Prunus persica Genome
Peach Genome on GDR
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At the Plant and Animal Genome XV Meeting on 01/16/07, Jerry Tuskan from the Joint Genome Institute (JGI) announced plans to sequence the peach genome. Since then, an international consortium (IPGI) coalesced to do the work cooperatively. This consortium, under the direction of Drs Bryon Sosinski, Ignazio Verde and Daniel Rokhsar, includes numerous researchers from countries around the globe including the US, Italy (Drupomics), Spain and Chile. The specific roles of the participants will be outlined in the publication of the peach genome.
Peach (Prunus persica) is considered one of the genetically most well characterized species in the Rosaceae, and it has distinct advantages that make it suitable as a model genome species for Prunus as well as for other species in the Rosaceae. While some Prunus species, such as cultivated plums and sour cherries, are polyploid, peach is a diploid with n = 8 and has a comparatively small genome currently estimated to be ~220-230 Mbp based upon the peach v1.0 assembly. Peach has a relatively short juvenility period of 2-3 years compared to most other fruit tree species that require 6-10 years. In addition, a number of genes for fundamentally important traits have been genetically described in peach, including genes controlling flower and fruit development, tree growth habit, dormancy, cold hardiness, and disease and pest resistance.
Genome facts and statistics
Peach v1.0 was generated using DNA from the doubled haploid cultivar ‘Lovell’ therefore the genes and intervening DNA are “fixed” or identical for all alleles and both chromosomal copies of the genome. This doubled haploid nature was confirmed by the evaluation of >200 SSRs, and has facilitated a highly accurate and consistent assembly of the peach genome.
Peach v1.0 currently consists of 8 pseudomolecules (scaffolds) representing the 8 chromosomes of peach, and are numbered according to their corresponding linkage groups. The genome sequencing consisted of approximately 7.7 fold whole genome shotgun sequencing employing the accurate Sanger methodology, and was assembled using Arachne. The assembled peach scaffolds cover nearly 99% of the peach genome, with over 92% having confirmed orientation. To further validate the quality of the assembly, 74,757 Prunus ESTs were queried against the genome at 90% identity and 85% coverage with approximately 2% missing. Current estimates indicate that peach has 28,689 transcripts and 27,852 genes.