Expressed Haplotypes and Polymorphisms in Prunus Species

Expressed sequence tags (ESTs) represent collective and redundant gene transcripts that contain alleles and paralogs of genes expressed in various genotypes, tissues, developmental stages, and environmental conditions. The former are primarily responsible for distinct individual phenotypes in a segregating manner, and the latter may additionally contribute to functional and phenotypic diversification. In this study, genome-wide analysis was performed to identify expressed haplotypes harboring simple sequence repeat (SSR) polymorphisms, single nucleotide polymorphisms (SNP), short insertions / deletions, introns, coding degeneracy statuses (non-synonymous vs. synonymous), and other genomic features, using ESTs from all Prunus species and the peach reference genome. In addition, some unigenes containing a single haplotype but sharing high identities among them likely are paralogous functional members in a same gene family. The distribution of all polymorphic haplotypes on the peach reference genome was also determined to facilitate selective use of these expressed allelic polymorphisms and genomic features in many genetic studies, such as mapping of whole genomes, tagging of important traits, comparison of genome evolution, classification of diverse clades, and many rapidly developing areas such as pharmacogenomics and functional proteomics.