Isolation and characterization of the highly repeated fraction of the banana genome
Language English Country Switzerland Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
18253041
DOI
10.1159/000112073
PII: 000112073
Knihovny.cz E-resources
- MeSH
- Musa genetics MeSH
- Clone Cells MeSH
- DNA, Plant genetics isolation & purification MeSH
- Genome, Plant genetics MeSH
- Gene Dosage MeSH
- Gene Library MeSH
- Primed In Situ Labeling MeSH
- Repetitive Sequences, Nucleic Acid genetics MeSH
- DNA, Ribosomal genetics MeSH
- Base Sequence MeSH
- Sequence Homology, Nucleic Acid MeSH
- Tandem Repeat Sequences MeSH
- Chromosomes, Artificial, Bacterial MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA, Plant MeSH
- DNA, Ribosomal MeSH
Although the nuclear genome of banana (Musa spp.) is relatively small (1C approximately 610 Mbp for M. acuminata), the results obtained from other sequenced genomes suggest that more than half of the banana genome may be composed of repetitive and non-coding DNA sequences. Knowledge of repetitive DNA can facilitate mapping of important traits, phylogenetic studies, BAC-based physical mapping, and genome sequencing/annotation. However, only a few repetitive DNA sequences have been characterized in banana. In this work, we used DNA reassociation kinetics to isolate the highly repeated fraction of the banana genome (M. acuminata 'Calcutta 4'). Two libraries, one prepared from Cot =0.05 DNA (2,688 clones) and one from Cot =0.1 sequences (4,608 clones), were constructed, and 614 DNA clones were chosen randomly for sequencing and further characterization. Dot-plot analysis revealed that 14% of the sequenced clones contained various semi-tandem and palindromic repeated sequences. 'BLAST' homology searches showed that, in addition to tandem repeats, the Cot libraries were composed mainly of different types of retrotransposons, the most frequent being the Ty3/gypsy type monkey retrotransposon. Selected sequences displaying tandem organization properties were mapped by PRimed IN Situ DNA labeling (PRINS) to the secondary constriction on metaphase chromosomes of M. acuminata 'Calcutta 4'. Southern hybridization with selected BAC clones carrying 45S rDNA confirmed the presence of the tandem repeats in the 45S rDNA unit. This work significantly expands the knowledge of the repetitive fraction of the Musa genome and organization of its chromosomes.
References provided by Crossref.org
Advances in the Molecular Cytogenetics of Bananas, Family Musaceae
Genome-wide analysis of repeat diversity across the family Musaceae
Flow sorting and sequencing meadow fescue chromosome 4F
Molecular analysis and genomic organization of major DNA satellites in banana (Musa spp.)
Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing