|Analysis Name||Fragaria x ananassa Royal Royce Genome v1.0 Assembly & Annotation |
|Source||PACBIO SMRT |
|Date performed||2021-10-26 |
Restrictions on Dataset Usage
We encourage investigators to use these data to advance their studies. Please cite “Fragaria x ananassa Royal Royce v1.0”. As a public service, the authors and their respective institutions and sponsors are making the Fragaria × ananassa ‘Royal Royce’ genome sequence available to the research community before scientific publication according to the Ft. Lauderdale Accord. Our policy, which is aligned with JGI policy, is that early release should aid the progress of science. This balances the imperative of making the genome and underlying data available with the desire of the contributing scientists to reserve a reasonable period of time to publish on the genome sequencing, assembly, and analysis without concerns about preemption by other groups.
By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by the developers of a comprehensive genome analysis ("Reserved Analyses"). "Reserved analyses" include the identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome or chromosome-scale comparisons with other species. The embargo on publication of Reserved Analyses by researchers outside of the Fragaria × ananassa ‘Royal Royce’ v1.1 Genome Sequencing Project is expected to extend until the publication of the results of the sequencing project are accepted.
Scientific users are free to publish papers dealing with specific genes or small sets of genes using the sequence data, not including analyses related to mapping or cloning the specific gene sequence required for the day-neutral/perpetual flowering trait in octoploid strawberry. If these data are used for publication, the following acknowledgment should be included: “These sequence data were produced through a collaboration between UC Davis, Pacific Biosciences, and Michigan State University”. This letter has been circulated to Journal Editors so that they are aware of the conditions of access and publication detailed above. These data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. The assembly and sequence data should not be redistributed or repackaged without permission from the Strawberry Genome Sequencing Consortium. Any redistribution of the data during the embargo period should carry this notice: "The Strawberry Genome Sequencing Consortium provides this data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used. Once the sequence is moved to unreserved status, the data will be freely available for any subsequent use."
We prefer that potential users of this genome assembly contact the individuals listed under Contacts with their plans to ensure that proposed usage of sequence data are not considered
Principal Collaborators: Steven J. Knapp (University of California, Davis) (e-mail: firstname.lastname@example.org) Michael A. Hardigan (USDA-ARS, Corvallis, Oregon): (e-mail: Michael.Hardigan@usda.gov) Mitchell J. Feldmann (University of California, Davis) (e-mail: email@example.com) Patrick P. Edger (Michigan State University): (e-mail: firstname.lastname@example.org)
The genome of the allo-octoploid (2n = 8x = 56) Fragaria × ananassa cultivar ‘Royal Royce’ was haplotype-phased and assembled to chromosome scale. ‘Royal Royce’ is a highly heterozygous outbred individual preserved by asexual propagation at the University of California, Davis. We are releasing haplotype A, haplotype B, and ’reference’ assemblies. The v1.1 reference assembly (FaRR1) was constructed by selecting the most contiguous of the haplotype A and B pseudomolecules for each chromosome.
The cultivars of strawberry found in gardens and markets around the globe originated from approximately 300 years of breeding in interspecific hybrid populations originally developed from crosses between allo-octoploid (2n = 8x = 56) beach strawberry (F. chiloensis) and allo-octoploid (2n = 8x = 56) meadow strawberry (F. virginiana) ecotypes (Hardigan et al. 2020, 2021). We have shown that the genomes of ‘Royal Royce’ and other modern descendants of these octoploid ancestors are mosaics inherited from ecotypes of seven of eight subspecies of F. chiloensis and F. virginiana (Pincot eet al. 2021).
The haplotype-resolved assembly of the ‘Royal Royce’ genome was achieved by breakthroughs in long-read DNA sequencing (Hon et al. 2020) and insights gained from the development of an unphased chromosome-scale assembly of the genome for the highly heterozygous outbred F. × ananassa cultivar ’Camarosa’ (FaCA1; Edger et al. 2019; https://phytozome-next.jgi.doe.gov/info/Fxananassa_v1_0_a1). The ‘Camarosa’ reference genome was developed before high-density genetic maps with fully resolved subgenomes or high-accuracy HiFi reads were available to guide and improve the assembly process. With the ‘Camarosa’ reference in place, Hardigan et al. (2020, 2021) identified millions of DNA variants in octoploid populations worldwide, developed high-density arrays for genotyping SNPs anchored to FaCA1, and genetically mapped 3.6M DNA variants using whole-genome shotgun genotyping-by-sequencing. The genome-wide distribution of heterozygosity in ecotypes of the octoploid ancestors facilitated telomere-to-telomere genetic mapping of DNA variants as complete haploblocks (Hardigan et al. 2020). These genomic resources, insights, and
breakthroughs were critical for applying a genetic mapping-guided approach to the problems of resolving haplotypes, breaking chimeras, and scaffolding the ‘Royal Royce’ genome.
The ‘Royal Royce’ genome was annotated using the chromosome nomenclature and physical orientations proposed by Hardigan et al. (2021). Homoeologous chromosomes in the A, B, C, and D genomes were identically numbered and oriented, e.g., chromosome 1 homoeologs were numbered 1A, 1B, 1C, and 1D and syntenically oriented. The physical coordinates for thousands of ‘Camarosa’ genome-anchored DNA markers were anchored to the ‘Royal Royce’ genome to facilitate cross-referencing genetic and physical mapping information (Hardigan et al. 2020, 2021a,b). DNA and RNA sequences, databases, and other genomic resources associated with the ‘Royal Royce’ genome assembly have been deposited in open-source public databases.
The Fragaria x ananassacv. Royal Royce Genome v1.0 assembly file is available in FASTA format.
The Fragaria x ananassacv. Royal Royce Genome v1.0 gene prediction files are available in FASTA and GFF3 formats.