An overview of the apple genome through BAC end sequence analysis.
The apple, Malus x domestica Borkh., is one of the most important fruit trees grown worldwide. A bacterial artificial chromosome (BAC)-based physical map of the apple genome has been recently constructed. Based on this physical map, a total of approximately 2,100 clones from different contigs (overlapping BAC clones) have been selected and sequenced at both ends, generating 3,744 high-quality BAC end sequences (BESs) including 1,717 BAC end pairs. Approximately 8.5% of BESs contain simple sequence repeats (SSRs), most of which are AT/TA dimer repeats. Potential transposable elements are identified in approximately 21% of BESs, and most of these elements are retrotransposons. About 11% of BESs have homology to the Arabidopsis protein database. The matched proteins cover a broad range of categories. The average GC content of the predicted coding regions of BESs is 42.4%; while, that of the whole BESs is 39%. A small number of BES pairs were mapped to neighboring chromosome regions of A. thaliana and Populus trichocarpa; whereas, no pairs are mapped to the Oryza sativa genome. The apple has a higher degree of synteny with the closely related Populus than with the distantly related Arabidopsis. BAC end sequencing can be used to anchor a small proportion of the apple genome to the Populus and possibly to the Arabidopsis genomes.
Han
Yuepeng
Y
Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA.
Korban
Schuyler S
SS
D022202:Chromosomes, Artificial, Bacterial; D004251:DNA Transposable Elements; D018745:Genome, Plant; D027845:Malus / Q000235:genetics*; D018895:Microsatellite Repeats; D020161:Physical Chromosome Mapping; D010940:Plant Proteins / Q000235:genetics; D018626:Retroelements; D017422:Sequence Analysis, DNA
D004251:DNA Transposable Elements; D010940:Plant Proteins; D018626:Retroelements