| Analysis Name | Prunus persica NCBIv2 Assembly & Annotation |
| Sequencing technology | ABI 3739 |
| Assembly method | ARACHNE v. 20071016_modified |
| Release Date | 2017-02-02 |
International Peach Genome Initiative; Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 2013 May;45(5):487-94. doi: 10.1038/ng.2586.
AbstractRosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
Assembly statistics
| Genome size | 227.4 Mb |
| Total ungapped length | 224.6 Mb |
| Number of chromosomes | 8 |
| Number of organelles | 1 |
| Number of scaffolds | 191 |
| Scaffold N50 | 27.4 Mb |
| Scaffold L50 | 4 |
| Number of contigs | 2,530 |
| Contig N50 | 255.4 kb |
| Contig L50 | 250 |
| GC percent | 37.5 |
| Genome coverage | 8.5x |
| Assembly level | Chromosome |
The Prunus persica NCBIv2 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCF_000346465.2_Prunus_persica_NCBIv2_genomic.fna.gz |
The Prunus persica NCBIv2 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GCF_000346465.2_Prunus_persica_NCBIv2_genomic.gff.gz |
| CDS sequences (FASTA file) | GCF_000346465.2_Prunus_persica_NCBIv2_cds_from_genomic.fna.gz |
| Protein sequences (FASTA file) | GCF_000346465.2_Prunus_persica_NCBIv2_protein.faa.gz |
Functional annotation for the Prunus persica NCBIv2 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Prunus_persica_NCBIv2.Pfam.tsv.gz |
Prunus S genes Nucleotide
Prunus S genes Protein