Prunus dulcis Nonpareil Genome v1.0 Assembly & Annotation

Overview
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

Abstract
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.

Assembly

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

Downloads

Chromosomes (FASTA file) pdulcis_Nonpareil_v1.0.fasta.gz

 

Gene Predictions

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

Downloads

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