title: Re-annotation of the woodland strawberry (Fragaria vesca) genome.
abstract: BACKGROUND
  Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1.
  
  
  RESULTS
  The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae ( http://www.rosaceae.org/ ). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results.
  
  
  CONCLUSIONS
  Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.
authors.affiliation: Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, Maryland, 21252, USA. ODARWISH@TOWSON.EDU.
authors.forename: Omar
authors.initials: O
authors.lastname: Darwish
authors.affiliation: Department of Cell Biology and Molecular Genetics, 0229 Biological Science Research Building, University of Maryland, College Park, Maryland, 20742, USA. RACHEL89@VT.EDU.
authors.forename: Rachel
authors.initials: R
authors.lastname: Shahan
authors.affiliation: Department of Cell Biology and Molecular Genetics, 0229 Biological Science Research Building, University of Maryland, College Park, Maryland, 20742, USA. ZLIU@UMD.EDU.
authors.forename: Zhongchi
authors.initials: Z
authors.lastname: Liu
authors.affiliation: USDA/ARS Genetic Improvement of Fruits and Vegetables Laboratory, BARC-W 10300 Baltimore Ave, Beltsville, Maryland, 20705, USA. JANET.SLOVIN@ARS.USDA.GOV.
authors.forename: Janet P
authors.initials: JP
authors.lastname: Slovin
authors.affiliation: Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, Maryland, 21252, USA. NALKHAROUF@TOWSON.EDU.
authors.forename: Nadim W
authors.initials: NW
authors.lastname: Alkharouf
mesh_terms: D001483:Base Sequence; D004171:Diploidy; D020224:Expressed Sequence Tags; D031985:Fragaria / Q000235:genetics*; D005638:Fruit / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D059467:Transcriptome / Q000235:genetics