Cell Biology & Molecular Genetics Research Works

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Author: search.filters.author.Alkharouf, Nadim WSubject: search.filters.subject.Strawberry

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    SGR: an online genomic resource for the woodland strawberry
    (Springer Nature, 2013-12-23) Darwish, Omar; Slovin, Janet P; Kang, Chunying; Hollender, Courtney A; Geretz, Aviva; Houston, Sam; Liu, Zhongchi; Alkharouf, Nadim W
    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. An ancestral F. vesca genome contributed to the genome of the octoploid dessert strawberry (F. ×ananassa), and the extant genome exhibits synteny with other commercially important members of the Rosaceae family such as apple and peach. To provide a molecular description of floral organ and fruit development at the resolution of specific tissues and cell types, RNAs from flowers and early developmental stage fruit tissues of the inbred F. vesca line YW5AF7 were extracted and the resulting cDNA libraries sequenced using an Illumina HiSeq2000. To enable easy access as well as mining of this two-dimensional (stage and tissue) transcriptome dataset, a web-based database, the Strawberry Genomic Resource (SGR), was developed. SGR is a web accessible database that contains sample description, sample statistics, gene annotation, and gene expression analysis. This information can be accessed publicly from a web-based interface at http://bioinformatics.towson.edu/strawberry/Default.aspx . The SGR website provides user friendly search and browse capabilities for all the data stored in the database. Users are able to search for genes using a gene ID or description or obtain differentially expressed genes by entering different comparison parameters. Search results can be downloaded in a tabular format compatible with Microsoft excel application. Aligned reads to individual genes and exon/intron structures are displayed using the genome browser, facilitating gene re-annotation by individual users. The SGR database was developed to facilitate dissemination and data mining of extensive floral and fruit transcriptome data in the woodland strawberry. It enables users to mine the data in different ways to study different pathways or biological processes during reproductive development.
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    Re-annotation of the woodland strawberry (Fragaria vesca) genome
    (Springer Nature, 2015-01-27) Darwis, Omar; Shahan, Rachel; Liu, Zhongchi; Slovin, Janet P; Alkharouf, Nadim W
    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. 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.