Rosa chinensis Old Blush homozygous genome v2.0

Overview
Analysis NameRosa chinensis Old Blush homozygous genome v2.0
MethodALLPathsLG
SourceRosa_chinensis_Old_Blush_homozygous_genome_v2.0
Date performed2018-06-19

Visit Rosa chinensis Old Blush Illumina genome v1.0 page from the same publication

Publication

Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C, Carrère S, Caissard JC, Couloux A, Cottret L, Aury JM, Szécsi J, Latrasse D, Madoui MA, François L, Fu X, Yang SH, Dubois A, Piola F, Larrieu A, Perez M, Labadie K, Perrier L, Govetto B, Labrousse Y, Villand P, Bardoux C, Boltz V, Lopez-Roques C, Heitzler P, Vernoux T, Vandenbussche M, Quesneville H, Boualem A, Bendahmane A, Liu C, Le Bris M, Salse J, Baudino S, Benhamed M, Wincker P, Bendahmane M. The Rosa genome provides new insights into the domestication of modern roses. Nature genetics. 2018 Apr 30.  | Journal | GDR |

Abstract

Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of 'La France', one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

Assembly

Downloads

Chromosome (FASTA file) Rchinensis_homozygous_v2.0.fasta.gz
Chromosome hardmasked (FASTA file) Rchinensis_homozygous_v2.0.hardmasked.fasta.gz
Chromosome softmasked (FASTA file) Rchinensis_homozygous_v2.0.softmasked.fasta.gz
Chromosome (GFF3 file) Rchinensis_homozygous_v2.0.gff3.gz

 

Gene Predictions

Downloads

Gene sequences (FASTA file) Rchinensis_homozygous_v2.0.gene.fasta.gz
Gene models (GFF3 file) Rchinensis_homozygous_v2.0_gene_models.gff3.gz
mRNA sequences (FASTA file) Rchinensis_homozygous_v2.0_CDs.fasta.gz
Protein sequences  (FASTA file) Rchinensis_homozygous_v2.0_prot.fasta.gz
ncRNA sequences  (FASTA file) Rchinensis_homozygous_v2.0_ncrna.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 Rosa chinensis homozygous genome v2.0 protein 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 2017-07) 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

Rosa chinensis homozygous genome-v2.0 v3.0 proteins with NCBI nr homologs (EXCEL file) Rchinensis_homozygous_v2.0_vs_nr.xlsx.gz
Rosa chinensis homozygous genome-v2.0 v3.0 proteins with NCBI nr (FASTA file) Rchinensis_homozygous_v2.0_vs_nr_hit.fasta.gz
Rosa chinensis homozygous genome-v2.0 v1.0 proteins without NCBI nr (FASTA file) Rchinensis_homozygous_v2.0_vs_nr_noHit.fasta.gz
Rosa chinensis homozygous genome-v2.0 v1.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) Rchinensis_homozygous_v2.0_vs_tair.xlsx.gz
Rosa chinensis homozygous genome-v2.0 v3.0 proteins with arabidopsis (TAIR10) (FASTA file) Rchinensis_homozygous_v2.0_vs_tair_hit.fasta.gz
Rosa chinensis homozygous genome-v2.0 proteins without arabidopsis (TAIR10) (FASTA file) Rchinensis_homozygous_v2.0_vs_tair_noHit.fasta.gz
Rosa chinensis homozygous genome-v2.0 proteins with SwissProt homologs (EXCEL file) Rchinensis_homozygous_v2.0_vs_swissprot.xlsx.gz
Rosa chinensis homozygous genome-v2.0 proteins with SwissProt (FASTA file) Rchinensis_homozygous_v2.0_vs_swissprot_hit.fasta.gz
Rosa chinensis homozygous genome-v2.0 proteins without SwissProt (FASTA file) Rchinensis_homozygous_v2.0_vs_swissprot_noHit.fasta.gz
Rosa chinensis homozygous genome-v2.0 proteins with TrEMBL homologs (EXCEL file) Rchinensis_homozygous_v2.0_vs_trembl.xlsx.gz
Rosa chinensis homozygous genome-v2.0 proteins with TrEMBL (FASTA file) Rchinensis_homozygous_v2.0_vs_trembl_hit.fasta.gz
Rosa chinensis homozygous genome-v2.0 proteins without TrEMBL (FASTA file) Rchinensis_homozygous_v2.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation for the Rosa chinensis homozygous genome-v2.0 genome are available for download below. The Rosa chinensis homozygous genome-v2.0 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 Rchinensis_homozygous_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Rchinensis_homozygous_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Rchinensis_homozygous_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Rchinensis_homozygous_v2.0_KEGG-pathways.xlsx.gz

 

Repeats

Repeats were predicted and provided as GFF3 and FASTA files below.

Downloads

TE annotation (REPET-release V2.5) (GFF3 file) R.chinensis_Old_Blush_homozygous_v2.0_TE.gff3.gz
TE annotation (REPET-release V2.5) (FASTA file) R.chinensis_Old_Blush_homozygous_v2.0_TE.fasta.gz