Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

0350031 - ÚEB 2011 RIV GB eng J - Journal Article
Hřibová, Eva - Neumann, Pavel - Matsumoto, T. - Roux, N. - Macas, Jiří - Doležel, Jaroslav
Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing.
BMC Plant Biology. Roč. 10, č. 204 (2010), s. 1-10. ISSN 1471-2229. E-ISSN 1471-2229
R&D Projects: GA AV ČR KJB500380901; GA AV ČR IAA600380703; GA MŠMT(CZ) LC06004
Institutional research plan: CEZ:AV0Z50380511; CEZ:AV0Z50510513
Keywords : IN-SITU HYBRIDIZATION * RIBOSOMAL-RNA GENES * DNA-SEQUENCES
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 4.085, year: 2010

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 (0.15x 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 demonstrated by analyzing the repeat composition of 62 genomic BAC clones.
Permanent Link: http://hdl.handle.net/11104/0190133