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


CONCLUSIONS
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.
Molecular Genetics Department, Center for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Jordi Girona, 18-26, 08034 Barcelona, Spain.
Víctor M
VM
González
Luis
L
Rodríguez-Moreno
Emilio
E
Centeno
Andrej
A
Benjak
Jordi
J
Garcia-Mas
Pere
P
Puigdomènech
Miguel A
MA
Aranda
D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D028463:Cucumis melo / Q000235:genetics*; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D018598:Minisatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D020161:Physical Chromosome Mapping; D017422:Sequence Analysis, DNA / Q000379:methods*; D026801:Synteny / Q000235:genetics