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Open Access Research article

Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries

Víctor M González1, Luis Rodríguez-Moreno2, Emilio Centeno1, Andrej Benjak3, Jordi Garcia-Mas3, Pere Puigdomènech1 and Miguel A Aranda2*

Author Affiliations

1 Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain

2 Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS) - CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain

3 IRTA, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Carretera de Cabrils Km 2, 08348 (Barcelona), Spain

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BMC Genomics 2010, 11:618  doi:10.1186/1471-2164-11-618

Published: 5 November 2010

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 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.