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Background   Musa  species contain the fourth most important crop in developing countries. Here, we report the analysis of 6,252 BAC end-sequences, in order to view the sequence composition of the  Musa acuminata  genome in a cost effective and efficient manner.    Results  BAC end sequencing generated 6,252 reads representing 4,420,944 bp, including 2,979 clone pairs with an average read length after cleaning and filtering of 707 bp. All sequences have been submitted to GenBank, with the accession numbers  DX451975  –  DX458350 . The BAC end-sequences, were searched against several databases and significant homology was found to mitochondria and chloroplast (2.6%), transposons and repetitive sequences (36%) and proteins (11%). Functional interpretation of the protein matches was carried out by Gene Ontology assignments from matches to  Arabidopsis  and was shown to cover a broad range of categories. From protein matching regions of  Musa  BAC end-sequences, it was determined that the GC content of coding regions was 47%. Where protein matches encompassed a start codon, GC content as a function of position (5' to 3') across 129 bp sliding windows generates a "rice-like" gradient. A total of 352 potential SSR markers were discovered. The most abundant simple sequence repeats in four size categories were AT-rich. After filtering mitochondria and chloroplast matches, thousands of BAC end-sequences had a significant BLASTN match to the  Oryza sativa  and  Arabidopsis  genome sequence. Of these, a small number of BAC end-sequence pairs were shown to map to neighboring regions of the  Oryza sativa  genome representing regions of potential microsynteny.    Conclusion  Database searches with the BAC end-sequences and  ab initio  analysis identified those reads likely to contain transposons, repeat sequences, proteins and simple sequence repeats. Approximately 600 BAC end-sequences contained protein sequences that were not found in the existing available  Musa  expressed sequence tags, repeat or transposon databases. In addition, gene statistics, GC content and profile could also be estimated based on the region matching the top protein hit. A small number of BAC end pair sequences can be mapped to neighboring regions of the  Oryza sativa  representing regions of potential microsynteny. These results suggest that a large-scale BAC end sequencing strategy has the potential to anchor a small proportion of the genome of  Musa acuminata  to the genomes of  Oryza sativa  and possibly  Arabidopsis .

A BAC end view of the Musa acuminata genome