Prunus mira Whole Genome v2.0 Assembly & Annotation

Analysis NamePrunus mira Whole Genome v2.0 Assembly & Annotation
SourcePrunus mira Illumina, PacBio and Hi-C Reads
Date performed2021-09-23


Cao K, Peng Z, Zhao X, Li Y, Liu K, Arus P, Fang W, Chen C, Wang X, Wu J, Fei Z, Wang L. Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance.. BMC biology. 2022 Jun 13; 20(1):139


As a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica. Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.

Homology Analysis

Homology of the Prunus mira Genome v2.0 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 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 


Protein Homologs

Prunus mira v2.0 proteins with NCBI nr homologs (EXCEL file) pmira_v2.0_vs_nr.xlsx.gz
Prunus mira v2.0 proteins with NCBI nr (FASTA file) pmira_v2.0_vs_nr_hit.fasta.gz
Prunus mira v2.0 proteins without NCBI nr (FASTA file) pmira_v2.0_vs_nr_noHit.fasta.gz
Prunus mira v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pmira_v2.0_vs_arabidopsis.xlsx.gz
Prunus mira v2.0 proteins with arabidopsis (Araport11) (FASTA file) pmira_v2.0_vs_arabidopsis_hit.fasta.gz
Prunus mira v2.0 proteins without arabidopsis (Araport11) (FASTA file) pmira_v2.0_vs_arabidopsis_noHit.fasta.gz
Prunus mira v2.0 proteins with SwissProt homologs (EXCEL file) pmira_v2.0_vs_swissprot.xlsx.gz
Prunus mira v2.0 proteins with SwissProt (FASTA file) pmira_v2.0_vs_swissprot_hit.fasta.gz
Prunus mira v2.0 proteins without SwissProt (FASTA file) pmira_v2.0_vs_swissprot_noHit.fasta.gz
Prunus mira v2.0 proteins with TrEMBL homologs (EXCEL file) pmira_v2.0_vs_trembl.xlsx.gz
Prunus mira v2.0 proteins with TrEMBL (FASTA file) pmira_v2.0_vs_trembl_hit.fasta.gz
Prunus mira v2.0 proteins without TrEMBL (FASTA file) pmira_v2.0_vs_trembl_noHit.fasta.gz



The Prunus mira Genome v2.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) pmira_v2.0.fasta.gz


Gene Predictions

The Prunus mira v2.0 genome gene prediction files are available in FASTA and GFF3 formats.


Protein sequences  (FASTA file) pmira_v2.0.proteins.fasta.gz
Genes (GFF3 file) pmira_v2.0.genes.gff3.gz


Functional Analysis

Functional annotation for the Prunus mira Genome v2.0 are available for download below. The Prunus mira Genome v2.0 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 pmira_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pmira_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs pmira_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways pmira_v2.0_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 mira 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 mira_v2.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus mira_v2.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus mira_v2.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus mira_v2.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus mira_v2.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus mira_v2.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus mira_v2.0_rubus_GDR_reftransV2