Prunus avium Big Star Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus avium Big Star Genome v1.0 Assembly & Annotation
MethodALLPATHS-LG (50900)
SourcePRJNA419491
Date performed2022-03-03

Publication

Pinosio S, Marroni F, Zuccolo A, Vitulo N, Mariette S, Sonnante G, Aravanopoulos FA, Ganopoulos I, Palasciano M, Vidotto M, Magris G, Iezzoni A, Giuseppe Vendramin G, Morgante M. A draft genome of sweet cherry (Prunus avium L.) reveals genome-wide and local effects of domestication.. The Plant journal : for cell and molecular biology. 2020 May 11.

Abstract

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of sweet cherry genome. We assembled and annotated the genome of the cultivated variety 'Big Star*' and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome-wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and 5 breeding sweeps covering respectively 11.0 Mb and 2.4 Megabases of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species P. persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions, involved in different processes such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.

Homology

Homology of the Prunus avium Big Star 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_avium v1.0 proteins with NCBI nr homologs (EXCEL file) pavium_Big_Star_v1.0_vs_nr.xlsx.gz
Prunus_avium v1.0 proteins with NCBI nr (FASTA file) pavium_Big_Star_v1.0_vs_nr_hit.fasta.gz
Prunus_avium v1.0 proteins without NCBI nr (FASTA file) pavium_Big_Star_v1.0_vs_nr_noHit.fasta.gz
Prunus_avium v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pavium_Big_Star_v1.0_vs_arabidopsis.xlsx.gz
Prunus_avium v1.0 proteins with arabidopsis (Araport11) (FASTA file) pavium_Big_Star_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus_avium v1.0 proteins without arabidopsis (Araport11) (FASTA file) pavium_Big_Star_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus_avium v1.0 proteins with SwissProt homologs (EXCEL file) pavium_Big_Star_v1.0_vs_swissprot.xlsx.gz
Prunus_avium v1.0 proteins with SwissProt (FASTA file) pavium_Big_Star_v1.0_vs_swissprot_hit.fasta.gz
Prunus_avium v1.0 proteins without SwissProt (FASTA file) pavium_Big_Star_v1.0_vs_swissprot_noHit.fasta.gz
Prunus_avium v1.0 proteins with TrEMBL homologs (EXCEL file) pavium_Big_Star_v1.0_vs_trembl.xlsx.gz
Prunus_avium v1.0 proteins with TrEMBL (FASTA file) pavium_Big_Star_v1.0_vs_trembl_hit.fasta.gz
Prunus_avium v1.0 proteins without TrEMBL (FASTA file) pavium_Big_Star_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

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

Downloads

Chromosomes (FASTA file) pa_BigStar_v1.0.fasta.gz

 

Gene Predictions

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

Downloads

Protein sequences  (FASTA file) pa_BigStar_v1.0.proteins.fasta.gz
CDS  (FASTA file) pa_BigStar_v1.0.cds.fasta.gz
Genes (GFF3 file) pa_BigStar_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus avium Big Star Genome v1.0 are available for download below. The Prunus_avium 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 pavium_Big_Star_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pavium_Big_Star_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pavium_Big_Star_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pavium_Big_Star_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 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 pavium_Big_Star_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 pavium_Big_Star_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 pavium_Big_Star_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 pavium_Big_Star_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 pavium_Big_Star_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 pavium_Big_Star_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 pavium_Big_Star_v1.0_pyrus_GDR_reftransV1