Genomes to Genes: Comparative genomic analysis in Prunoideae

Comparative genomic analysis can facilitate rapid biological discovery. We compared genomic and transcriptomic data from Prunus avium (sweet cherry) and Prunus dulcis (almond) against publicly available Prunus persica (peach) genome to understand the underlying genetic and genomic differences among these sub-family members. Reference based assemblies with each of 4 almond varieties and sweet cherry Illumina reads were completed. Genomic and transcriptomic 454 sequence reads from sweet cherry were also assembled against peach. Analysis of the SNP reports enabled identification of several almond and sweet cherry specific polymorphisms. Among sweet cherry and almond, SNPs were analyzed against the predicted genes from peach to identify the ones resulting in amino acid changes. Annotation of mis-sense and non-sense SNPs and INDELs was performed to identify pathways that are more or less conserved across the three species. Additionally, R values were calculated to compare almond and sweet cherry to peach, as well as between the 4 almond cultivars. This analysis is expected to serve as a foundation for unraveling biological phenomenon within Prunoideae. This comparative analysis was combined with existing genetic information to identify the putative genetic cause for bitterness, a major agro-economic trait in almonds. Of the sequenced almond varieties, two are sweet and two are bitter with each being homozygous for the respective trait. Polymorphisms, that are different between the sweet and bitter varieties, were identified in the 3 Mb region around the Sweet kernel (Sk) locus. Further analysis of a correlation of these putative polymorphisms with the sweet/bitterness trait is underway and the ensuing results will be presented.