Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries
González Miguel, Víctor Manuel (Centre de Recerca en Agrigenòmica)
Rodríguez Moreno, Luis (Centro de Edafología y Biología Aplicada del Segura)
Centeno, Emilio (Centre de Recerca en Agrigenòmica)
Benjak, Andrej (Centre de Recerca en Agrigenòmica)
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica)
Aranda, Miguel A. (Centro de Edafología y Biología Aplicada del Segura)

Data:	2010
Resum:	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 non-redundant, 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.
Ajuts:	Ministerio de Ciencia e Innovación CSD2007-00036
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Publicat a:	BMC genomics, Vol. 11 (2010) , art. 618, ISSN 1471-2164

DOI: 10.1186/1471-2164-11-618
PMID: 21054843

11 p, 935.2 KB

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