Prunus dulcis Nonpareil Genome v1.0 Assembly & Annotation

Analysis NamePrunus dulcis Nonpareil Genome v1.0 Assembly & Annotation
MethodFALCON (FALCON v.0.3.0)
SourceIllumina, PacBio sequence, Prunus dulcis Nonpareil
Date performed2022-07-27


D'Amico-Willman KM, Ouma WZ, Meulia T, Sideli GM, Gradziel TM, Fresnedo-Ramírez J. Whole-genome sequence and methylome profiling of the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar 'Nonpareil'. G3 (Bethesda). 2022 May 6;12(5):jkac065. doi: 10.1093/g3journal/jkac065. (GDR | Journal)

Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including ‘Nonpareil,’ which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for ‘Nonpareil’ is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment.


This work was supported through the Ohio State University CFAES-SEEDS program grant 2019-125, the Almond Board of California Grant HORT35, the Translational Plant Sciences Graduate Fellowship, the Cancer Center Support Grant (CCSG) P30CA016058, the AFRI-EWD Predoctoral Fellowship 2019-67011-29558 from the USDA National Institute of Food and Agriculture.


Homology of the Prunus dulcis Nonpareil 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 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 dulcis Nonpareil v1.0 proteins with NCBI nr homologs (EXCEL file) pdulcis_Nonpareil_v1.0_vs_nr.xlsx.gz
Prunus dulcis Nonpareil v1.0 proteins with NCBI nr (FASTA file) pdulcis_Nonpareil_v1.0_vs_nr_hit.fasta.gz
Prunus dulcis Nonpareil v1.0 proteins without NCBI nr (FASTA file) pdulcis_Nonpareil_v1.0_vs_nr_noHit.fasta.gz
Prunus dulcis Nonpareil v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pdulcis_Nonpareil_v1.0_vs_arabidopsis.xlsx.gz
Prunus dulcis Nonpareil v1.0 proteins with arabidopsis (Araport11) (FASTA file) pdulcis_Nonpareil_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus dulcis Nonpareil v1.0 proteins without arabidopsis (Araport11) (FASTA file) pdulcis_Nonpareil_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus dulcis Nonpareil v1.0 proteins with SwissProt homologs (EXCEL file) pdulcis_Nonpareil_v1.0_vs_swissprot.xlsx.gz
Prunus dulcis Nonpareil v1.0 proteins with SwissProt (FASTA file) pdulcis_Nonpareil_v1.0_vs_swissprot_hit.fasta.gz
Prunus dulcis Nonpareil v1.0 proteins without SwissProt (FASTA file) pdulcis_Nonpareil_v1.0_vs_swissprot_noHit.fasta.gz
Prunus dulcis Nonpareil v1.0 proteins with TrEMBL homologs (EXCEL file) pdulcis_Nonpareil_v1.0_vs_trembl.xlsx.gz
Prunus dulcis Nonpareil v1.0 proteins with TrEMBL (FASTA file) pdulcis_Nonpareil_v1.0_vs_trembl_hit.fasta.gz
Prunus dulcis Nonpareil v1.0 proteins without TrEMBL (FASTA file) pdulcis_Nonpareil_v1.0_vs_trembl_noHit.fasta.gz



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


Chromosomes (FASTA file) pdulcis_Nonpareil_v1.0.fasta.gz
Repeats (GFF3 file) pdulcis_Nonpareil_v1.0.repeats.gff3.gz
Repeats (FASTA file) pdulcis_Nonpareil_v1.0.repeats.fasta.gz


Gene Predictions

The Prunus dulcis Nonpareil v1.0 genome gene prediction file is available in GFF3 format.


Genes (GFF3 file) pdulcis_Nonpareil_v1.0.genes.gff3.gz
Protein sequences  (FASTA file) pdulcis_Nonpareil_v1.0.proteins.fasta.gz
Transcript sequences  (FASTA file) pdulcis_Nonpareil_v1.0.transcripts.fasta.gz


Functional Analysis

Functional annotation for the Prunus dulcis Nonpareil Genome v1.0 are available for download below. The Prunus dulcis Nonpareil 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 pdulcis_Nonpareil_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pdulcis_Nonpareil_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs pdulcis_Nonpareil_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways pdulcis_Nonpareil_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 dulcis Nonpareil 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 pdulcis_Nonpareil_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 pdulcis_Nonpareil_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 pdulcis_Nonpareil_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 pdulcis_Nonpareil_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 pdulcis_Nonpareil_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 pdulcis_Nonpareil_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 pdulcis_Nonpareil_v1.0_pyrus_GDR_reftransV1