DOI: 10.5061/dryad.cc2fqz6fh
title: 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

description: 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 (2n=5x=35), and all three assemblies are chromosome-level. Note
 that the assemblies only contain pseudochromosomal sequences, no unplaced
 contigs. The PacBio HiFi and Hi-C data of Rosa canina S27 were sequenced
 in-house and can be downloaded by NCBI BioProject: PRJNA1111045, while the
 sequencing data of Rosa canina (DToL) and Rosa agrestis (DToL)
 are from Darwin Tree of Life (DToL). The NCBI BioProject accessions for
 the two DToL Rosa data are PRJEB79802 and PRJEB79880,
 respectively. The chromosomes of Rosa canina are named as
 "Rca#_Subgenome", in which # denotes the chromosome number
 (possible value: 1-7) and 'Subgenome' can only be one of S1_h1,
 S1_h2, S2, R3, and R4. Similarly, the chromosomes of Rosa
 agrestis are named as "Rag#_Subgenome", where # also denotes the
 chromosome number and 'Subgenome' can only be one of S1, S2, R3,
 R4_h1, and R4_h2. Please check our publication if you want to learn about
 how we resolve the haplotypes.
description: # 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 concatenated into subgenome-specific sequences, together with sample specifice SCO refereces used for aqlignment analysis. ## Description of the data and file structure The dataset include a file called `sample.tab` containing relevant information about .fasta files and sample source. Sequence data as .fasta files containing assembled SCO loci. A file called `loci.list` represents all loci which were used for concatenating, alignment, and phylogenetic analysis because of single copy characteristics. Loci names come from *Rosa chinensis* haploid line genome v.1.0 (Hibrand Saint-Oyant et al., 2018, [https://doi.org/10.1038/s41477-018-0166-1](https://doi.org/10.1038/s41477-018-0166-1)). These names describe the gene annotation and the region where SCO loci are located, e.g. RC7G0579500_0_602. The alignment file is also included as `2xphyl.align7.fasta`. Additionally, the data set contain variant calling format (.vcf) files within a zip archive (`pollen_leaf_vcfs.zip`) for SNP count analysis between *Rosa* section *Caninae* somatic leaf tissue and pollen DNA samples. The original target based on Rosa chinensis haploid line genome v.1.0 is also included as `Supplementary_Dataset_12.fasta`. The dataset also includes 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`). All three *Rosa* samples are pentaploid (2n=5x=35), and all three assemblies are chromosome-level. Note that the assemblies only contain pseudochromosomal sequences, no unplaced contigs. The PacBio HiFi and Hi-C data of *Rosa canina* S27 were sequenced in-house and can be downloaded by NCBI BioProject: [PRJNA1111045](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1111045), while the sequencing data of *Rosa canina* (DToL) and *Rosa agrestis* (DToL) are from Darwin Tree of Life (DToL). The NCBI BioProject accessions for the two DToL *Rosa* data are [PRJEB79802](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB79802) and [PRJEB79880](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB79880), respectively. The chromosomes of *Rosa canina* are named as "Rca#_Subgenome", in which # denotes the chromosome number (possible value: 1-7) and 'Subgenome' can only be one of S1_h1, S1_h2, S2, R3, and R4. Similarly, the chromosomes of *Rosa agrestis* are named as "Rag#_Subgenome", where # also denotes the chromosome number and 'Subgenome' can only be one of S1, S2, R3, R4_h1, and R4_h2. Please check our publication if you want to learn about how we assembled and resolve the haplotypes. Gene annotation files (GFF3) for subgenomes S1, S2 , R3, R4 of Rosa canina (S27) were also uploaded (`rosCan_S27_[x]_mercator_annotation.gff3.gz`). ## Sharing/Access information NCBI BioProject: PRJNA1111045 ## Code/Software For any code and bioinformatic information please contact the autor: [veit.herklotz@senckenberg.de](mailto:veit.herklotz@senckenberg.de)