Rosa rugosa Whole Genome v1.0 Assembly & Annotation

Analysis NameRosa rugosa Whole Genome v1.0 Assembly & Annotation
MethodHiCanu, Juicerbox tool ( v2.2.1)
Date performed2021-08-31


Chen F, Su L, Hu S, Xue JY, Liu H, Liu G, Jiang Y, Du J, Qiao Y, Fan Y, Liu H, Yang Q, Lu W, Shao ZQ, Zhang J, Zhang L, Chen F, Cheng ZM. A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics. Hortic Res 8, 141 (2021).


Rosa rugosa, commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for R. rugosa to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of R. rugosa, and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of R. rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred ~100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of R. rugosa and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose R. chinensis and a retroposition in strawberry caused by post-WGT events. We also found that floral development- and stress response signaling-related gene modules were retained after the WGT. Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 (DRIP2) and PEPTIDE TRANSPORTER 3 (PTR3) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of R. rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.

Homology Analysis

Homology of the Rosa rugosa 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

Rosa rugosa v1.0 proteins with NCBI nr homologs (EXCEL file) Rosa_rugosa_v1.0_vs_nr.xlsx.gz
Rosa rugosa v1.0 proteins with NCBI nr (FASTA file) Rosa_rugosa_v1.0_vs_nr_hit.fasta.gz
Rosa rugosa v1.0 proteins without NCBI nr (FASTA file) Rosa_rugosa_v1.0_vs_nr_noHit.fasta.gz
Rosa rugosa v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Rosa_rugosa_v1.0_vs_arabidopsis.xlsx.gz
Rosa rugosa v1.0 proteins with arabidopsis (Araport11) (FASTA file) Rosa_rugosa_v1.0_vs_arabidopsis_hit.fasta.gz
Rosa rugosa v1.0 proteins without arabidopsis (Araport11) (FASTA file) Rosa_rugosa_v1.0_vs_arabidopsis_noHit.fasta.gz
Rosa rugosa v1.0 proteins with SwissProt homologs (EXCEL file) Rosa_rugosa_v1.0_vs_swissprot.xlsx.gz
Rosa rugosa v1.0 proteins with SwissProt (FASTA file) Rosa_rugosa_v1.0_vs_swissprot_hit.fasta.gz
Rosa rugosa v1.0 proteins without SwissProt (FASTA file) Rosa_rugosa_v1.0_vs_swissprot_noHit.fasta.gz
Rosa rugosa v1.0 proteins with TrEMBL homologs (EXCEL file) Rosa_rugosa_v1.0_vs_trembl.xlsx.gz
Rosa rugosa v1.0 proteins with TrEMBL (FASTA file) Rosa_rugosa_v1.0_vs_trembl_hit.fasta.gz
Rosa rugosa v1.0 proteins without TrEMBL (FASTA file) Rosa_rugosa_v1.0_vs_trembl_noHit.fasta.gz



The Rosa rugosa Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) Rosa_rugosa_v1.0.fasta.gz


Gene Predictions

The Rosa rugosa v1.0 genome gene prediction files are available in FASTA and GFF3 formats.


Protein sequences  (FASTA file) Rosa_rugosa_v1.0.proteins.fasta.gz
CDS  (FASTA file) Rosa_rugosa_v1.0.cds.fasta.gz
Genes (GFF3 file) Rosa_rugosa_v1.0.genes.gff3.gz


Functional Analysis

Functional annotation for the Rosa rugosa Genome v1.0 are available for download below. The Rosa rugosa 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).


GO assignments from InterProScan Rosa_rugosa_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Rosa_rugosa_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Rosa_rugosa_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Rosa_rugosa_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 Rosa rugosa 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 Rosa_rugosa_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 Rosa_rugosa_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Rosa_rugosa_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Rosa_rugosa_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Rosa_rugosa_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Rosa_rugosa_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Rosa_rugosa_v1.0_pyrus_GDR_reftransV1