Přispěvatelé: | Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Amélioration des Plantes et Biotechnologies Végétales (APBV), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) |
| Rok vydání: | 2009 |
| Předmět: |
MESH: Genome
Plant 0106 biological sciences Chromosomes Artificial Bacterial MESH: Sequence Analysis DNA caféier Coffea Plant Science [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics Phylogenetics and taxonomy 01 natural sciences Genome lcsh:Botany MESH: Genes Plant Vitis BANQUE DE GENES Conserved Sequence MESH: Evolution Molecular Plant Proteins MESH: Receptors Cell Surface 2. Zero hunger Genetics 0303 health sciences Expressed sequence tag Vegetal Biology MESH: Conserved Sequence MESH: Plant Proteins [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM] biology [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] adn food and beverages [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular Networks [q-bio.MN] Physical Chromosome Mapping [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] lcsh:QK1-989 [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry Molecular Biology/Biomolecules [q-bio.BM] [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry Molecular Biology/Biomolecules [q-bio.BM] Genome Plant Research Article MESH: Chromosomes Artificial Bacterial DNA Plant BIOLOGIE MOLECULAIRE Canephora Molecular Sequence Data MESH: Sequence Alignment Receptors Cell Surface Locus (genetics) [SDV.BC]Life Sciences [q-bio]/Cellular Biology Genes Plant Coffea canephora MESH: Vitis MESH: Physical Chromosome Mapping Evolution Molecular [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics 03 medical and health sciences vitis vinifera [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] Gene density MESH: Gene Library [SDV.BV]Life Sciences [q-bio]/Vegetal Biology [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry Molecular Biology/Biochemistry [q-bio.BM] MESH: DNA Plant Genome size Gene Library 030304 developmental biology Whole genome sequencing [SDV.GEN]Life Sciences [q-bio]/Genetics MESH: Molecular Sequence Data MESH: Coffea génome fungi [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biology Sequence Analysis DNA biology.organism_classification [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] vigne Sequence Alignment Biologie végétale 010606 plant biology & botany |
| Zdroj: | BMC Plant Biology BMC Plant Biology, 2009, 9 (22), pp.22. ⟨10.1186/1471-2229-9-22⟩ BMC Plant Biology, BioMed Central, 2009, 9, pp.22. ⟨10.1186/1471-2229-9-22⟩ BMC Plant Biology, BioMed Central, 2009, 9 (22), pp.22. ⟨10.1186/1471-2229-9-22⟩ BMC Plant Biology 22 (9), 1-15. (2009) BMC Plant Biology, Vol 9, Iss 1, p 22 (2009) |
| ISSN: | 1471-2229 |
| DOI: | 10.1186/1471-2229-9-22 |
| Popis: | 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 ≈ 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. |
| Databáze: | OpenAIRE |
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