Re-annotation of the woodland strawberry (Fragaria vesca) genome

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dc.contributor.authorDarwis, Omar
dc.contributor.authorShahan, Rachel
dc.contributor.authorLiu, Zhongchi
dc.contributor.authorSlovin, Janet P
dc.contributor.authorAlkharouf, Nadim W
dc.date.accessioned2021-08-27T14:34:41Z
dc.date.available2021-08-27T14:34:41Z
dc.date.issued2015-01-27
dc.description.abstractFragaria 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. 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. 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.en_US
dc.description.urihttps://doi.org/10.1186/s12864-015-1221-1
dc.identifierhttps://doi.org/10.13016/wywk-fk4e
dc.identifier.citationDarwish, O., Shahan, R., Liu, Z. et al. Re-annotation of the woodland strawberry (Fragaria vesca) genome. BMC Genomics 16, 29 (2015).en_US
dc.identifier.urihttp://hdl.handle.net/1903/27654
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCell Biology & Molecular Geneticsen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectAnnotationen_US
dc.subjectStrawberryen_US
dc.subjectFragaria vescaen_US
dc.subjectTranscriptomeen_US
dc.subjectGenomeen_US
dc.subjectRNA-Seqen_US
dc.subjectGeneen_US
dc.subjectRosaceaeen_US
dc.titleRe-annotation of the woodland strawberry (Fragaria vesca) genomeen_US
dc.typeArticleen_US

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