An Update on Rosaceae Genomes

The draft genome assemblies of double haploid apple (Malus x domestica cv. “Golden Delicious”), double haploid pear (Pyrus communis cv “Doyenne du Comice”), sweet cherry (Prunus avium cv “Stella”) and almond (Pyrus amygdalus – 2 selections S3067 and Lauranne) have been made available to the research community prior to publication via the Genome Portal http://genomicsdata.wsu.edu/public_access/index.php. For gene prediction, FGenesH, Augustus and Glimmer were used. FGenesH and Augustus predictions used the Tomato model. Glimmer predictions used the Arabidposis model. Consensus gene models were developed by combining the outputs of FGenesH, Glimmer and Augustus. A community wide effort is ongoing to perform analysis of the genomes. Initial comparative genomics analyses of sweet cherry and almond genomes has resulted in identification of 13 million identified single nucleotide polymorphisms (SNPs) out of which 70,000 account for non-sense mutations . Blast2GO analyses revealed that non-sense SNPs were not evenly distributed across all gene ontology terms. In comparison with peach, sweet cherry possesses non-sense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the non-climacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were also identified by comparing sweet and bitter almond sequences.