Inference of the Fragaria vesca's transcriptome through the re-annotation of its genome

The diploid Fragaria vesca, is recognized as model for more complex octoploid species such as F. × ananassa (the commercial strawberry) and F. chiloensis (the native Chilean strawberry). The genome of F. vesca has been recently sequenced nevertheless the annotation in its 1.1 version presented some inconsistencies. Therefore, in order to improve the annotation of its transcriptome the following steps were followed: 1) Prediction of open reading frames from scaffolds; 2) Assembling of ORFs in a contig or coding sequences (CDS); 3) Annotation of genes; 4) Functional classification of the genes through KOG, followed by homology with reference genomes using Blast (Arabidopsis, Populus and Prunus). From the 256 scaffolds available a total of 217,766 ORFs, longer than 150 bp, were predicted using Glimmer. A total of 17,818 ORFs were annotated: 6451 sequences were classified within the main KOG categories (737 in Information, storage and processing category; 4858 in Cellular processing and signalling; and 856 in Metabolism), 5409 sequences were classified as poorly characterized and 5958 as unknown. A total of 53,586 ORFs with a biological description were annotated by homology. The entire data has been deposited initially in a local database. The search of genes related to important quality traits of strawberry fruit was performed particularly on fruit softening. The search provided an entire list of genes including those previously described as main players in the softening of strawberry fruit. Research supported by Anillo ACT-1110 project.