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

TitleRepetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing.
Publication TypeJournal Article
Year of Publication2010
AuthorsHribová E, Neumann P, Matsumoto T, Roux N, Macas J, Dolezel J
JournalBMC Plant Biol
Volume10
Pagination204
Date Published2010 Sep 16
ISSN1471-2229
KeywordsDNA, Plant, DNA Transposable Elements, Genome, Plant, Microsatellite Repeats, Musa, Retroelements, Sequence Analysis, DNA
Abstract

<p><b>BACKGROUND: </b>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.</p><p><b>RESULTS: </b>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 demonstrated by analyzing the repeat composition of 62 genomic BAC clones.</p><p><b>CONCLUSION: </b>A low-depth 454 sequencing of banana nuclear genome provided the largest amount of DNA sequence data available until now for Musa and permitted reconstruction of most of the major types of DNA repeats. The information obtained in this study improves the knowledge of the long-range organization of banana chromosomes, and provides sequence resources needed for repeat masking and annotation during the Musa genome sequencing project. It also provides sequence data for isolation of DNA markers to be used in genetic diversity studies and in marker-assisted selection.</p>

DOI10.1186/1471-2229-10-204
Alternate JournalBMC Plant Biol.
PubMed ID20846365
PubMed Central IDPMC2956553
Showing 1 of 1 accessions
Accession Name Pictures Accession number Species / Group SubSpecies / SubGroup Origin Collection Available for distribution
Calcutta 4 ITC0249 acuminata subsp. burmannicoides India ITC