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

Authors:González, Víctor M.
Rodríguez Moreno, Luis
Centeno, Emilio
Benjak, Andrej
García-Mas, Jordi
Puigdomènech, Pere
Aranda, Miguel A.
Issue Date:5-Nov-2010
Publisher:BioMed Central
Citation:BMC Genomics 11:618 (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 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.
Description:11 pages, 1 figure, 6 tables.-- PMID: 21054843 [PubMed].-- Supporting information available at: http://www.biomedcentral.com/1471-2164/11/618/additional
Publisher version (URL):http://dx.doi.org/10.1186/1471-2164-11-618
URI:http://hdl.handle.net/10261/29972
E-ISSNmetadata.dc.identifier.doi = DOI:1471-2164
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