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

Overview
Analysis NameRosa wichuraiana Basye's Thornless Genome v1.0 Assembly & Annotation
MethodCANU and WTBDG2 (1.4)
SourcePRJNA542225
Date performed2022-03-03

Publication

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, https://doi.org/10.1093/nsr/nwab092

Abstract

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.

 

Assembly

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

Downloads

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.

Downloads

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