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Microcollinearity in an Ethylene Receptor Coding Gene Region of The 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. Romain Guyot, Marion de la Mare, Véronique Viader, Perla Hamon, Olivier Coriton, José Bustamante-Porras, Valérie Poncet, Claudine Campa, Serge Hamon, Alexandre de Kochko To cite this version: Romain Guyot, Marion de la Mare, Véronique Viader, Perla Hamon, Olivier Coriton, et al.. Micro- collinearity 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- ogy, BioMed Central, 2009, 9 (22), pp.22. 10.1186/1471-2229-9-22. hal-00695701 HAL Id: hal-00695701 https://hal.archives-ouvertes.fr/hal-00695701 Submitted on 30 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. BMC Plant Biology BioMed Central Research article Open Access 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 Romain Guyot*1, Marion de la Mare2, Véronique Viader2, Perla Hamon2, Olivier Coriton3, José Bustamante-Porras2, Valérie Poncet2, Claudine Campa2, Serge Hamon2 and Alexandre de Kochko2 Address: 1UMR GDP, IRD BP 64501, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France, 2UMR DIA-PC, IRD Génomique Comparative et Fonctionnelle de l'Adaptation, Centre IRD de Montpellier, BP 64501, Montpellier Cedex 5, France and 3UMR 118, INRA Agrocampus Rennes Amélioration des Plantes, Domaine de la Motte – BP 35327, 35650 Le Rheu cedex, France Email: Romain Guyot* - romain.guyot@mpl.ird.fr; Marion de la Mare - marion.de-la-mare@ird.fr; Véronique Viader - veronique.viader@mpl.ird.fr; Perla Hamon - perla.hamon@ird.fr; Olivier Coriton - olivier.coriton@rennes.inra.fr; José Bustamante-Porras - Jose.Bustamante@mpl.ird.fr; Valérie Poncet - Valerie.Poncet@ird.fr; Claudine Campa - claudine.campa@ird.fr; Serge Hamon - serge.hamon@ird.fr; Alexandre de Kochko - alexandre.dekochko@mpl.ird.fr * Corresponding author Published: 25 February 2009 Received: 25 November 2008 Accepted: 25 February 2009 BMC Plant Biology 2009, 9:22 doi:10.1186/1471-2229-9-22 This article is available from: http://www.biomedcentral.com/1471-2229/9/22 © 2009 Guyot et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 ≈ 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. Page 1 of 15 (page number not for citation purposes) BMC Plant Biology 2009, 9:22 http://www.biomedcentral.com/1471-2229/9/22 Background library [12] and the availability of 55,840 C. canephora Twenty years ago, the availability of several plant genetic ESTs from different tissues and stages of seed develop- maps allowed the development of the first comparative ment [13] to facilitate the isolation and the characteriza- genetic mapping studies [1]. Results indicated that the tion of genes with agronomic interest. However, despite marker content and order were globally conserved within its agronomical importance, very little information con- plant families, between species that sometimes display cerning the composition, the structure and the evolution huge differences in genome size and organization. Thus, of the C. canephora genome is now available. Particularly, macrosynteny was established within the Brassicaceae, the it remains unclear so far how the distantly related Fabaceae, the Solanaceae and the Poaceae families [2]. In sequenced dicotyledonous reference genomes such as Poaceae, the spectacular conservation of macrosynteny Arabidopsis, Medicago, Populus, grapevine and tomato gave the opportunity to draw a consensus map for seven will have a predictive value to study the genome structure different grass genomes that diverged more than 50 mil- and to isolate genes of interest in C. canephora. Recently, lion years ago [3]. In contrast to within family compara- in an effort to identify factors implicated in ethylene per- tive mapping, macrosynteny appears less conserved ception during the ripening of the C. canephora berries, between distantly related species belonging to distant several ethylene receptors and transcription factors genes families or different clades [4,5]. With such a comparison, were isolated [14-16]. One of them called CcEIN4 was the overall conservation of the genome organization identified on an isolated BAC clone [15]. appears scrambled by mechanisms of genome evolution such as chromosome rearrangements and genome dupli- In this study, we present the complete sequencing of the cations, to such an extent that the synteny was frequently C. canephora BAC clone 46C02, carrying the CcEIN4 gene. limited over small genetic intervals. Recently, the increase Sequence analysis of the 160 kb of the BAC indicates a of complete or partial genomic sequence of reference high density of active genes and few transposable ele- plant species from different families and the development ments. Sequence comparisons reveal a high microcolline- of the BAC clones sequencing in experimental species arity between the C. canephora BAC clone and most of the gave the opportunity to perform direct comparisons at the current dicotyledonous sequenced genomes that diverged genomic sequence level. Beside intra-family comparisons, 114 to 125 Million Years Ago (MYA). microcollinearity was investigated between Arabidopsis and tomato [6,7], Arabidopsis, tomato and Capsella [8], Results Arabidopsis, M. truncatula, P. trichocarpa and Lotus japoni- The C. canephora BAC clone 46C02 carries the mono cus [5] and Arabidopsis, Medicago, Populus and Cucumis locus CcEIN4 gene melo [9]. Despite a lack of macrosynteny, a significant The CcEIN4 gene, used as a probe for hybridization, microcollinearity was established between these phyloge- revealed eight positive BAC clones on the high-density fil- netically distant species. In addition, direct sequences ters of the C. canephora BAC library. Among these clones, comparisons allowed the detection of a complex network the BAC clone 46C02 was randomly chosen for further of microcollinearity between Arabidospis and tomato [7] analyses. Low-pass sequencing of about 70 sub-clones and between Arabidospsis, Medicago and Populus [5] from BAC 46C02 suggested the presence of several poten- suggesting the presence of ancient segmental duplication tial coding regions and
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