Abstract
BackgroundFragaria 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.ResultsThe 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.ConclusionsUsing 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.
Highlights
Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry
The time, cost, and difficulty of generating transcriptome sequences has been greatly reduced due to recent advances in sequencing technology, and RNA-Seq is dominant over microarrays for in-depth transcriptome studies
All de novo assembled transcripts were aligned to the F. vesca genome using GMAP [14] within Program to Assemble Spliced Alignments (PASA), with the aims of eliminating sequences not aligning to the genome and merging de novo assembled sequences to remove redundancy
Summary
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. The diploid strawberry Fragaria vesca is native to temperate regions of Eurasia and North America and is commonly known as the alpine or woodland strawberry. Due to its small size and small genome it is a versatile experimental perennial plant system and an emerging model for the Rosaceae family. The Illumina HiSeq 2000 platform was previously used to sequence 50 RNA-Seq libraries of 25 different F. vesca tissue types from early developing fruit at various stages, young leaves, and seedlings [2] of the 7th generation inbred line Yellow Wonder 5AF7 (YW5AF7) [3]. The 50 libraries represent two biological replicates of 25 tissue types, and each library yielded between 12 and 40 million 51 bp, single end reads, for a total of ~70 Giga bytes of sequence data [2,4]
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