Analysis of the Musa genome from BAC sequencing and its comparison with rice

Piffanelli, Pietro; Ciampi, Ana; Ruiz, Manuel; Rodrigues da Silva, Felipe; Lescot, Magali; Papas, Georgios J.; Ronning, Catherine; Haas, Brian; Wortman, Jennifer; Frison, Emile A.; Roux, Nicolas; Miller, Roberto Neil Gerard; Côte, François-Xavier; D'Hont, Angélique; Souza, Manoel; Glaszmann, Jean-Christophe; Town, Christopher

Analysis of the Musa genome from BAC sequencing and its comparison with rice

2005

Within the MusaGenomics Consortium three BAC libraries were constructed from the genomes of Musa acuminata (diploid Calcutta-4, triploid Cavendish) and Musa balbisiana (diploid PKW). To study the structure and evolution of Musa genomes in relation to those of rice and sorghum, 50 Sorghum bicolor cDNA clones (EGRAM genes), were used as probes to screen the M. acuminata BAC library. Nine BAC clones were selected using EGRAM probes of known function, analysed by BAC-end sequencing and RFLP-fingerprinting, and sequenced. In addition, BAC clones believed to arise from the homeologous region on the A and B Musa genomes were identified using M. acuminata probes encoding for genes of agronomic interest. We have completely sequenced thirteen Musa BACs (~1.4 Mb), having a gene density of approximately one per 5 kb. The base composition of the CDSs ranges from 35% GC to 75% GC and shows a bimodal distribution. A subset of the genes shows a gradient in GC content along the coding sequence similar to rice, while the other set has a uniform base composition like Arabidopsis. At least one region of microsynteny was observed between Musa and rice, in which 6 genes are found in the same order of rice chromosome 5. Comparison of presumed homeologous BACs from the A and B genomes showed almost complete conservation of gene content and order. Retrotransposon content of these gene rich BACs was low. Preliminary phylogenetic analysis of individual genes suggests that Musa is as close to members of the Asparagales as to the Poales. (Texte intégral)

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