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Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries
dc.contributor.author | González, Víctor M | |
dc.contributor.author | Rodríguez-Moreno, Luis | |
dc.contributor.author | Centeno, Emilio | |
dc.contributor.author | Benjak, Andrej | |
dc.contributor.author | Garcia-Mas, Jordi | |
dc.contributor.author | Puigdomènech, Pere | |
dc.contributor.author | Aranda, Miguel A | |
dc.contributor.other | Producció Vegetal | ca |
dc.date.accessioned | 2024-08-12T12:26:20Z | |
dc.date.available | 2024-08-12T12:26:20Z | |
dc.date.issued | 2010-11-05 | |
dc.identifier.citation | González, Víctor M, Luis Rodríguez-Moreno, Emilio Centeno, Andrej Benjak, Jordi Garcia-Mas, Pere Puigdomènech, and Miguel A Aranda. 2010. “Genome-wide BAC-end Sequencing of Cucumis Melo Using Two BAC Libraries.” BMC Genomics 11 (1): 618. doi: 10.1186/1471-2164-11-618 | ca |
dc.identifier.issn | 1471-2164 | ca |
dc.identifier.uri | http://hdl.handle.net/20.500.12327/3123 | |
dc.description.abstract | Background: Although melon (Cucumis melo L.) is an economically important fruit crop, no genome-wide sequence information is openly available at the current time. We therefore sequenced BAC-ends representing a total of 33,024 clones, half of them from a previously described melon BAC library generated with restriction endonucleases and the remainder from a new random-shear BAC library. Results: We generated a total of 47,140 high-quality BAC-end sequences (BES), 91.7% of which were paired-BES. Both libraries were assembled independently and then cross-assembled to obtain a final set of 33,372 nonredundant, high-quality sequences. These were grouped into 6,411 contigs (4.5 Mb) and 26,961 non-assembled BES (14.4 Mb), representing ~4.2% of the melon genome. The sequences were used to screen genomic databases, identifying 7,198 simple sequence repeats (corresponding to one microsatellite every 2.6 kb) and 2,484 additional repeats of which 95.9% represented transposable elements. The sequences were also used to screen expressed sequence tag (EST) databases, revealing 11,372 BES that were homologous to ESTs. This suggests that ~30% of the melon genome consists of coding DNA. We observed regions of microsynteny between melon paired-BES and six other dicotyledonous plant genomes. Conclusion: The analysis of nearly 50,000 BES from two complementary genomic libraries covered ~4.2% of the melon genome, providing insight into properties such as microsatellite and transposable element distribution, and the percentage of coding DNA. The observed synteny between melon paired-BES and six other plant genomes showed that useful comparative genomic data can be derived through large scale BAC-end sequencing by anchoring a small proportion of the melon genome to other sequenced genomes. | ca |
dc.description.sponsorship | Acknowledgements We gratefully acknowledge Núria Aventín (CRAG, Barcelona, Spain) for technical assistance in the culture and replica plating of BAC clones. This project was carried out in the frame of the MELONOMICS project (2009- 2012) of the Fundación Genoma España, and also supported by funding of the Consolider-Ingenio 2010 Programme of the Spanish Ministerio de Ciencia e Innovación (CSD2007-00036 “Center for Research in Agrigenomics”). Note: The Cucumis melo BAC-end sequences are available in the DDBJ/ EMBL/GenBank databases under the accession numbers HN291986- HN339125 as well as in the Spanish melon genome sequencing project webpage http://melonomics.upv.es/public_files. | ca |
dc.format.extent | 11 | ca |
dc.language.iso | eng | ca |
dc.publisher | BMC | ca |
dc.relation.ispartof | BMC Genomics | ca |
dc.rights | Attribution 4.0 International | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.title | Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries | ca |
dc.type | info:eu-repo/semantics/article | ca |
dc.description.version | info:eu-repo/semantics/publishedVersion | ca |
dc.rights.accessLevel | info:eu-repo/semantics/openAccess | |
dc.embargo.terms | cap | ca |
dc.relation.projectID | MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/ | ca |
dc.subject.udc | 575 | ca |
dc.subject.udc | 633 | ca |
dc.identifier.doi | https://doi.org/10.1186/1471-2164-11-618 | ca |
dc.contributor.group | Genòmica i Biotecnologia | ca |
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