Three haplotype-resolved pentaploid Rosa assemblies with assembled and extracted single copy orthologue (SCO) sequences from Rosa canina genome, diploid Rosa species, and sect. Caninae pollen

This dataset was created to analyze nuclear single copy regions in Rosa canina genome assembly based on single copy orthologue (SCO) tags (Debray et al. 2019). We used 24 diploid rose species, pollen data from sekt. Caninae roses, Rosa canina subgenome specific SCO sequences, and outgroup species from the Rosaceae family. Target capturing baits were designed by Agilent Technologies covered exons, UTRs, and small introns.
The raw reads of target capturer sequencing were processed with GATK to obtain a sample specific reference for each SCO locus and each sample. Additionally, single copy loci for all whole genome assemblies (Rosa canina, Rubus idaeus, and Fragaria species) were extracted and concatenated into subgenome-specific sequences and together with sample specific SCO references used for alignment analysis.
The dataset also includes haplotype-resolved genome assemblies of Rosa canina S27, Rosa canina (DToL), and Rosa agrestis (DToL). All three Rosa samples are pentaploid..., , , # Three haplotype-resolved pentaploid Rosa assemblies with assembled and extracted single copy orthologue (SCO) sequences from Rosa canina genome, diploid Rosa species and sect. Caninae pollen

[https://doi.org/10.5061/dryad.cc2fqz6fh](https://doi.org/10.5061/dryad.cc2fqz6fh)

This dataset was created to analyze nuclear single copy regions in *Rosa canina* genome assembly based on single copy orthologue (SCO) tags (Debray et al. 2019). We used 24 diploid rose species, pollen data from sekt. *Caninae* roses, *Rosa canina* subgenome specific SCO sequences and outgroup species from the *Rosaceae* family. Target capturing baits were designed by Agilent Technologies covered exons, UTRs, and small introns.

The raw reads from target  capturer sequencing were processed with GATK to obtain a sample specific reference for each SCO locus and each sample. Additionaly, single copy loci for all whole genome assemblies (*Rosa canina*, *Rubus idaeus* and *Fragaria* species) were extracted and concaten..., , **Changes after Jul 17, 2024:** The haplotype-resolved genome assemblies of Rosa canina S27 (rosCan_S27_v1.fasta.gz), Rosa canina DToL (rosCan_DTOL_5n_chrsOnly.fasta.gz), and Rosa agrestis DToL (rosArg_DTOL_5n_chrsOnly.fasta.gz) were added to the dataset. Volker Wissemann was added as author, author order was changed and journal was specified. Title was changed indicating the three genome assemblies.

**Changes after May 5, 2025:** The file Supplementary_Dataset_2.fasta was renamed into Supplementary_Dataset_12.fasta in order to fit with the article.

**Changes after Jun 3, 2025:** Upload gene annotation files (GFF3) for subgenomes S1, S2 , R3, R4 of Rosa canina (S27).