Genome assembly and transcriptome profiling of the woodland strawberry (<i>Fragaria vesca</i>) 'Ruegen'

The diploid woodland strawberry, <italic>Fragaria vesca</italic> (2n = 2x = 14), has emerged as a premier model system for Rosaceae functional genomics due to its compact genome, low heterozygosity, and tractable genetic transformation. Commonly used research accessions for woodland strawberry include 'Ruegen' with red fruits, 'Yellow Wonder', and 'Hawaii 4' with yellow fruits. While reference genomes are available for 'Yellow Wonder' and 'Hawaii 4', 'Ruegen' has remained lacking in this regard. In this study, SMRT and Hi-C technology were employed to assemble the 'Ruegen' genome, yielding a total size of 221.31 Mb with a contig N50 of 8.35 Mb. Gene prediction identified 36,071 protein-coding genes, of which 85.79% exhibited significant homology to sequences in the NCBI NR database. RNA-seq of fruits from the diploid 'Ruegen' and octoploid 'Yanli' varieties was conducted across multiple developmental stages. Comparative transcriptomic analysis revealed divergence in anthocyanin-related gene expression patterns. Notably, <italic>MYB1</italic> homologs exhibited diametrically opposed expression profiles during fruit development between 'Ruegen' and 'Yanli'. These integrated genomic and transcriptomic resources significantly advance strawberry functional genomics research.