Prunus domestica Draft Genome Assembly v1.0 Assembly & Annotation

Overview

Analysis Name Prunus domestica Draft Genome Assembly v1.0 Assembly & Annotation
Sequencing technology Illumina/10x Genomics
Assembly method NRGene
Release Date 2018-12-18
Reference Publication(s)

Callahan AM, Zhebentyayeva TN, Humann JL, Saski CA, Galimba KD, Georgi LL, Scorza R, Main D, Dardick CD. Defining the 'HoneySweet' insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica). Hortic Res. 2021 Jan 1;8(1):8. doi: 10.1038/s41438-020-00438-2.

Abstract

‘HoneySweet’ plum (Prunus domestica) is resistant to Plum pox potyvirus, through an RNAi-triggered mechanism. Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum. DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event. To confirm the transgene arrangement of the insertion event, ‘HoneySweet’ DNA was subjected to whole genome sequencing using Illumina short-read technology. Results indicated two different insertion events, one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side, flanked by plum DNA. To determine the locations of the two transgene insertions, a phased plum genome assembly was developed from the commercial plum ‘Improved French’. A subset of the scaffolds (2447) that were >10 kb in length and representing, >95% of the genome were annotated and used for alignment against the ‘HoneySweet’ transgene reads. Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart, however we were unable to identify which scaffold(s) represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars. Regardless, there was no evidence of any gene(s) being interrupted as a result of the insertions. Furthermore, RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.

Assembly statistics

Assembly

The Prunus domestica Draft Genome Assembly v1.0 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) plum_phased_scaffolds_subset.fasta.gz

Gene Predictions

The Prunus domestica Draft Genome Assembly v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) P.domestica_Genome-Dardick_v1.0.genes.gff3.gz
CDS sequences (FASTA file) P.domestica_Genome-Dardick_v1.0.cds.fasta.gz
Protein sequences (FASTA file) P.domestica_Genome-Dardick_v1.0.proteins.faa.gz

Functional Analysis

Functional annotation for the Prunus domestica Draft Genome Assembly v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Prunus_domestica_Draft_Genome_Assembly_v1.0.Pfam.tsv.gz

S genes

Prunus S genes Nucleotide

Prunus S genes Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences