Hi Folks,
Great news! The International Peach Genome Initiative (IPGA) has released version 1.0 of the peach genome sequence.
Peach v1.0 currently consists of 8 pseudomolecules (the first 8 scaffolds) representing the 8 chromosomes of peach and are numbered according to their corresponding linkage groups (a total of 202 scaffolds were generated). 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 (total of 202) 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, and we found that only ~2% were missing. This is truly a high quality genome! Gene prediction and annotation, is an ongoing process that may take years to complete, but current estimates indicate that peach has 28,689 transcripts and 27,852 genes.
Peach v1.0 was generated from DNA from the doubled haploid cultivar 'Lovell' which means that the genes and intervening DNA is "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 and assembly of the peach genome.
For more information about the project and access to the peach genome data and tools go GDR(www.rosaceae.org/peach/genome/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://www.rosaceae.o…> ), JGI (www.phytozome.org/peach/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://www.phytozome.…> ) or the Istituto di Genomica Applicata (http://services.appliedgenomics.org/gbrowse/prunus_public/ <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=http://services.appli…> )
Cheers
The IPGA folks
p.s. please note that GDR is now located at www.rosaceae.org <https://mail.cahnrs.wsu.edu/exchweb/bin/redir.asp?URL=https://mail.cahnrs.w…> , you will be redirected from the old GDR site to the new one. We will be sending out a newsletter about GDR very soon.
Dorrie Main, PhD
Associate Professor of Bioinformatics
Dept of Horticulture and Landscape Architecture
Washington State University
45 Johnson Hall, Pullman, WA 99164-6414
Email: dorrie(a)wsu.edu
Tel: (509) 335 2774
Fax: (509) 335 8690
URL: www.bioinfo.wsu.edu <http://www.bioinfo.wsu.edu/>
Randall Svancara
Systems Administrator/DBA/Developer
Main Bioinformatics Laboratory
Randall Svancara
Systems Administrator/DBA/Developer
Main Bioinformatics Laboratory
