Rosa chinensis Old Blush Illumina genome v1.0

Overview
Analysis NameRosa chinensis Old Blush Illumina genome v1.0
MethodIllumina
SourceRosa_chinensis_Old_Blush_Illumina_genome_v1.0
Date performed2018-07-23

Visit Rosa chinensis Old Blush homozygous genome v2.0 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_Illumina_v1.0.fasta.gz
Chromosome hardmasked (FASTA file) Rchinensis_Illumina_v1.0.hardmasked.fasta.gz
Chromosome softmasked (FASTA file) Rchinensis_Illumina_v1.0.softmasked.fasta.gz

 

Gene Predictions

Downloads

Gene sequences (FASTA file) Rchinensis_Illumina_v1.0.gene.fasta.gz
Gene models (GFF3 file) Rchinensis_Illumina_v1.0_gene_models.gff3.gz
mRNA sequences (FASTA file) Rchinensis_Illumina_v1.0_CDs.fasta.gz
Protein sequences  (FASTA file) Rchinensis_Illumina_v1.0_prot.fasta.gz
mRNA sequences  (FASTA file) Rchinensis_Illumina_v1.0_mrna.fasta.gz
ncRNA sequences  (FASTA file) Rchinensis_Illumina_v1.0_ncrna.fasta.gz
Repeats (GFF3 file) Rchinensis_Illumina_v1.0_repeats.gff3.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.

Repeats

Repeats were predicted and provided as GFF3 file below.

Downloads

TE annotation (REPET-release V2.5) (GFF3 file) R.chinensis_Old_Blush_Illumina_v1.0_TE.gff3.gz