Prunus persica Lovell 2D Genome v3.0

Overview
Analysis NamePrunus persica Lovell 2D Genome v3.0
Methodn/a (na)
SourceLovell 2D
Date performed2025-05-13

Publication: Gottschalk, C., Brock, J. R., Mansfeld, B. N., Main, D., Jung, S., Zheng, P., Vann, C., Demuth, M., Bennett, D., Liu, Z., & Dardick, C. (Year). Improved genome assembly of double haploid Prunus persica siblings ‘Lovell 2D’ and ‘Lovell 5D’ and the peach NLRome. Submitted to Genes, Genomes, and Genetics (G3)

Abstract: Prunus persica (peach) has long served as a model fruit tree for studying phenological events. It has a relatively small genome and exhibits tremendous plasticity in climate tolerances due to the high variation of chill requirements, bloom times, and fruit ripening times. The peach variety ‘Lovell 2D’ was used to generate one of the first high-quality genome assemblies for a tree species, using Sanger sequencing of genetic-map ordered BAC clones. A key to the high quality of this early assembly was the use of a doubled haploid variety, which eliminates the challenges posed by mixed haplotypes. Here, we re-sequenced and assembled the ‘Lovell 2D’ genome along with a doubled haploid sibling ‘Lovell 5D’ using 3rd generation technologies. The resulting genomes were significantly more contiguous than the current ‘Lovell 2D’ reference genome (ver2.0 updated in 2017) and are closer to the estimated total genome size for peach (265 Mb). In addition, new gene, transposable element (TE), and Nucleotide-binding domain and Leucine-rich repeat receptor (NLR) annotations were performed to enhance the integrity and utility of the genome. These updated peach doubled-haploid reference assemblies will provide the research community with an improved reference genome for genomics-guided studies and breeding efforts.

Homology

Homology of the Prunus persica Lovell 2D genome v3.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2025-02), and UniProtKB/TrEMBL (Release 2025-02) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

P. persica Lovell 2D v3.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Ppersica_Lovell_2D_v3.0_vs_arabidopsis.xlsx.gz
P. persica Lovell 2D v3.0 proteins with arabidopsis (Araport11) (FASTA file) Ppersica_Lovell_2D_v3.0_vs_arabidopsis_hit.fasta.gz
P. persica Lovell 2D v3.0 proteins without arabidopsis (Araport11) (FASTA file) Ppersica_Lovell_2D_v3.0_vs_arabidopsis_noHit.fasta.gz
P. persica Lovell 2D v3.0 proteins with SwissProt homologs (EXCEL file) Ppersica_Lovell_2D_v3.0_vs_swissprot.xlsx.gz
P. persica Lovell 2D v3.0 proteins with SwissProt (FASTA file) Ppersica_Lovell_2D_v3.0_vs_swissprot_hit.fasta.gz
P. persica Lovell 2D v3.0 proteins without SwissProt (FASTA file) Ppersica_Lovell_2D_v3.0_vs_swissprot_noHit.fasta.gz
P. persica Lovell 2D v3.0 proteins with TrEMBL homologs (EXCEL file) Ppersica_Lovell_2D_v3.0_vs_trembl.xlsx.gz
P. persica Lovell 2D v3.0 proteins with TrEMBL (FASTA file) Ppersica_Lovell_2D_v3.0_vs_trembl_hit.fasta.gz
P. persica Lovell 2D v3.0 proteins without TrEMBL (FASTA file) Ppersica_Lovell_2D_v3.0_vs_trembl_noHit.fasta.gz
Assembly

The Prunus persica Lovell 2D v3.0 assembly file is available in FASTA format.

Downloads

Scaffolds and Chromosomes (FASTA file) ppersica_Lovell_2D_v3.0.fasta.gz
Scaffolds and Chromosomes (Masked FASTA file) ppersica_Lovell_2D_v3.0.fasta.gz
Gene Predictions

The Prunus persica Lovell 2D v3.0 genome gene prediction files are available in GFF3 and FASTA formats.

Downloads

Genes (GFF3 file) ppersica_Lovell_2D_v3.0.genes.gff3.gz
Transcripts (FASTA file) ppersica_Lovell_2D_v3.0.transcript.fasta.gz
Protein sequences (FASTA file) ppersica_Lovell_2D_v3.0.protein.fasta.gz
TE (GFF3 file) ppersica_Lovell_2D_v3.0.TE.gff3.gz
Functional Analysis

Functional annotation for the Prunus persica Lovell 2D genome v3.0 are available for download below. The Prunus persica Lovell 2D genome v3.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan Ppersica_Lovell_2D_v3.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Ppersica_Lovell_2D_v3.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Ppersica_Lovell_2D_v3.0_KEGG-orthologis.xlsx.gz
Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Prunus persica Lovell 2D genome v3.0 assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.

 

Fragaria x ananassa GDR RefTrans v1 Ppersica_Lovell_2D_v3.0_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 Ppersica_Lovell_2D_v3.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Ppersica_Lovell_2D_v3.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Ppersica_Lovell_2D_v3.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Ppersica_Lovell_2D_v3.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Ppersica_Lovell_2D_v3.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Ppersica_Lovell_2D_v3.0_pyrus_GDR_reftransV1