The domesticated Apple (Malus x domestica) is the most consumed fruit of the temperate regions of the world. Apples are members of the Rose family, the Rosaceae, and members of a larger group of plants collectively known as the Rosids, which staggeringly includes more than one third of all the flowering plants. Numerous plants within the Rosaceae have now either had their genomes sequenced (Peach, Strawberry) or are in the works or slated for sequencing (Almond, Pear, Plum, Cherry, Rose, Raspberry, and Apricot, for example). The latest member of the Rosaceae to have a genome sequence completed (just behind Peach and just ahead of Strawberry) is the ‘Golden Delicious’ cultivar of Apple (photo link).
The Apple Genome Consortium recently reported (see Velasco et al.) on the draft genome in the October issue of the journal Nature Genetics (see here also). This genome was sequenced using a combination of Roche/454 pyrosequencing and traditional Sanger sequencing. The estimated size of Apple genome is 742.3 Mb and the length of assembled contigs (603.9 Mb) is estimated to be 81% of the genome. Repetitive elements correspond to 67% of the assembled portion of the genome (500 Mb) and 98% of the unassembled portion of the genome (138.4 Mb).
When comparing the genome of Apple to other plants there were striking differences. A large number of putative genes have been identified in Apple (57,386). This value is considerably higher than most plants with sequenced genomes, such as Arabidopsis thaliana (27,228), Poplar (45,654), Papaya (28,027), Brachypodium distachyon (25,532), Grape (33,514), Rice (40,577), Sorghum (34,496), Cucumber (26,682) Soybean (46,430), Maize (32,540), Strawberry (34,809) and Cocoa (28,798). There were a total of 11,444 Apple-specific genes identified in the study. Gene density of the Apple genome is approximately equal to that of Poplar and Grape, but is less dense than the genomes of Arabidopsis, Brachypodium, and Rice. Like many plant genomes, the Apple genome has a large number of repeated elements which made the assembly of the genome more difficult than most.
One aspect of the Apple’s biology that has been elucidated by this genome is the development of the characteristic fruit, also known as the pome. This fruit is only found in the tribe Pyreae, which includes both Apple and Pear. The fruit probably evolved from the widespread duplication of MADS-box genes that, in the case of Apple, regulate the transition from flower to fruit. The tribe Pyreae had a relatively recent (in geological time that is, less that 50 million years ago) genome wide duplication event which has contributed to the wide diversity of MADS-box genes, as well as other gene families. In addition to this recent genome wide duplication event, there were prior duplication events which have contributed to the large size of the Apple genome.
Genes corresponding to Apple development, flowering, aroma and taste have been identified by the consortium, as well as genes within the plant that respond to disease and environmental factors, such as temperature and air pollution. Having the genome sequence of Apple will contribute to understanding the biology of Apple and accelerate the breeding of this economically important crop.