Theor Appl Genet (2004) 109:129–139 DOI 10.1007/s00122-004-1603-2 ORIGINAL PAPER R. Aert · L. Sµgi · G. Volckaert Gene content and density in banana (Musa acuminata) as revealed by genomic sequencing of BAC clones Received: 4 December 2003 / Accepted: 20 January 2004 / Published online: 18 February 2004  Springer-Verlag 2004 Abstract The complete sequence of Musa acuminata bacterial artificial chromosome (BAC) clones is presented and, consequently, the first analysis of the banana genome organization. One clone (MuH9) is 82,723 bp long with an overall G+C content of 38.2%. Twelve putative protein-coding sequences were identified, representing a gene density of one per 6.9 kb, which is slightly less than that previously reported for Arabidopsis but similar to rice. One coding sequence was identified as a partial M. acuminata malate synthase, while the remaining se- quences showed a similarity to predicted or hypothetical proteins identified in genome sequence data. A second BAC clone (MuG9) is 73,268 bp long with an overall G+C content of 38.5%. Only seven putative coding regions were discovered, representing a gene density of only one gene per 10.5 kb, which is strikingly lower than that of the first BAC. One coding sequence showed significant homology to the soybean ribonucleotide re- ductase (large subunit). A transition point between coding regions and repeated sequences was found at approxi- mately 45 kb, separating the coding upstream BAC end from its downstream end that mainly contained transpo- son-like sequences and regions similar to known repet- itive sequences of M. acuminata. This gene organization resembles Gramineae genome sequences, where genes are clustered in gene-rich regions separated by gene-poor DNA containing abundant transposons. Introduction The continuous advance in high-throughput DNA au- tomation and sequencing technologies has resulted in important breakthroughs in plant science. An example of this progress is the recent release of the high-accuracy complete sequence of rice chromosomes 1 (Sasaki et al. 2002) and 4 (Feng et al. 2002). High-quality sequencing becomes more desirable in view of current data, which demonstrate that the degree of collinearity between rice and Arabidopsis (currently the only other plant species with a draft genome sequence) is rather low at the level of the whole genome (Liu et al. 2001; Salse et al. 2002). An additional consequence is that ongoing genome projects in other plant species might not be able to rely on the information obtained from genomes already sequenced to the extent that had been expected. Therefore, despite the development of ever more intelligent algorithms for comparative genome analysis, the importance of individ- ual genome projects in higher organisms cannot be underestimated. With an annual production of about 100 million tons, banana and plantain (Musa sp.) are the most important fruit crop on worldwide and a staple food for about 400 million people in more than 120, mainly less- developed countries, in which it accounts for up to 90% of the carbohydrates consumed. However, this species has not been extensively used in genetic studies as triploidy and sterility is prevalent in most cultivars, which also results in low genetic variability. On the other hand, with a haploid genome size of 500–600 Mbp (Lysµk et al. 1999), the banana genome is among the smaller ones found within non-graminaceous monocotyledons. Natural hybridizations between the wild diploid species, Musa acuminata Colla (A genome, 2n=2x=22) and Musa balbisiana Colla (B genome, 2n=2x=22) have given rise to various genome combinations at three ploidy levels. This characteristic turns banana into an interesting candidate for comparative genomics. Being a mono- cotyledon but distantly related to rice, banana could represent a useful comparison point between dicotyle- Communicated by J.S. Heslop-Harrison R. Aert · G. Volckaert Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium Present address: R. Aert ( ) ) · L. Sµgi, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13, 3001 Leuven, Belgium e-mail: Rita.Aert@agr.kuleuven.ac.be Tel.: +32-16-321683 Fax: +32-16-321993