Fragaria vesca ‘Yellow Wonder’ Genome v1.0 Assembly & Annotation
Dirk Joldersma,, Norah Sadowski, Winston Timp, and Zhongchi Liu. Assembly and annotation of Fragaria vesca ‘Yellow Wonder’ genome, a model diploid strawberry for molecular genetic research. Fruit Research 2:13 doi: 10.48130/FruRes-2022-0013
Fragaria vesca, a wild diploid strawberry, serves as a fundamental research model for cultivated strawberry. The current reference genomes available are limited to two closely-related accessions, Hawaii 4 and CFRA2339. The widely-used model accession 'Yellow Wonder' does not yet have its reference genome. In this study, the genome of a 7th generation inbred 'Yellow Wonder' was assembled using a combination of Oxford Nanopore long reads and Illumina short reads. The de novo chromosome-scale assembly of this 220 megabase genome possesses 34,007 genes which were annotated through lift over from the Hawaii 4 genome annotation. Genome comparisons show that the 'Yellow Wonder' genome is relatively distinct from the two previously published F. vesca accessions, Hawaii 4 and CFRA2339. The availability of a 'Yellow Wonder' reference genome adds another important genomic resource to Fragaria vesca and enables rapid research progress in strawberry.
Homology of the Fragaria vesca ‘Yellow Wonder’ 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 2021-09) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.
Functional annotation for the Fragaria vesca ‘Yellow Wonder’ Genome v1.0 are available for download below. The Fragaria vesca ‘Yellow Wonder’ 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 vesca genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.