Rosa wichuraiana Basye's Thornless Genome v1.0 Assembly & Annotation

Analysis NameRosa wichuraiana Basye's Thornless Genome v1.0 Assembly & Annotation
MethodCANU and WTBDG2 (1.4)
Date performed2022-03-03


Mi-Cai Zhong, Xiao-Dong Jiang, Guo-Qian Yang, Wei-Hua Cui, Zhi-Quan Suo, Wei-Jia Wang, Yi-Bo Sun, Dan Wang, Xin-Chao Cheng, Xu-Ming Li, Xue Dong, Kai-Xue Tang, De-Zhu Li, Jin-Yong Hu, Rose without prickle: genomic insights linked to moisture adaptation, National Science Review, Volume 8, Issue 12, December 2021, nwab092,


Prickles act against herbivores, pathogens or mechanical injury, while also preventing water loss. However, whether prickles have new function and the molecular genetics of prickle patterning remain poorly explored. Here, we generated a high-quality reference genome assembly for ‘Basye's Thornless’ (BT), a prickle-free cultivar of Rosa wichuraiana, to identify genetic elements related to stem prickle development. The BT genome harbors a high level of sequence diversity in itself and with cultivar ‘Old Blush’ (R. chinensis), a founder genotype in rose domestication. Inheritance of stem prickle density was determined and two QTL were identified. Differentially expressed genes in QTL were involved in water-related functions, suggesting that prickle density may hitchhike with adaptations to moist environments. While the prickle-related gene-regulatory-network (GRN) was highly conserved, the expression variation of key candidate genes was associated with prickle density. Our study provides fundamental resources and insights for genome evolution in the Rosaceae. Ongoing efforts on identification of the molecular bases for key rose traits may lead to improvements for horticultural markets.



Homology of the Rosa wichuraiana Basye's Thornless 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

Rosa wichuraiana v1.0 proteins with NCBI nr homologs (EXCEL file) rwichuraiana_BasyesThornless_v1.0_vs_nr.xlsx.gz
Rosa wichuraiana v1.0 proteins with NCBI nr (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_nr_hit.fasta.gz
Rosa wichuraiana v1.0 proteins without NCBI nr (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_nr_noHit.fasta.gz
Rosa wichuraiana v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) rwichuraiana_BasyesThornless_v1.0_vs_arabidopsis.xlsx.gz
Rosa wichuraiana v1.0 proteins with arabidopsis (Araport11) (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_arabidopsis_hit.fasta.gz
Rosa wichuraiana v1.0 proteins without arabidopsis (Araport11) (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_arabidopsis_noHit.fasta.gz
Rosa wichuraiana v1.0 proteins with SwissProt homologs (EXCEL file) rwichuraiana_BasyesThornless_v1.0_vs_swissprot.xlsx.gz
Rosa wichuraiana v1.0 proteins with SwissProt (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_swissprot_hit.fasta.gz
Rosa wichuraiana v1.0 proteins without SwissProt (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_swissprot_noHit.fasta.gz
Rosa wichuraiana v1.0 proteins with TrEMBL homologs (EXCEL file) rwichuraiana_BasyesThornless_v1.0_vs_trembl.xlsx.gz
Rosa wichuraiana v1.0 proteins with TrEMBL (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_trembl_hit.fasta.gz
Rosa wichuraiana v1.0 proteins without TrEMBL (FASTA file) rwichuraiana_BasyesThornless_v1.0_vs_trembl_noHit.fasta.gz



The Rosa_wichuraiana Basye's Thornless Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) rwichuraiana_BasyesThornless_v1.0.fasta.gz
Repeats (GFF3 file) rwichuraiana_BasyesThornless_v1.0.repeats.gff3.gz


Gene Predictions

The Rosa wichuraiana Basye's Thornless v1.0 genome gene prediction files are available in FASTA and GFF3 formats.


Protein sequences  (FASTA file) rwichuraiana_BasyesThornless_v1.0.proteins.fasta.gz
CDS  (FASTA file) rwichuraiana_BasyesThornless_v1.0.cds.fasta.gz
Genes (GFF3 file) rwichuraiana_BasyesThornless_v1.0.genes.gff3.gz


Functional Analysis

Functional annotation for the Rosa wichuraiana Basye's Thornless Genome v1.0 are available for download below. The Rosa wichuraiana 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 rwichuraiana_BasyesThornless_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan rwichuraiana_BasyesThornless_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs rwichuraiana_BasyesThornless_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways rwichuraiana_BasyesThornless_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 wichuraiana 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 rwichuraiana_BasyesThornless_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 rwichuraiana_BasyesThornless_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 rwichuraiana_BasyesThornless_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 rwichuraiana_BasyesThornless_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 rwichuraiana_BasyesThornless_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 rwichuraiana_BasyesThornless_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 rwichuraiana_BasyesThornless_v1.0_pyrus_GDR_reftransV1