Prunus avium Tieton Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus avium Tieton Genome v1.0 Assembly & Annotation
MethodSupernova assembler (2.0)
SourcePrunus avium Tieton v1.0
Date performed2020-06-16

Publication:

Wang J, Liu W, Zhu D, Zhou X, Hong P, Zhao H, Tan Y, Chen X, Zong X, Xu L, Zhang L, Wei H, Liu Q. A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology. PeerJ. 2020 Jun 5;8:e9114. doi: 10.7717/peerj.9114. 

Overview:

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

 

Assembly

The Prunus avium Tieton Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) paviumTieton_chromosome_v1.0.fasta.gz
Scaffolds (FASTA file) paviumTieton_scaffold_v1.0.fasta.gz

 

Gene Predictions

The Prunus avium Tieton v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) paviumTieton_v1.0.proteins.fasta.gz
Genes (GFF3 file) paviumTieton_v1.0.genes.gff3.gz

 

Homology

Homology of the Prunus avium Tieton 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 (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Prunus avium Tieton v1.0 proteins with NCBI nr homologs (EXCEL file) paviumTieton_v1.0_vs_nr.xlsx.gz
Prunus avium Tieton v1.0 proteins with NCBI nr (FASTA file) paviumTieton_v1.0_vs_nr_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without NCBI nr (FASTA file) paviumTieton_v1.0_vs_nr_noHit.fasta.gz
Prunus avium Tieton v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) paviumTieton_v1.0_vs_arabidopsis.xlsx.gz
Prunus avium Tieton v1.0 proteins with arabidopsis (Araport11) (FASTA file) paviumTieton_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without arabidopsis (Araport11) (FASTA file) paviumTieton_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus avium Tieton v1.0 proteins with SwissProt homologs (EXCEL file) paviumTieton_v1.0_vs_swissprot.xlsx.gz
Prunus avium Tieton v1.0 proteins with SwissProt (FASTA file) paviumTieton_v1.0_vs_swissprot_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without SwissProt (FASTA file) paviumTieton_v1.0_vs_swissprot_noHit.fasta.gz
Prunus avium Tieton v1.0 proteins with TrEMBL homologs (EXCEL file) paviumTieton_v1.0_vs_trembl.xlsx.gz
Prunus avium Tieton v1.0 proteins with TrEMBL (FASTA file) paviumTieton_v1.0_vs_trembl_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without TrEMBL (FASTA file) paviumTieton_v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation for the Prunus avium Tieton genome v1.0 are available for download below. The Prunus avium Tieton 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).

Downloads

GO assignments from InterProScan paviumTieton_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan paviumTieton_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways paviumTieton_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs paviumTieton_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 avium Tieton 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 avium Tieton_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus avium Tieton_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus avium Tieton_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus avium Tieton_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus avium Tieton_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus avium Tieton_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus avium Tieton_v1.0_rubus_GDR_reftransV2
Download

All assembly and 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 to download.  Alternatively, you can browse all available files on the FTP repository.