Re-Annotation of the Strawberry (Fragaria vesca) Genome

Fragaria vesca, a diploid strawberry species commonly known as the alpine or woodland strawberry, is a versatile experimental plant system and an emerging model for the Rosaceae family. The F. vesca genome was sequenced in 2010. The current gene model (version 1.1) was developed using GeneMark program. Gene predictions are hosted on Genome Database of Rosaceae (GDR). We have generated 50 different Illumina RNA-Seq libraries from flowers and early developmental stage fruit tissues of the inbred F. vesca line YW5AF7. The sequence reads were aligned to the genome (version 1.1) and visualized in GBrowse, which revealed a significant number of mis-annotated genes. Examples included reads aligning to genome locations without any known annotated genes, reads aligning to introns, and reads aligning to 5’ and 3’ sequences of existing exons. Therefore, we set out to re-annotate the 7 chromosomes of the F. vesca genome taking advantage of our RNA-seq data. We used the MAKER annotation pipeline; the annotation is based on RNA-seq reference-based and de novo assembly of all 50 tissues and plants reference proteins. The re-annotation resulted in an increase in the number of coding regions and thus the total coding length across all chromosomes due to:  1) Discovery of new genes, 2) Addition of exons to current genes, 3) extension of current exons, 4) merging of current exons, and among others. This complete genome re-annotation will significantly benefit the strawberry and Rosaceae research community as a whole.