Prunus davidiana Whole Genome v1.0 Assembly & Annotation

Analysis NamePrunus davidiana Whole Genome v1.0 Assembly & Annotation
MethodALLPATHS-LG (na)
SourcePrunus davidiana Illumina Reads
Date performed2020-07-09

Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation (to be submitted by Cao Ke at Zhengzhou fruit research institute, CAAS, China)

Peach (Prunus persica) is the third most produced fruit crop, and is widely cultivated in temperate and subtropical regions. Due to its small genome size, peach has been used as a model plant for comparative and functional genomic researches of the Rosaceae family. In 2013, a high-quality reference genome sequence of peach constructed with the Sanger whole-genome shotgun approach was released by International Peach Genome Initiative. It is well known that wild germplasm contributes a significant proportion of the genetic resources of major crop species, and significant phenotypic differences in fruit size, flavor, and stress tolerance were found among P. persica and its wild relatives, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. It is necessary to study genetic variations of peach and its wild relatives from a broader perspective, such as pan-genome analyses. P. dvaidiana is an attractive model for studying resistance mechanism for aphid, drought, and low temperature.

Genome facts and statistics
The genome of P. davidiana was assembled using variety “Zhouxing Shan Tao” through Illumina platforms. Illumina reads from the wild species of P. persica were assembled using ALLPATHS-LG, and gaps in the assemblies were filled using GapCloser V1.12. Mate-paired reads were then used to generate scaffolds using SSPACE.
Draft genome of the wild peach specie, P. davidiana, was generated using only Illumina sequencing reads. We ultimately obtained 220.5 Mb assemblies, covering about 92.9% of the estimated genome sizes and having the scaffold N50 lengths of 0.64 Mb. The quality of the assemblies was demonstrated using the BUSCO analysis and RNA-Seq read mapping rates.
Gene prediction was performed using a combination of homology, ab initio and transcriptome based approaches. Finally, gene prediction and annotation were performed resulting in 26,527 protein-coding genes in P. davidiana.

Homology Analysis

Homology of the Prunus davidiana 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-9 was used for the NCBI nr (Release 2018-05) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 


Protein Homologs

Prunus davidiana v1.0 proteins with NCBI nr homologs (EXCEL file) pdavidiana_v1.0_vs_nr.xlsx.gz
Prunus davidiana v1.0 proteins with NCBI nr (FASTA file) pdavidiana_v1.0_vs_nr_hit.fasta.gz
Prunus davidiana v1.0 proteins without NCBI nr (FASTA file) pdavidiana_v1.0_vs_nr_noHit.fasta.gz
Prunus davidiana v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pdavidiana_v1.0_vs_arabidopsis.xlsx.gz
Prunus davidiana v1.0 proteins with arabidopsis (Araport11) (FASTA file) pdavidiana_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus davidiana v1.0 proteins without arabidopsis (Araport11) (FASTA file) pdavidiana_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus davidiana v1.0 proteins with SwissProt homologs (EXCEL file) pdavidiana_v1.0_vs_swissprot.xlsx.gz
Prunus davidiana v1.0 proteins with SwissProt (FASTA file) pdavidiana_v1.0_vs_swissprot_hit.fasta.gz
Prunus davidiana v1.0 proteins without SwissProt (FASTA file) pdavidiana_v1.0_vs_swissprot_noHit.fasta.gz
Prunus davidiana v1.0 proteins with TrEMBL homologs (EXCEL file) pdavidiana_v1.0_vs_trembl.xlsx.gz
Prunus davidiana v1.0 proteins with TrEMBL (FASTA file) pdavidiana_v1.0_vs_trembl_hit.fasta.gz
Prunus davidiana v1.0 proteins without TrEMBL (FASTA file) pdavidiana_v1.0_vs_trembl_noHit.fasta.gz



All assembly and annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links to download.  Alternatively, you can browse all available files on the FTP repository.


The Prunus davidiana Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) pdavidiana_v1.0.fasta.gz


Gene Predictions

The Prunus davidiana v1.0 genome gene prediction files are available in FASTA and GFF3 formats.


Protein sequences  (FASTA file) pdavidiana_v1.0.proteins.fasta.gz
Genes (GFF3 file) pdavidiana_v1.0.genes.gff3.gz


Functional Analysis

Functional annotation for the Prunus davidiana genome v1.0 are available for download below. The Prunus davidiana 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).


GO assignments from InterProScan pdavidiana_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pdavidiana_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pdavidiana_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pdavidiana_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 davidiana genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.


Fragaria x ananassa GDR RefTrans v1 Prunus davidiana_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus davidiana_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus davidiana_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus davidiana_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus davidiana_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus davidiana_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus davidiana_v1.0_rubus_GDR_reftransV2