An overview of the apple genome through BAC end sequence analysis

Abstract

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.

Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences

“…The top six GO functional categories were associated with binding to nucleic acids (17.8%), ions (15.6%) and proteins (8.7%); and also transferase-(17.1%), hydrolase-(13.5%), and oxidoreductase activities (10.9%). The distribution of molecular functional categories in the carrot BES is comparable to previous Wndings in other dicot (Han and Korban 2008) and monocot (Huo et al 2008) species.…”

Characterizing the walnut genome through analyses of BAC end sequences

“…The most represented biological processes were metabolic process, cellular process, localization, biological regulation, and response to stimulus. The frequencies of genes in each category for walnut were comparable to those reported for other trees (Barakat et al 2009;Cheung and Town 2007;Han and Korban 2008).…”

Identification of Four New Est-Based Markers on the Apple (MALUS ⋉ DOMESTICA) Genetic Map

“…Comparative mapping is the manner to determine the level of colinearity of the genome of genetically distant plants (Han & Korban 2008) and predicts the location of genes coding an important trait in another species (Frary et al 2008, Velasco et al 2010.…”