Prunus domestica Draft Genome Assembly v1.0 & Annotation v1.0.a1

Overview
Analysis NamePrunus domestica Draft Genome Assembly v1.0 & Annotation v1.0.a1
MethodNRGene, Illumina/10x Genomics
SourcePrunus domestica Draft Genome Assembly v1.0 & Annotation v1.0.a1
Date performed2018-12-18

Publication

Genome paper is in preparation. Available details are given below. We appreciate your patience. Please also see: 
Zhebentyayeva T, Shankar V, Scorza R, Callahan A, Ravelonandro M, Castro S, DeJong T, Saski CA, Dardick C. (2019) Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping. Hortic Res. 6:12.

 

About the Assembly

Overview

European plum (Prunus domestica) is a hexaploid fruit tree species used predominately for drying as prunes. Currently, almost all known commercial production is based on ‘French’ cultivars which were recently shown to have been clonally selected (Zhebentyayeva et al., 2019). Thus, the worldwide industry is largely a monoculture. Current evidence suggests that P. domestica originated as an interspecific hybrid of a diploid P. cerasifera and a tetraploid P. spinosa that itself may have been an interspecific hybrid of P. cerasifera and an unknown Eurasian plum species (Zhebentyayeva et al., 2019). This complexity of the P. domestica genome makes the sequencing and assembly of the genome particularly challenging.

Sequencing and assembly

Sequencing and assembly was performed by NRGene using 2nd generation sequencing technology with total depth (coverage) of 210X using Illumina™ technologies. The sequencing data was processed and assembled using DeNovoMAGIC™ assembler application version 3.0. Total of 27,870 phased assembled scaffolds were generated. The integrity of the assembly was verified using several quality-assurance procedures including the independent BUSCO benchmark (http://busco.ezlab.org/) which is used to specifically indicating the genic region integrity, ploidy and zygosity characteristics of the assembled genome.

Genome annotation

2,747 scaffolds (>10Kb in length) from the genome assembly were annotated using GenSAS (www.gensas.org) by GDR team.  The genome sequence was masked using RepeatMasker (other dicots RepBase dataset) and RepeatModeler.  The gene models were predicted using BRAKER2 which was trained with a BAM file which contained aligned RNA-seq reads from HISAT2 (RNA-seq reads were provided by Chris Dardick, see below).  A total of 130,866 gene models were identified.  tRNA and rRNA were identified using tRNAscan-SE and RNAmmer, respectively.  Functional annotation was performed using InterProScan, Pfam, SignalP, TargetP, and protein alignments with BLAST and DIAMOND.  BUSCO was run on the predicted proteins, and the genome annotation contains 92.4% of the complete, conserved BUSCOs.

A set of approximately 10 billion raw RNAseq reads (150bp paired-end) derived from vegetative bud and leaf tissues at various stages of development were used for gene prediction. This RNAseq set was created using the translatome profiling technique where epitope tagged ribosomes are immunopurified to enrich for actively translating mRNAs. This technique enriches the mRNA fraction for fully spliced transcripts (Collum et al. 2019; Collum TD, Stone AL, Sherman DJ, Rogers EE, Dardick C, and Culver JN. (2019) Translatome profiling of plum pox virus infected leaves in Prunus European plum reveals post-dormancy temporal and spatial coordination of defense responses in phloem tissues. MPMI. In press).

 
Contacts
Project Leaders: Dr. Chris Dardick chris.dardick@ars.usda.gov
Dr. Tetyana Zhebentyayeva tnz4@psu.edu
 

This work was supported by the USDA National Institute of Food and Agriculture, Plant-Associated Microbes and Plant-Microbe Interactions Program (2015–67013-23004) and the NSF Division of Integrative Organismal Systems (ISO-1644713).

Assembly

The Prunus domestica Genome  assembly v1.0 files are available in FASTA and GFF3 formats.

Downloads

Chromosome (FASTA file) P.domestica_v1.0.fasta.gz

 

Gene Predictions

The Prunus domestica Genome  v1.0 gene prediction files are available in FASTA and GFF3 formats.

Downloads

Gene sequences (FASTA file) P.domestica_v1.0.gene.fasta.gz
Gene models (GFF3 file) P.domestica_v1.0_gene_models.gff3.gz
CDS sequences (FASTA file) P.domestica_v1.0_CDs.fasta.gz
Protein sequences  (FASTA file) P.domestica_v1.0_proteins.fasta.gz

 

Downloads

All 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 do download.  Alternatively, you can use the FTP repository for bulk download.

Homology

Homology of the Prunus_domestica  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 (TAIR10), UniProtKB/SwissProt (Release 2018-04), and UniProtKB/TrEMBL (Release 2018-04) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Prunus_domestica v1.0 transcripts with NCBI nr homologs (EXCEL file) p.domestica_v1.0_vs_nr.xlsx.gz
Prunus_domestica v1.0 transcripts with NCBI nr (FASTA file) p.domestica_v1.0_vs_nr_hit.fasta.gz
Prunus_domestica v1.0 transcripts without NCBI nr (FASTA file) p.domestica_v1.0_vs_nr_noHit.fasta.gz
Prunus_domestica v1.0 transcripts with arabidopsis (TAIR10) homologs (EXCEL file) p.domestica_v1.0_vs_tair.xlsx.gz
Prunus_domestica v1.0 transcripts with arabidopsis (TAIR10) (FASTA file) p.domestica_v1.0_vs_tair_hit.fasta.gz
Prunus_domestica v1.0 transcripts without arabidopsis (TAIR10) (FASTA file) p.domestica_v1.0_vs_tair_noHit.fasta.gz
Prunus_domestica v1.0 transcripts with SwissProt homologs (EXCEL file) p.domestica_v1.0_vs_swissprot.xlsx.gz
Prunus_domestica v1.0 transcripts with SwissProt (FASTA file) p.domestica_v1.0_vs_swissprot_hit.fasta.gz
Prunus_domestica v1.0 transcripts without SwissProt (FASTA file) p.domestica_v1.0_vs_swissprot_noHit.fasta.gz
Prunus_domestica v1.0 transcripts with TrEMBL homologs (EXCEL file) p.domestica_v1.0_vs_trembl.xlsx.gz
Prunus_domestica v1.0 transcripts with TrEMBL (FASTA file) p.domestica_v1.0_vs_trembl_hit.fasta.gz
Prunus_domestica v1.0 transcripts without TrEMBL (FASTA file) p.domestica_v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation files for the Prunus domestica Genome v1.0 are available for download below. The Prunus domesticaGenome-Dardick 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).

Downloads

GO assignments from InterProScan P.domestica_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan P.domestica_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways P.domestica_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs P.domestica_v1.0_KEGG-pathways.xlsx.gz