repetitive part of the banana (musa acuminata) genome investigated by low-depth 454 sequencing重复的部分香蕉(穆萨acuminata)基因组调查low-depth 454测序.pdfVIP

Hřibová et al. BMC Plant Biology 2010, 10:204 /1471-2229/10/204 RESEARCH ARTICLE Open Access Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing 1* 2 3 4 2 1 Eva Hřibová , Pavel Neumann , Takashi Matsumoto , Nicolas Roux , Jiří Macas , Jaroslav Doležel Abstract Background: Bananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement. Results: In this work, we report on the first thorough characterization of the repeat component of the banana (M. acuminata cv. ‘Calcutta 4′) genome. Analysis of almost 100 Mb of sequence data (0.15× genome coverage) permitted partial sequence reconstruction and characterization of repetitive DNA, making up about 30% of the genome. The results showed that the banana repeats are predominantly made of various types of Ty1/copia and Ty3/gypsy retroelements representing 16 and 7% of the genome respectively. On the other hand, DNA transposons were found to be rare. In addition to new families of transposable elements, two new satellite repeats were discovered and found useful as cytogenetic markers. To help in banana sequence annotation, a specific Musa repeat database was created, and its utility was demons