Fragaria viridis SCBG Genome v1.0 Assembly & Annotation
Whole genome sequences of F. nilgerrensis, F. nubicola, and F. viridis were made available in the study of the diploid ancestry of the cultivated octoploid strawberry.
Feng C, Wang J, Harris AJ, Folta KM, Zhao M, Kang M. Tracing the diploid ancestry of the cultivated octoploid strawberry. Mol Biol Evol. 2020 Sep 17:msaa238. doi: 10.1093/molbev/msaa238.
The commercial strawberry, Fragaria × ananassa, is a recent allo-octoploid that is cultivated worldwide. However, other than F. vesca, which is universally accepted one of its diploid ancestors, its other early diploid progenitors remain unclear. Here, we performed comparative analyses of the genomes of five diploid strawberries, F. iinumae, F. vesca, F. nilgerrensis, F. nubicola, and F. viridis, of which the latter three are newly sequenced. We found that the genomes of these species share highly conserved gene content and gene order. Using an alignment-based approach, we show that F. iinumae and F. vesca are the diploid progenitors to the octoploid F. × ananassa, whereas the other three diploids that we analyzed in this study are not parental species. We generated a fully resolved, dated phylogeny of Fragaria and determined that the genus arose ca. 6.37 million years ago. Our results effectively resolve conflicting hypotheses regarding the putative diploid progenitors of the cultivated strawberry, establish a reliable backbone phylogeny for the genus, and provide genetic resources for molecular breeding.
Homology of the Fragaria viridis SCBG 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 2018-05) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.
All assembly and annotation files are available for download by selecting the desired data type in the left-hand side bar. Each data type page will provide a description of the available files and links to download.
The Fragaria viridis SCBG Genome v1.0 assembly file is available in FASTA format.
The Fragaria viridis SCBG v1.0 genome gene prediction files are available in FASTA and GFF3 formats.
Functional annotation for the Fragaria viridis SCBG genome v1.0 are available for download below. The fragaria viridis SCBG 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).
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 fragaria viridis SCBG genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.