Prunus avium Regina Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus avium Regina Genome v1.0 Assembly & Annotation
MethodFALCON-Unzip
SourcePacBio Reads
Date performed2023-11-30

Data Source:

https://doi.org/10.15454/KEW474

Description

This dataset includes the preliminary assembly and structural annotation of the version 1 (V1) of 'Regina' sweet cherry genome, following genome sequencing using PacBio long reads and optical mapping. We have reconstructed the pseudomolecules at near chromosome level using high density genetic linkage maps with GBS data. (2020-05-11)

Related Publication

Le Dantec L, Girollet N, Gouzy J, Sallet E, Fouché M, Quero-Garcia J, Dirlewanger E (2019) An Improved Assembly of the Diploid ‘Regina’ Sweet Cherry Genome. International Plant & Animal Genome XXVII / January 12-16, 2019 - San Diego, CA, USA.

 

Homology

Homology of the Prunus avium Regina genome v1.0 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 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

Prunus avium Regina v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Pavium_Regina_v1.0_vs_arabidopsis.xlsx.gz
Prunus avium Regina v1.0 proteins with arabidopsis (Araport11) (FASTA file) Pavium_Regina_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus avium Regina v1.0 proteins without arabidopsis (Araport11) (FASTA file) Pavium_Regina_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus avium Regina v1.0 proteins with SwissProt homologs (EXCEL file) Pavium_Regina_v1.0_vs_swissprot.xlsx.gz
Prunus avium Regina v1.0 proteins with SwissProt (FASTA file) Pavium_Regina_v1.0_vs_swissprot_hit.fasta.gz
Prunus avium Regina v1.0 proteins without SwissProt (FASTA file) Pavium_Regina_v1.0_vs_swissprot_noHit.fasta.gz
Prunus avium Regina v1.0 proteins with TrEMBL homologs (EXCEL file) Pavium_Regina_v1.0_vs_trembl.xlsx.gz
Prunus avium Regina v1.0 proteins with TrEMBL (FASTA file) Pavium_Regina_v1.0_vs_trembl_hit.fasta.gz
Prunus avium Regina v1.0 proteins without TrEMBL (FASTA file) Pavium_Regina_v1.0_vs_trembl_noHit.fasta.gz
Assembly

The Prunus avium Regina genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes(FASTA file) PRUAV_Regina_V1.0.a1.fasta.gz
Gene Predictions

The Prunus avium Regina genome v1.0 gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) PRUAV_Regina_V1.0.a1.genes.gff3.gz
Protein sequences (FASTA file) GDR_PRUAV_Regina_V1.0.a1.pep.fasta.gz
CDS sequences (FASTA file) GDR_PRUAV_Regina_V1.0.a1.cds.fasta.gz
Functional Analysis

Functional annotation for the Prunus avium Regina genome v1.0 are available for download below. The Prunus avium Regina genome v1.0 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 Pavium_Regina_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Pavium_Regina_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Pavium_Regina_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Pavium_Regina_v1.0_KEGG-pathways.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 avium Regina genome 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 Pavium_Regina_v1.0_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 Pavium_Regina_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Pavium_Regina_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pavium_Regina_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pavium_Regina_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Pavium_Regina_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Pavium_Regina_v1.0_pyrus_GDR_reftransV1